Starting phenix.real_space_refine on Wed Jul 24 19:24:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/07_2024/8jmh_36421_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/07_2024/8jmh_36421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/07_2024/8jmh_36421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/07_2024/8jmh_36421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/07_2024/8jmh_36421_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/07_2024/8jmh_36421_neut_trim.cif" } resolution = 2.5 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= 0.003 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 8872 2.51 5 N 2212 2.21 5 O 2264 1.98 5 H 13812 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 233": "OD1" <-> "OD2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "C GLU 313": "OE1" <-> "OE2" Residue "C PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D ASP 316": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 27256 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "B" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "C" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "D" Number of atoms: 6791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 6791 Classifications: {'peptide': 407} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 390} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'FRU': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'FRU': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'FRU': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'FRU': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.53, per 1000 atoms: 0.46 Number of scatterers: 27256 At special positions: 0 Unit cell: (116.25, 116.25, 101.37, 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 96 16.00 O 2264 8.00 N 2212 7.00 C 8872 6.00 H 13812 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 Links applied ALPHA1-2 " GLC E 1 " - " FRU E 2 " ~> Even though FRU is a beta isomer, an alpha linkage is required... " GLC F 1 " - " FRU F 2 " " GLC G 1 " - " FRU G 2 " " GLC H 1 " - " FRU H 2 " Time building additional restraints: 24.10 Conformation dependent library (CDL) restraints added in 2.6 seconds 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 58 through 73 Proline residue: A 65 - end of helix removed outlier: 3.858A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 95 through 123 Processing helix chain 'A' and resid 128 through 164 removed outlier: 3.927A pdb=" N LEU A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 177 through 214 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 242 through 287 removed outlier: 4.551A pdb=" N ASP A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 319 removed outlier: 3.592A pdb=" N PHE A 298 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 339 Processing helix chain 'A' and resid 347 through 382 removed outlier: 4.137A pdb=" N ILE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 421 through 443 removed outlier: 4.085A pdb=" N GLN A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 442 " --> pdb=" O VAL A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 removed outlier: 3.843A pdb=" N GLY A 450 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 73 Proline residue: B 65 - end of helix removed outlier: 3.856A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 89 Processing helix chain 'B' and resid 95 through 123 Processing helix chain 'B' and resid 128 through 164 removed outlier: 3.927A pdb=" N LEU B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 177 through 214 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 242 through 287 removed outlier: 4.557A pdb=" N ASP B 264 " --> pdb=" O TRP B 260 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 319 removed outlier: 3.591A pdb=" N PHE B 298 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 339 Processing helix chain 'B' and resid 347 through 382 removed outlier: 4.135A pdb=" N ILE B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 387 Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 421 through 443 removed outlier: 4.081A pdb=" N GLN B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE B 442 " --> pdb=" O VAL B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 450 removed outlier: 3.842A pdb=" N GLY B 450 " --> pdb=" O ASN B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 73 Proline residue: C 65 - end of helix removed outlier: 3.852A pdb=" N VAL C 73 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 95 through 123 Processing helix chain 'C' and resid 128 through 164 removed outlier: 4.022A pdb=" N LEU C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 168 Processing helix chain 'C' and resid 177 through 214 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 242 through 287 removed outlier: 4.554A pdb=" N ASP C 264 " --> pdb=" O TRP C 260 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 319 removed outlier: 3.590A pdb=" N PHE C 298 " --> pdb=" O CYS C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 339 Processing helix chain 'C' and resid 347 through 382 removed outlier: 4.132A pdb=" N ILE C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 387 Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 421 through 443 removed outlier: 4.064A pdb=" N GLN C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE C 442 " --> pdb=" O VAL C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 450 removed outlier: 3.843A pdb=" N GLY C 450 " --> pdb=" O ASN C 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 73 Proline residue: D 65 - end of helix removed outlier: 3.729A pdb=" N VAL D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 Processing helix chain 'D' and resid 95 through 123 Processing helix chain 'D' and resid 128 through 164 removed outlier: 4.137A pdb=" N LEU D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 168 Processing helix chain 'D' and resid 177 through 214 Processing helix chain 'D' and resid 223 through 232 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 242 through 287 removed outlier: 4.342A pdb=" N ASP D 264 " --> pdb=" O TRP D 260 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 339 removed outlier: 3.536A pdb=" N PHE D 298 " --> pdb=" O CYS D 294 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER D 321 " --> pdb=" O SER D 317 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 387 removed outlier: 4.015A pdb=" N ILE D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ASN D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL D 385 " --> pdb=" O ARG D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 421 through 440 Processing helix chain 'D' and resid 443 through 450 removed outlier: 3.734A pdb=" N GLY D 450 " --> pdb=" O ASN D 446 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2916 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: 9.94 Time building geometry restraints manager: 25.29 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: 13772 1.03 - 1.23: 40 1.23 - 1.42: 5796 1.42 - 1.61: 7828 1.61 - 1.81: 156 Bond restraints: 27592 Sorted by residual: bond pdb=" C4 FRU G 2 " pdb=" C5 FRU G 2 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4 FRU E 2 " pdb=" C5 FRU E 2 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4 FRU F 2 " pdb=" C5 FRU F 2 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C4 FRU H 2 " pdb=" C5 FRU H 2 " ideal model delta sigma weight residual 1.528 1.301 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C5 FRU F 2 " pdb=" O5 FRU F 2 " ideal model delta sigma weight residual 1.420 1.619 -0.199 2.00e-02 2.50e+03 9.94e+01 ... (remaining 27587 not shown) Histogram of bond angle deviations from ideal: 80.97 - 91.58: 3 91.58 - 102.18: 52 102.18 - 112.78: 32028 112.78 - 123.38: 15664 123.38 - 133.98: 2081 Bond angle restraints: 49828 Sorted by residual: angle pdb=" CG2 THR A 54 " pdb=" CB THR A 54 " pdb=" HB THR A 54 " ideal model delta sigma weight residual 108.00 80.97 27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" OG1 THR A 54 " pdb=" CB THR A 54 " pdb=" HB THR A 54 " ideal model delta sigma weight residual 109.00 82.70 26.30 3.00e+00 1.11e-01 7.69e+01 angle pdb=" CA THR A 54 " pdb=" CB THR A 54 " pdb=" HB THR A 54 " ideal model delta sigma weight residual 109.00 83.66 25.34 3.00e+00 1.11e-01 7.13e+01 angle pdb=" OG1 THR A 54 " pdb=" CB THR A 54 " pdb=" CG2 THR A 54 " ideal model delta sigma weight residual 109.30 120.58 -11.28 2.00e+00 2.50e-01 3.18e+01 angle pdb=" CA THR A 54 " pdb=" CB THR A 54 " pdb=" CG2 THR A 54 " ideal model delta sigma weight residual 110.50 118.56 -8.06 1.70e+00 3.46e-01 2.25e+01 ... (remaining 49823 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 11348 14.72 - 29.44: 1208 29.44 - 44.16: 354 44.16 - 58.89: 153 58.89 - 73.61: 25 Dihedral angle restraints: 13088 sinusoidal: 7084 harmonic: 6004 Sorted by residual: dihedral pdb=" CG LYS D 449 " pdb=" CD LYS D 449 " pdb=" CE LYS D 449 " pdb=" NZ LYS D 449 " ideal model delta sinusoidal sigma weight residual -180.00 -122.72 -57.28 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 449 " pdb=" CD LYS B 449 " pdb=" CE LYS B 449 " pdb=" NZ LYS B 449 " ideal model delta sinusoidal sigma weight residual -180.00 -123.57 -56.43 3 1.50e+01 4.44e-03 9.40e+00 dihedral pdb=" CG LYS A 449 " pdb=" CD LYS A 449 " pdb=" CE LYS A 449 " pdb=" NZ LYS A 449 " ideal model delta sinusoidal sigma weight residual -180.00 -123.57 -56.43 3 1.50e+01 4.44e-03 9.40e+00 ... (remaining 13085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.280: 2175 0.280 - 0.559: 0 0.559 - 0.839: 0 0.839 - 1.118: 0 1.118 - 1.398: 1 Chirality restraints: 2176 Sorted by residual: chirality pdb=" CB THR A 54 " pdb=" CA THR A 54 " pdb=" OG1 THR A 54 " pdb=" CG2 THR A 54 " both_signs ideal model delta sigma weight residual False 2.55 1.15 1.40 2.00e-01 2.50e+01 4.89e+01 chirality pdb=" C1 GLC E 1 " pdb=" C2 GLC E 1 " pdb=" O5 GLC E 1 " pdb=" O2 FRU E 2 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 9.66e+00 chirality pdb=" C1 GLC F 1 " pdb=" C2 GLC F 1 " pdb=" O5 GLC F 1 " pdb=" O2 FRU F 2 " both_signs ideal model delta sigma weight residual False 2.40 2.34 0.06 2.00e-02 2.50e+03 8.51e+00 ... (remaining 2173 not shown) Planarity restraints: 3836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 211 " -0.181 9.50e-02 1.11e+02 6.05e-02 4.26e+00 pdb=" NE ARG D 211 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG D 211 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 211 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 211 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG D 211 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG D 211 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 211 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG D 211 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE D 164 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO D 165 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 165 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 165 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 164 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO B 165 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " 0.016 5.00e-02 4.00e+02 ... (remaining 3833 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 1846 2.21 - 2.81: 58108 2.81 - 3.41: 79260 3.41 - 4.00: 102843 4.00 - 4.60: 159628 Nonbonded interactions: 401685 Sorted by model distance: nonbonded pdb=" O ILE D 249 " pdb="HD22 ASN D 253 " model vdw 1.615 1.850 nonbonded pdb=" OD2 ASP A 264 " pdb="HD21 ASN A 330 " model vdw 1.648 1.850 nonbonded pdb=" O PHE B 367 " pdb=" HG1 THR B 371 " model vdw 1.654 1.850 nonbonded pdb=" O PHE C 367 " pdb=" HG1 THR C 371 " model vdw 1.655 1.850 nonbonded pdb=" OD2 ASP C 264 " pdb="HD21 ASN C 330 " model vdw 1.656 1.850 ... (remaining 401680 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 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.420 Extract box with map and model: 1.080 Check model and map are aligned: 0.180 Set scattering table: 0.250 Process input model: 88.310 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.007 0.227 13780 Z= 0.418 Angle : 0.570 11.277 18704 Z= 0.288 Chirality : 0.047 1.398 2176 Planarity : 0.003 0.080 2276 Dihedral : 15.006 73.607 5168 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.07 % Allowed : 11.41 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 3.05 (0.21), residues: 1620 helix: 2.80 (0.15), residues: 1172 sheet: None (None), residues: 0 loop : -0.13 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 355 HIS 0.001 0.000 HIS D 197 PHE 0.012 0.001 PHE C 64 TYR 0.011 0.001 TYR D 241 ARG 0.009 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 2.278 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 2.7006 time to fit residues: 521.7320 Evaluate side-chains 175 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13780 Z= 0.185 Angle : 0.522 11.249 18704 Z= 0.280 Chirality : 0.047 1.394 2176 Planarity : 0.003 0.043 2276 Dihedral : 5.516 30.143 1996 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.20 % Allowed : 11.55 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.77 (0.20), residues: 1620 helix: 2.56 (0.14), residues: 1228 sheet: None (None), residues: 0 loop : -0.61 (0.29), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 355 HIS 0.001 0.000 HIS D 197 PHE 0.013 0.001 PHE C 64 TYR 0.012 0.001 TYR D 241 ARG 0.004 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 2.322 Fit side-chains REVERT: A 94 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7163 (tptp) REVERT: B 94 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7173 (tptp) REVERT: C 94 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7176 (tptp) outliers start: 3 outliers final: 0 residues processed: 174 average time/residue: 2.6526 time to fit residues: 507.3871 Evaluate side-chains 175 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 172 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain C residue 94 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 80 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13780 Z= 0.347 Angle : 0.537 11.293 18704 Z= 0.290 Chirality : 0.049 1.408 2176 Planarity : 0.003 0.045 2276 Dihedral : 4.526 19.362 1996 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.20 % Allowed : 11.96 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.79 (0.20), residues: 1620 helix: 2.61 (0.14), residues: 1184 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 355 HIS 0.003 0.001 HIS D 197 PHE 0.015 0.001 PHE D 66 TYR 0.013 0.002 TYR C 276 ARG 0.005 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 2.131 Fit side-chains REVERT: A 94 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7167 (tptt) REVERT: B 94 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7156 (tptt) REVERT: C 94 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7168 (tptt) outliers start: 3 outliers final: 0 residues processed: 174 average time/residue: 2.7966 time to fit residues: 534.4849 Evaluate side-chains 177 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 174 time to evaluate : 2.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain C residue 94 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13780 Z= 0.171 Angle : 0.487 11.268 18704 Z= 0.262 Chirality : 0.046 1.395 2176 Planarity : 0.003 0.050 2276 Dihedral : 3.742 13.775 1996 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.87 (0.20), residues: 1620 helix: 2.68 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.52 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 355 HIS 0.001 0.000 HIS D 197 PHE 0.012 0.001 PHE A 64 TYR 0.012 0.001 TYR D 241 ARG 0.007 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 2.172 Fit side-chains REVERT: D 180 ARG cc_start: 0.8087 (tpp-160) cc_final: 0.7804 (tpp80) outliers start: 0 outliers final: 1 residues processed: 174 average time/residue: 2.6541 time to fit residues: 507.5483 Evaluate side-chains 170 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 124 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13780 Z= 0.251 Angle : 0.504 11.257 18704 Z= 0.270 Chirality : 0.047 1.398 2176 Planarity : 0.003 0.053 2276 Dihedral : 3.668 13.913 1996 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.07 % Allowed : 13.11 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.88 (0.20), residues: 1620 helix: 2.71 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.56 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 355 HIS 0.002 0.001 HIS D 197 PHE 0.013 0.001 PHE D 64 TYR 0.012 0.001 TYR B 241 ARG 0.006 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.995 Fit side-chains REVERT: D 180 ARG cc_start: 0.8121 (tpp-160) cc_final: 0.7842 (tpp80) outliers start: 1 outliers final: 1 residues processed: 173 average time/residue: 2.8089 time to fit residues: 530.5723 Evaluate side-chains 170 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 154 optimal weight: 0.0870 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 81 optimal weight: 0.4980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13780 Z= 0.160 Angle : 0.475 11.230 18704 Z= 0.255 Chirality : 0.046 1.391 2176 Planarity : 0.004 0.057 2276 Dihedral : 3.488 14.094 1996 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.27 % Allowed : 12.91 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 3.03 (0.20), residues: 1620 helix: 2.80 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.49 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 355 HIS 0.001 0.000 HIS D 197 PHE 0.012 0.001 PHE D 64 TYR 0.012 0.001 TYR D 241 ARG 0.007 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 2.503 Fit side-chains REVERT: A 180 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7750 (tpp80) REVERT: D 180 ARG cc_start: 0.8043 (tpp-160) cc_final: 0.7759 (tpp80) outliers start: 4 outliers final: 5 residues processed: 181 average time/residue: 2.7756 time to fit residues: 554.9631 Evaluate side-chains 174 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13780 Z= 0.316 Angle : 0.518 11.255 18704 Z= 0.279 Chirality : 0.048 1.399 2176 Planarity : 0.004 0.059 2276 Dihedral : 3.625 13.993 1996 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.48 % Allowed : 12.70 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.91 (0.20), residues: 1620 helix: 2.73 (0.14), residues: 1200 sheet: None (None), residues: 0 loop : -0.55 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 355 HIS 0.003 0.001 HIS D 197 PHE 0.015 0.001 PHE D 66 TYR 0.012 0.002 TYR B 276 ARG 0.008 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 2.313 Fit side-chains REVERT: A 180 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7840 (tpp80) REVERT: D 180 ARG cc_start: 0.8142 (tpp-160) cc_final: 0.7863 (tpp80) outliers start: 7 outliers final: 4 residues processed: 172 average time/residue: 2.8484 time to fit residues: 535.5478 Evaluate side-chains 171 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 98 optimal weight: 0.4980 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13780 Z= 0.239 Angle : 0.498 11.264 18704 Z= 0.268 Chirality : 0.047 1.398 2176 Planarity : 0.004 0.061 2276 Dihedral : 3.560 13.989 1996 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.27 % Allowed : 13.25 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.91 (0.20), residues: 1620 helix: 2.72 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 355 HIS 0.002 0.001 HIS D 197 PHE 0.013 0.001 PHE D 66 TYR 0.012 0.001 TYR A 241 ARG 0.009 0.000 ARG D 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 2.384 Fit side-chains REVERT: A 180 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7840 (tpp80) REVERT: D 180 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7851 (tpp80) outliers start: 4 outliers final: 4 residues processed: 174 average time/residue: 2.8175 time to fit residues: 535.5952 Evaluate side-chains 172 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13780 Z= 0.246 Angle : 0.504 11.254 18704 Z= 0.270 Chirality : 0.047 1.396 2176 Planarity : 0.004 0.076 2276 Dihedral : 3.546 13.949 1996 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.34 % Allowed : 13.38 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.93 (0.20), residues: 1620 helix: 2.73 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 355 HIS 0.002 0.001 HIS D 197 PHE 0.013 0.001 PHE D 64 TYR 0.012 0.001 TYR B 241 ARG 0.011 0.000 ARG C 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 167 time to evaluate : 2.180 Fit side-chains REVERT: A 180 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7838 (tpp80) REVERT: D 180 ARG cc_start: 0.8125 (tpp-160) cc_final: 0.7851 (tpp80) outliers start: 5 outliers final: 4 residues processed: 171 average time/residue: 2.9372 time to fit residues: 554.4142 Evaluate side-chains 171 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 146 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13780 Z= 0.174 Angle : 0.481 11.238 18704 Z= 0.258 Chirality : 0.046 1.392 2176 Planarity : 0.004 0.069 2276 Dihedral : 3.465 13.912 1996 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.27 % Allowed : 13.32 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 3.05 (0.20), residues: 1620 helix: 2.80 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.44 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 355 HIS 0.001 0.000 HIS D 197 PHE 0.012 0.001 PHE D 64 TYR 0.012 0.001 TYR A 241 ARG 0.009 0.000 ARG C 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3240 Ramachandran restraints generated. 1620 Oldfield, 0 Emsley, 1620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 169 time to evaluate : 2.366 Fit side-chains REVERT: A 180 ARG cc_start: 0.8068 (tpp80) cc_final: 0.7761 (tpp80) REVERT: D 180 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.7776 (tpp80) outliers start: 4 outliers final: 5 residues processed: 173 average time/residue: 2.9044 time to fit residues: 551.2452 Evaluate side-chains 174 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 169 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.080369 restraints weight = 47326.242| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.89 r_work: 0.2768 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 13780 Z= 0.298 Angle : 0.517 11.259 18704 Z= 0.277 Chirality : 0.048 1.398 2176 Planarity : 0.004 0.067 2276 Dihedral : 3.551 13.884 1996 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.27 % Allowed : 13.25 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 2.94 (0.20), residues: 1620 helix: 2.74 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.51 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 355 HIS 0.002 0.001 HIS D 197 PHE 0.015 0.001 PHE D 66 TYR 0.012 0.001 TYR A 241 ARG 0.009 0.000 ARG D 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9303.35 seconds wall clock time: 161 minutes 48.66 seconds (9708.66 seconds total)