Starting phenix.real_space_refine on Sat Apr 13 02:47:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/04_2024/8jmh_36421_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/04_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_36421/04_2024/8jmh_36421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/04_2024/8jmh_36421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/04_2024/8jmh_36421_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jmh_36421/04_2024/8jmh_36421_neut_trim_updated.pdb" } 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-5288/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: 11.71, per 1000 atoms: 0.43 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: 24.03 Conformation dependent library (CDL) restraints added in 2.8 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... running ksdssp... Secondary structure from input PDB file: 63 helices and 0 sheets defined 73.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.47 Creating SS restraints... Processing helix chain 'A' and resid 59 through 72 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 96 through 122 Processing helix chain 'A' and resid 129 through 163 Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 178 through 213 Processing helix chain 'A' and resid 224 through 231 Processing helix chain 'A' and resid 233 through 236 No H-bonds generated for 'chain 'A' and resid 233 through 236' Processing helix chain 'A' and resid 243 through 288 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) removed outlier: 3.908A pdb=" N LEU A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 318 Processing helix chain 'A' and resid 320 through 340 removed outlier: 3.783A pdb=" N ASN A 340 " --> pdb=" O TYR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 381 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) Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.857A pdb=" N ARG A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'A' and resid 422 through 442 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 444 through 449 Processing helix chain 'B' and resid 59 through 72 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 96 through 122 Processing helix chain 'B' and resid 129 through 163 Proline residue: B 153 - end of helix Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 178 through 213 Processing helix chain 'B' and resid 224 through 231 Processing helix chain 'B' and resid 233 through 236 No H-bonds generated for 'chain 'B' and resid 233 through 236' Processing helix chain 'B' and resid 243 through 288 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) removed outlier: 3.903A pdb=" N LEU B 288 " --> pdb=" O ARG B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 318 Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.777A pdb=" N ASN B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 381 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) Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.857A pdb=" N ARG B 388 " --> pdb=" O GLY B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'B' and resid 422 through 442 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 444 through 449 Processing helix chain 'C' and resid 59 through 72 Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 96 through 122 Processing helix chain 'C' and resid 129 through 163 Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 178 through 213 Processing helix chain 'C' and resid 224 through 231 Processing helix chain 'C' and resid 233 through 236 No H-bonds generated for 'chain 'C' and resid 233 through 236' Processing helix chain 'C' and resid 243 through 288 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) removed outlier: 3.895A pdb=" N LEU C 288 " --> pdb=" O ARG C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 318 Processing helix chain 'C' and resid 320 through 340 removed outlier: 3.777A pdb=" N ASN C 340 " --> pdb=" O TYR C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 381 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) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.864A pdb=" N ARG C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 Processing helix chain 'C' and resid 422 through 442 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 444 through 449 Processing helix chain 'D' and resid 59 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 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 96 through 122 Processing helix chain 'D' and resid 128 through 163 Proline residue: D 153 - end of helix Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 178 through 215 removed outlier: 3.615A pdb=" N CYS D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 231 Processing helix chain 'D' and resid 233 through 236 No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 243 through 288 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) removed outlier: 3.837A pdb=" N LEU D 288 " --> pdb=" O ARG D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 340 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) removed outlier: 3.625A pdb=" N ASN D 340 " --> pdb=" O TYR D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 381 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) Processing helix chain 'D' and resid 383 through 388 removed outlier: 3.809A pdb=" N ARG D 388 " --> pdb=" O GLY D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 407 Processing helix chain 'D' and resid 422 through 439 Processing helix chain 'D' and resid 444 through 449 897 hydrogen bonds defined for protein. 2601 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: 9.41 Time building geometry restraints manager: 23.63 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: 1911 2.21 - 2.81: 58157 2.81 - 3.41: 79325 3.41 - 4.00: 102981 4.00 - 4.60: 159746 Nonbonded interactions: 402120 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 402115 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: 0.930 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: 0.370 Extract box with map and model: 4.680 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 87.270 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.130 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:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.700 ------------------------------------------------------------------------------- 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= 0.422 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 : 2.159 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 2.8055 time to fit residues: 541.2760 Evaluate side-chains 175 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.156 ------------------------------------------------------------------------------- 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: 0.3980 chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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: 0.8087 moved from start: 0.0526 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= 0.198 Angle : 0.517 11.238 18704 Z= 0.277 Chirality : 0.047 1.394 2176 Planarity : 0.003 0.040 2276 Dihedral : 5.335 28.043 1996 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 11.82 % Favored : 88.18 % 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: 2.67 (0.14), residues: 1184 sheet: None (None), residues: 0 loop : -0.12 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 152 HIS 0.002 0.000 HIS D 197 PHE 0.014 0.001 PHE C 64 TYR 0.011 0.001 TYR D 241 ARG 0.005 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 171 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.192 Fit side-chains REVERT: A 94 LYS cc_start: 0.7495 (tptt) cc_final: 0.7096 (tptp) REVERT: B 94 LYS cc_start: 0.7546 (tptt) cc_final: 0.7149 (tptp) REVERT: C 94 LYS cc_start: 0.7555 (tptt) cc_final: 0.7152 (tptp) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 2.9072 time to fit residues: 552.4868 Evaluate side-chains 170 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 40 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.0759 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= 0.293 Angle : 0.516 11.281 18704 Z= 0.278 Chirality : 0.048 1.405 2176 Planarity : 0.004 0.050 2276 Dihedral : 4.095 15.881 1996 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.27 % Allowed : 11.82 % Favored : 87.91 % 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: 2.62 (0.20), residues: 1620 helix: 2.44 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.45 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 355 HIS 0.003 0.001 HIS D 197 PHE 0.014 0.001 PHE D 66 TYR 0.012 0.001 TYR D 241 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 178 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 2.163 Fit side-chains REVERT: A 94 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7136 (tptt) REVERT: B 94 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7138 (tptt) REVERT: C 94 LYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7142 (tptt) REVERT: D 180 ARG cc_start: 0.8118 (tpp-160) cc_final: 0.7832 (tpp80) outliers start: 4 outliers final: 0 residues processed: 174 average time/residue: 2.8607 time to fit residues: 545.8419 Evaluate side-chains 176 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 173 time to evaluate : 2.360 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 97 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.0842 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= 0.211 Angle : 0.485 11.261 18704 Z= 0.261 Chirality : 0.046 1.397 2176 Planarity : 0.003 0.050 2276 Dihedral : 3.562 11.565 1996 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.27 % Allowed : 12.16 % Favored : 87.57 % 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: 2.71 (0.21), residues: 1620 helix: 2.51 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.40 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 355 HIS 0.002 0.000 HIS D 197 PHE 0.013 0.001 PHE A 64 TYR 0.012 0.001 TYR B 241 ARG 0.006 0.000 ARG D 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 178 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 2.228 Fit side-chains REVERT: B 94 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.7129 (tptt) REVERT: C 94 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7115 (tptt) REVERT: D 180 ARG cc_start: 0.8126 (tpp-160) cc_final: 0.7839 (tpp80) outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 2.9416 time to fit residues: 563.4799 Evaluate side-chains 174 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 171 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain D residue 215 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 128 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 2 optimal weight: 0.0170 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.5424 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.0941 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= 0.225 Angle : 0.492 11.245 18704 Z= 0.263 Chirality : 0.047 1.396 2176 Planarity : 0.004 0.055 2276 Dihedral : 3.476 11.388 1996 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.20 % Allowed : 12.84 % Favored : 86.96 % 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: 2.74 (0.21), residues: 1620 helix: 2.53 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.44 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 355 HIS 0.002 0.000 HIS D 197 PHE 0.013 0.001 PHE B 64 TYR 0.012 0.001 TYR A 241 ARG 0.006 0.000 ARG B 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 181 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 2.136 Fit side-chains REVERT: A 94 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7102 (tptt) REVERT: D 94 LYS cc_start: 0.7706 (tptp) cc_final: 0.7390 (tptt) REVERT: D 180 ARG cc_start: 0.8128 (tpp-160) cc_final: 0.7841 (tpp80) outliers start: 3 outliers final: 2 residues processed: 180 average time/residue: 2.8364 time to fit residues: 562.8912 Evaluate side-chains 178 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B 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: 5.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13780 Z= 0.217 Angle : 0.483 11.230 18704 Z= 0.259 Chirality : 0.046 1.393 2176 Planarity : 0.004 0.055 2276 Dihedral : 3.417 11.537 1996 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.20 % Allowed : 13.18 % Favored : 86.62 % 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 (0.21), residues: 1620 helix: 2.55 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.41 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 355 HIS 0.002 0.000 HIS D 197 PHE 0.013 0.001 PHE C 64 TYR 0.012 0.001 TYR D 241 ARG 0.009 0.000 ARG D 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 178 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 2.091 Fit side-chains REVERT: A 94 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7107 (tptt) REVERT: D 180 ARG cc_start: 0.8136 (tpp-160) cc_final: 0.7854 (tpp80) outliers start: 3 outliers final: 2 residues processed: 177 average time/residue: 2.9116 time to fit residues: 563.7212 Evaluate side-chains 178 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 175 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain C residue 215 CYS 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: 3.9990 chunk 17 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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: 0.8089 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13780 Z= 0.214 Angle : 0.492 11.241 18704 Z= 0.261 Chirality : 0.047 1.395 2176 Planarity : 0.004 0.061 2276 Dihedral : 3.376 11.485 1996 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.27 % Allowed : 13.45 % 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: 2.79 (0.21), residues: 1620 helix: 2.57 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.42 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 355 HIS 0.002 0.000 HIS D 197 PHE 0.013 0.001 PHE B 64 TYR 0.012 0.001 TYR D 241 ARG 0.008 0.000 ARG A 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 182 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 178 time to evaluate : 2.174 Fit side-chains REVERT: D 180 ARG cc_start: 0.8134 (tpp-160) cc_final: 0.7852 (tpp80) outliers start: 4 outliers final: 4 residues processed: 182 average time/residue: 2.8431 time to fit residues: 566.4287 Evaluate side-chains 180 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 176 time to evaluate : 2.221 ------------------------------------------------------------------------------- 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: 1.9990 chunk 98 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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: 0.8092 moved from start: 0.1031 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= 0.229 Angle : 0.484 11.243 18704 Z= 0.260 Chirality : 0.047 1.395 2176 Planarity : 0.004 0.063 2276 Dihedral : 3.389 11.380 1996 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.34 % Allowed : 13.04 % Favored : 86.62 % 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 (0.21), residues: 1620 helix: 2.57 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.40 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 355 HIS 0.002 0.000 HIS D 197 PHE 0.013 0.001 PHE A 64 TYR 0.012 0.001 TYR D 241 ARG 0.009 0.000 ARG A 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 181 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 176 time to evaluate : 2.199 Fit side-chains REVERT: D 180 ARG cc_start: 0.8133 (tpp-160) cc_final: 0.7852 (tpp80) outliers start: 5 outliers final: 5 residues processed: 181 average time/residue: 2.8717 time to fit residues: 569.8068 Evaluate side-chains 180 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 175 time to evaluate : 2.228 ------------------------------------------------------------------------------- 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 75 ILE 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: 2.9990 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: 0.9990 chunk 129 optimal weight: 0.6980 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: 0.8095 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13780 Z= 0.242 Angle : 0.502 11.249 18704 Z= 0.266 Chirality : 0.047 1.396 2176 Planarity : 0.004 0.067 2276 Dihedral : 3.385 11.318 1996 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.54 % Allowed : 13.18 % 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: 2.78 (0.21), residues: 1620 helix: 2.56 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.40 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 355 HIS 0.002 0.000 HIS D 197 PHE 0.013 0.001 PHE B 64 TYR 0.012 0.001 TYR B 241 ARG 0.008 0.000 ARG A 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 186 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 178 time to evaluate : 2.213 Fit side-chains REVERT: D 180 ARG cc_start: 0.8140 (tpp-160) cc_final: 0.7860 (tpp80) outliers start: 8 outliers final: 8 residues processed: 186 average time/residue: 2.8471 time to fit residues: 581.9179 Evaluate side-chains 184 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 176 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain D residue 75 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 151 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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: 0.8089 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13780 Z= 0.205 Angle : 0.481 11.241 18704 Z= 0.258 Chirality : 0.046 1.394 2176 Planarity : 0.004 0.067 2276 Dihedral : 3.350 11.353 1996 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.48 % Allowed : 13.04 % 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: 2.85 (0.21), residues: 1620 helix: 2.60 (0.14), residues: 1208 sheet: None (None), residues: 0 loop : -0.34 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 355 HIS 0.002 0.000 HIS D 197 PHE 0.013 0.001 PHE A 64 TYR 0.012 0.001 TYR D 241 ARG 0.010 0.000 ARG A 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 182 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 2.158 Fit side-chains REVERT: D 94 LYS cc_start: 0.7538 (tptt) cc_final: 0.7063 (tptp) REVERT: D 180 ARG cc_start: 0.8142 (tpp-160) cc_final: 0.7858 (tpp80) outliers start: 7 outliers final: 7 residues processed: 182 average time/residue: 2.8784 time to fit residues: 574.1748 Evaluate side-chains 182 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 175 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain C residue 75 ILE 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 135 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 35 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.081727 restraints weight = 47104.942| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.89 r_work: 0.2790 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1124 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= 0.186 Angle : 0.489 11.227 18704 Z= 0.258 Chirality : 0.046 1.392 2176 Planarity : 0.004 0.076 2276 Dihedral : 3.311 11.295 1996 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.61 % Allowed : 13.59 % Favored : 85.80 % 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 (0.21), residues: 1620 helix: 2.65 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -0.31 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 355 HIS 0.002 0.000 HIS D 197 PHE 0.013 0.001 PHE C 64 TYR 0.012 0.001 TYR B 241 ARG 0.011 0.000 ARG C 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9488.97 seconds wall clock time: 169 minutes 9.43 seconds (10149.43 seconds total)