Starting phenix.real_space_refine on Sat Jul 20 01:00:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl1_36386/07_2024/8jl1_36386.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl1_36386/07_2024/8jl1_36386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl1_36386/07_2024/8jl1_36386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl1_36386/07_2024/8jl1_36386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl1_36386/07_2024/8jl1_36386.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jl1_36386/07_2024/8jl1_36386.cif" } resolution = 2.8 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= 0.001 sd= 0.035 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 P 6 5.49 5 S 40 5.16 5 C 6458 2.51 5 N 1364 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 9384 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4189 Classifications: {'peptide': 527} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 501} Chain breaks: 3 Chain: "B" Number of atoms: 4189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4189 Classifications: {'peptide': 527} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 501} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 447 Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 1, 'OCT': 16, 'R16': 1} Classifications: {'undetermined': 36} Link IDs: {None: 35} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 447 Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 1, 'OCT': 16, 'R16': 1} Classifications: {'undetermined': 36} Link IDs: {None: 35} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.57, per 1000 atoms: 0.70 Number of scatterers: 9384 At special positions: 0 Unit cell: (108.73, 87.15, 105.41, 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 40 16.00 P 6 15.00 O 1516 8.00 N 1364 7.00 C 6458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 443 " - pdb=" SG CYS A 462 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 107 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 443 " - pdb=" SG CYS B 462 " distance=2.03 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 802 " - " ASN A 94 " " NAG B 803 " - " ASN B 94 " " NAG C 1 " - " ASN A 142 " " NAG D 1 " - " ASN A 162 " " NAG E 1 " - " ASN B 142 " " NAG F 1 " - " ASN B 162 " Time building additional restraints: 3.88 Conformation dependent library (CDL) restraints added in 1.5 seconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1948 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 56.5% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 191 through 215 Processing helix chain 'A' and resid 268 through 287 removed outlier: 3.593A pdb=" N ASP A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.545A pdb=" N TYR A 292 " --> pdb=" O GLY A 289 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TRP A 293 " --> pdb=" O GLY A 290 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR A 294 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 296 " --> pdb=" O TRP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 Processing helix chain 'A' and resid 308 through 331 removed outlier: 3.538A pdb=" N TRP A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 356 Processing helix chain 'A' and resid 367 through 371 Processing helix chain 'A' and resid 375 through 394 Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 437 removed outlier: 3.546A pdb=" N TRP A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 removed outlier: 3.559A pdb=" N LYS A 458 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 475 Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.952A pdb=" N VAL A 488 " --> pdb=" O SER A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 524 Processing helix chain 'A' and resid 527 through 551 removed outlier: 3.549A pdb=" N ILE A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 590 Proline residue: A 587 - end of helix Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 606 through 617 Processing helix chain 'A' and resid 632 through 657 Processing helix chain 'B' and resid 191 through 215 Processing helix chain 'B' and resid 268 through 287 removed outlier: 3.593A pdb=" N ASP B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.545A pdb=" N TYR B 292 " --> pdb=" O GLY B 289 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP B 293 " --> pdb=" O GLY B 290 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TYR B 294 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS B 296 " --> pdb=" O TRP B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 307 Processing helix chain 'B' and resid 308 through 331 removed outlier: 3.538A pdb=" N TRP B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 356 Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 375 through 394 Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 417 through 437 removed outlier: 3.546A pdb=" N TRP B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.559A pdb=" N LYS B 458 " --> pdb=" O ASP B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 475 Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.952A pdb=" N VAL B 488 " --> pdb=" O SER B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 524 Processing helix chain 'B' and resid 527 through 551 removed outlier: 3.550A pdb=" N ILE B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 590 Proline residue: B 587 - end of helix Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 606 through 617 Processing helix chain 'B' and resid 632 through 657 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132 removed outlier: 8.935A pdb=" N TYR A 163 " --> pdb=" O GLN A 81 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU A 83 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU A 165 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 85 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL A 167 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N HIS A 87 " --> pdb=" O VAL A 167 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN A 162 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 168 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115 removed outlier: 6.841A pdb=" N VAL A 97 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ASN A 114 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU A 95 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A 151 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132 removed outlier: 8.936A pdb=" N TYR B 163 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 83 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N LEU B 165 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU B 85 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL B 167 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS B 87 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN B 162 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 168 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115 removed outlier: 6.840A pdb=" N VAL B 97 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ASN B 114 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU B 95 " --> pdb=" O ASN B 114 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS B 151 " --> pdb=" O LEU B 141 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1356 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: 2.73 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1403 1.32 - 1.45: 2457 1.45 - 1.57: 5642 1.57 - 1.69: 6 1.69 - 1.82: 54 Bond restraints: 9562 Sorted by residual: bond pdb=" CG LEU B 279 " pdb=" CD1 LEU B 279 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.10e+00 bond pdb=" CG LEU A 279 " pdb=" CD1 LEU A 279 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.08e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.81e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.73e+00 bond pdb=" CB PRO B 311 " pdb=" CG PRO B 311 " ideal model delta sigma weight residual 1.492 1.427 0.065 5.00e-02 4.00e+02 1.70e+00 ... (remaining 9557 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.66: 283 106.66 - 114.29: 5905 114.29 - 121.92: 4984 121.92 - 129.56: 1484 129.56 - 137.19: 100 Bond angle restraints: 12756 Sorted by residual: angle pdb=" N MET B 282 " pdb=" CA MET B 282 " pdb=" CB MET B 282 " ideal model delta sigma weight residual 110.28 116.08 -5.80 1.55e+00 4.16e-01 1.40e+01 angle pdb=" N MET A 282 " pdb=" CA MET A 282 " pdb=" CB MET A 282 " ideal model delta sigma weight residual 110.28 116.08 -5.80 1.55e+00 4.16e-01 1.40e+01 angle pdb=" C LEU A 281 " pdb=" N MET A 282 " pdb=" CA MET A 282 " ideal model delta sigma weight residual 120.31 114.75 5.56 1.52e+00 4.33e-01 1.34e+01 angle pdb=" C LEU B 281 " pdb=" N MET B 282 " pdb=" CA MET B 282 " ideal model delta sigma weight residual 120.31 114.82 5.49 1.52e+00 4.33e-01 1.30e+01 angle pdb=" C MET A 282 " pdb=" CA MET A 282 " pdb=" CB MET A 282 " ideal model delta sigma weight residual 110.67 104.32 6.35 1.92e+00 2.71e-01 1.10e+01 ... (remaining 12751 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.47: 5073 15.47 - 30.94: 623 30.94 - 46.41: 158 46.41 - 61.88: 72 61.88 - 77.35: 12 Dihedral angle restraints: 5938 sinusoidal: 2896 harmonic: 3042 Sorted by residual: dihedral pdb=" CB CYS B 443 " pdb=" SG CYS B 443 " pdb=" SG CYS B 462 " pdb=" CB CYS B 462 " ideal model delta sinusoidal sigma weight residual 93.00 170.35 -77.35 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS A 443 " pdb=" SG CYS A 443 " pdb=" SG CYS A 462 " pdb=" CB CYS A 462 " ideal model delta sinusoidal sigma weight residual 93.00 170.34 -77.34 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS B 151 " pdb=" SG CYS B 151 " pdb=" SG CYS B 179 " pdb=" CB CYS B 179 " ideal model delta sinusoidal sigma weight residual 93.00 138.30 -45.30 1 1.00e+01 1.00e-02 2.85e+01 ... (remaining 5935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 704 0.029 - 0.059: 490 0.059 - 0.088: 148 0.088 - 0.117: 69 0.117 - 0.147: 15 Chirality restraints: 1426 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 142 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 142 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.26e-01 chirality pdb=" CA PRO A 460 " pdb=" N PRO A 460 " pdb=" C PRO A 460 " pdb=" CB PRO A 460 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.38e-01 ... (remaining 1423 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 420 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" CD GLN A 420 " -0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN A 420 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN A 420 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 420 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.92e+00 pdb=" CD GLN B 420 " 0.024 2.00e-02 2.50e+03 pdb=" OE1 GLN B 420 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 GLN B 420 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 192 " -0.021 5.00e-02 4.00e+02 3.16e-02 1.59e+00 pdb=" N PRO B 193 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 193 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 193 " -0.018 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1462 2.76 - 3.30: 7932 3.30 - 3.83: 14570 3.83 - 4.37: 18790 4.37 - 4.90: 32457 Nonbonded interactions: 75211 Sorted by model distance: nonbonded pdb=" OD1 ASN A 191 " pdb=" OH TYR A 294 " model vdw 2.226 2.440 nonbonded pdb=" OD1 ASN B 191 " pdb=" OH TYR B 294 " model vdw 2.226 2.440 nonbonded pdb=" O ILE B 559 " pdb=" OG SER B 569 " model vdw 2.372 2.440 nonbonded pdb=" O ILE A 559 " pdb=" OG SER A 569 " model vdw 2.373 2.440 nonbonded pdb=" O LYS A 296 " pdb=" OG1 THR A 304 " model vdw 2.392 2.440 ... (remaining 75206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 663 or resid 805 through 806 or (resid 808 and \ (name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C0 \ 9 or name C10 or name C11 or name C12 or name C13 or name C14)) or resid 809 thr \ ough 811 or resid 818 or resid 823 through 825 or (resid 827 and (name C03 or na \ me C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 o \ r name C11 or name C12 or name C13 or name C14)) or resid 828 through 829 or res \ id 831 or resid 834 through 835)) selection = (chain 'B' and (resid 75 through 663 or resid 805 through 806 or resid 808 throu \ gh 811 or resid 818 or resid 823 through 825 or resid 827 through 829 or resid 8 \ 31 or resid 834 through 835)) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.820 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 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 0.067 9562 Z= 0.427 Angle : 0.611 6.355 12756 Z= 0.313 Chirality : 0.044 0.147 1426 Planarity : 0.004 0.032 1446 Dihedral : 15.095 75.183 3972 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1038 helix: 1.63 (0.22), residues: 498 sheet: 0.96 (0.43), residues: 122 loop : -0.35 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 647 HIS 0.010 0.001 HIS A 614 PHE 0.013 0.002 PHE A 322 TYR 0.020 0.002 TYR A 620 ARG 0.003 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 0.982 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 1.2375 time to fit residues: 104.0307 Evaluate side-chains 62 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.0770 chunk 78 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9562 Z= 0.182 Angle : 0.477 6.205 12756 Z= 0.248 Chirality : 0.039 0.135 1426 Planarity : 0.004 0.035 1446 Dihedral : 12.420 59.749 2080 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.20 % Allowed : 8.32 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.14 (0.26), residues: 1038 helix: 2.73 (0.22), residues: 496 sheet: 1.25 (0.41), residues: 128 loop : -0.17 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.004 0.001 HIS A 614 PHE 0.014 0.001 PHE A 322 TYR 0.010 0.001 TYR B 570 ARG 0.005 0.001 ARG B 337 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 64 time to evaluate : 1.033 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.9866 time to fit residues: 69.4757 Evaluate side-chains 65 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9562 Z= 0.252 Angle : 0.491 6.290 12756 Z= 0.250 Chirality : 0.041 0.144 1426 Planarity : 0.004 0.033 1446 Dihedral : 12.042 56.816 2080 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.53 % Allowed : 9.52 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.29 (0.26), residues: 1038 helix: 2.92 (0.22), residues: 498 sheet: 1.25 (0.41), residues: 130 loop : -0.18 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.005 0.001 HIS B 614 PHE 0.015 0.001 PHE A 322 TYR 0.010 0.001 TYR B 294 ARG 0.002 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 58 time to evaluate : 0.985 Fit side-chains REVERT: A 148 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7387 (ptmt) REVERT: A 416 SER cc_start: 0.8750 (p) cc_final: 0.8548 (m) REVERT: B 148 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7362 (ptmt) REVERT: B 416 SER cc_start: 0.8749 (p) cc_final: 0.8545 (m) outliers start: 14 outliers final: 8 residues processed: 60 average time/residue: 0.9259 time to fit residues: 61.7725 Evaluate side-chains 62 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 52 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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: 0.8541 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9562 Z= 0.237 Angle : 0.476 6.311 12756 Z= 0.244 Chirality : 0.040 0.151 1426 Planarity : 0.003 0.033 1446 Dihedral : 11.624 58.039 2080 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.53 % Allowed : 10.83 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.42 (0.26), residues: 1038 helix: 3.05 (0.22), residues: 498 sheet: 1.26 (0.41), residues: 130 loop : -0.13 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 647 HIS 0.005 0.001 HIS B 614 PHE 0.014 0.001 PHE A 322 TYR 0.010 0.001 TYR A 570 ARG 0.002 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 56 time to evaluate : 0.967 Fit side-chains REVERT: A 148 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7354 (ptmt) REVERT: B 148 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7327 (ptmt) outliers start: 14 outliers final: 6 residues processed: 62 average time/residue: 0.8908 time to fit residues: 61.4816 Evaluate side-chains 59 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 51 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 9562 Z= 0.527 Angle : 0.625 6.513 12756 Z= 0.315 Chirality : 0.047 0.162 1426 Planarity : 0.005 0.037 1446 Dihedral : 12.991 57.734 2080 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.74 % Allowed : 10.50 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.00 (0.26), residues: 1038 helix: 2.53 (0.21), residues: 498 sheet: 1.34 (0.41), residues: 128 loop : -0.19 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 647 HIS 0.005 0.001 HIS B 483 PHE 0.017 0.002 PHE B 322 TYR 0.018 0.002 TYR A 496 ARG 0.004 0.001 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 55 time to evaluate : 1.027 Fit side-chains REVERT: A 148 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7346 (ptmt) REVERT: A 337 ARG cc_start: 0.7500 (mtp-110) cc_final: 0.7275 (ttm110) REVERT: A 391 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 556 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7680 (mt-10) REVERT: B 148 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7341 (ptmt) REVERT: B 337 ARG cc_start: 0.7510 (mtp-110) cc_final: 0.7284 (ttm110) REVERT: B 391 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7704 (mm-30) REVERT: B 556 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7687 (mt-10) outliers start: 25 outliers final: 14 residues processed: 65 average time/residue: 1.1962 time to fit residues: 84.6792 Evaluate side-chains 70 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 52 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 483 HIS Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 483 HIS Chi-restraints excluded: chain B residue 556 GLU Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 358 ASN B 87 HIS B 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9562 Z= 0.232 Angle : 0.482 6.313 12756 Z= 0.247 Chirality : 0.040 0.157 1426 Planarity : 0.004 0.032 1446 Dihedral : 11.959 58.396 2080 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.30 % Allowed : 11.49 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.37 (0.26), residues: 1038 helix: 2.96 (0.22), residues: 498 sheet: 1.28 (0.41), residues: 128 loop : -0.10 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.002 0.001 HIS A 483 PHE 0.014 0.001 PHE A 322 TYR 0.013 0.001 TYR A 570 ARG 0.002 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 52 time to evaluate : 1.025 Fit side-chains REVERT: A 148 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7318 (ptmt) REVERT: A 391 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7667 (mm-30) REVERT: B 148 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7323 (ptmt) REVERT: B 391 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7676 (mm-30) outliers start: 21 outliers final: 12 residues processed: 58 average time/residue: 1.0694 time to fit residues: 68.2218 Evaluate side-chains 65 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 51 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 84 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9562 Z= 0.192 Angle : 0.453 6.325 12756 Z= 0.232 Chirality : 0.039 0.153 1426 Planarity : 0.003 0.032 1446 Dihedral : 10.844 58.436 2080 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.31 % Allowed : 12.80 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.55 (0.26), residues: 1038 helix: 3.14 (0.22), residues: 502 sheet: 1.23 (0.42), residues: 130 loop : -0.05 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.004 0.001 HIS B 614 PHE 0.013 0.001 PHE B 322 TYR 0.011 0.001 TYR A 570 ARG 0.001 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.885 Fit side-chains REVERT: A 325 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7893 (tpp) REVERT: A 556 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: A 630 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.8086 (t0) REVERT: B 325 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7881 (tpp) REVERT: B 630 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.8111 (t0) outliers start: 12 outliers final: 4 residues processed: 58 average time/residue: 1.1293 time to fit residues: 71.6383 Evaluate side-chains 58 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 556 GLU Chi-restraints excluded: chain A residue 630 ASN Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 630 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 0.0670 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9562 Z= 0.166 Angle : 0.440 6.336 12756 Z= 0.226 Chirality : 0.039 0.152 1426 Planarity : 0.003 0.034 1446 Dihedral : 10.252 57.472 2080 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.88 % Allowed : 13.57 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.64 (0.26), residues: 1038 helix: 3.25 (0.21), residues: 502 sheet: 1.30 (0.42), residues: 130 loop : -0.05 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.002 0.001 HIS B 614 PHE 0.013 0.001 PHE B 322 TYR 0.011 0.001 TYR B 570 ARG 0.001 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 1.024 Fit side-chains REVERT: A 325 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7884 (tpp) REVERT: B 325 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7873 (tpp) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 1.0721 time to fit residues: 60.1921 Evaluate side-chains 53 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 478 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 60 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9562 Z= 0.147 Angle : 0.427 6.309 12756 Z= 0.219 Chirality : 0.038 0.150 1426 Planarity : 0.003 0.036 1446 Dihedral : 9.743 58.635 2080 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.77 % Allowed : 13.68 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.75 (0.26), residues: 1038 helix: 3.37 (0.21), residues: 502 sheet: 1.32 (0.42), residues: 130 loop : -0.03 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 647 HIS 0.002 0.001 HIS B 614 PHE 0.013 0.001 PHE A 322 TYR 0.010 0.001 TYR A 570 ARG 0.001 0.000 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 51 time to evaluate : 0.878 Fit side-chains REVERT: A 148 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7365 (ptmt) REVERT: A 325 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7893 (tpp) REVERT: A 478 ASP cc_start: 0.7549 (p0) cc_final: 0.7285 (m-30) REVERT: B 325 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7883 (tpp) REVERT: B 478 ASP cc_start: 0.7570 (p0) cc_final: 0.7283 (m-30) outliers start: 7 outliers final: 4 residues processed: 55 average time/residue: 1.0152 time to fit residues: 61.3380 Evaluate side-chains 56 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 0.0370 chunk 8 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9562 Z= 0.177 Angle : 0.439 6.394 12756 Z= 0.226 Chirality : 0.039 0.149 1426 Planarity : 0.003 0.035 1446 Dihedral : 9.772 59.961 2080 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.98 % Allowed : 13.46 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.73 (0.26), residues: 1038 helix: 3.32 (0.21), residues: 502 sheet: 1.39 (0.42), residues: 130 loop : -0.01 (0.32), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.002 0.001 HIS B 614 PHE 0.014 0.001 PHE B 322 TYR 0.011 0.001 TYR B 570 ARG 0.001 0.000 ARG B 152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.962 Fit side-chains REVERT: A 148 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7365 (ptmt) REVERT: A 325 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7883 (tpp) REVERT: B 325 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7873 (tpp) outliers start: 9 outliers final: 5 residues processed: 53 average time/residue: 1.0166 time to fit residues: 59.3675 Evaluate side-chains 57 residues out of total 914 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 CYS Chi-restraints excluded: chain A residue 148 LYS Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain B residue 104 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 478 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 82 optimal weight: 0.0970 chunk 34 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS B 87 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.135814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.100773 restraints weight = 10141.997| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.79 r_work: 0.3013 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9562 Z= 0.170 Angle : 0.439 6.372 12756 Z= 0.225 Chirality : 0.039 0.150 1426 Planarity : 0.003 0.035 1446 Dihedral : 9.648 57.675 2080 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.98 % Rotamer: Outliers : 1.31 % Allowed : 13.13 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 2.76 (0.26), residues: 1038 helix: 3.32 (0.21), residues: 502 sheet: 1.44 (0.42), residues: 130 loop : 0.01 (0.33), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 647 HIS 0.002 0.001 HIS A 614 PHE 0.014 0.001 PHE B 322 TYR 0.011 0.001 TYR A 570 ARG 0.001 0.000 ARG A 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2526.58 seconds wall clock time: 45 minutes 37.99 seconds (2737.99 seconds total)