Starting phenix.real_space_refine on Fri Mar 6 00:25:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r8u_4761/03_2026/6r8u_4761_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r8u_4761/03_2026/6r8u_4761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6r8u_4761/03_2026/6r8u_4761_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r8u_4761/03_2026/6r8u_4761_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6r8u_4761/03_2026/6r8u_4761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r8u_4761/03_2026/6r8u_4761.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.136 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 88 5.16 5 C 8524 2.51 5 N 2420 2.21 5 O 2500 1.98 5 H 13176 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26712 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6661 Chain: "B" Number of atoms: 6655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6661 Chain: "D" Number of atoms: 6655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6661 Chain: "C" Number of atoms: 6655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6661 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AALA A 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA A 220 " occ=0.43 residue: pdb=" N AALA B 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA B 220 " occ=0.43 residue: pdb=" N AALA D 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA D 220 " occ=0.43 residue: pdb=" N AALA C 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA C 220 " occ=0.43 Time building chain proxies: 7.78, per 1000 atoms: 0.29 Number of scatterers: 26712 At special positions: 0 Unit cell: (103.653, 103.653, 105.747, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 4 15.00 O 2500 8.00 N 2420 7.00 C 8524 6.00 H 13176 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 0 sheets defined 24.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 11 through 16 removed outlier: 3.530A pdb=" N GLN A 15 " --> pdb=" O MET A 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 16' Processing helix chain 'A' and resid 30 through 37 removed outlier: 3.689A pdb=" N LYS A 34 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 35 " --> pdb=" O ARG A 32 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR A 37 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 55 through 63 removed outlier: 3.629A pdb=" N ASN A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS A 61 " --> pdb=" O ALA A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.824A pdb=" N ASP A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 232 removed outlier: 4.007A pdb=" N GLU A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 250 removed outlier: 3.662A pdb=" N LYS A 247 " --> pdb=" O ASP A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 289 removed outlier: 3.627A pdb=" N TYR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'A' and resid 418 through 424 Processing helix chain 'B' and resid 11 through 16 removed outlier: 3.530A pdb=" N GLN B 15 " --> pdb=" O MET B 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 30 through 37 removed outlier: 3.689A pdb=" N LYS B 34 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP B 35 " --> pdb=" O ARG B 32 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR B 37 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 44 Processing helix chain 'B' and resid 55 through 63 removed outlier: 3.629A pdb=" N ASN B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 151 through 159 removed outlier: 3.824A pdb=" N ASP B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 232 removed outlier: 4.007A pdb=" N GLU B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 250 removed outlier: 3.662A pdb=" N LYS B 247 " --> pdb=" O ASP B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 289 removed outlier: 3.627A pdb=" N TYR B 283 " --> pdb=" O THR B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'B' and resid 418 through 424 Processing helix chain 'D' and resid 11 through 16 removed outlier: 3.529A pdb=" N GLN D 15 " --> pdb=" O MET D 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 11 through 16' Processing helix chain 'D' and resid 30 through 37 removed outlier: 3.689A pdb=" N LYS D 34 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP D 35 " --> pdb=" O ARG D 32 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR D 37 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 44 Processing helix chain 'D' and resid 55 through 63 removed outlier: 3.629A pdb=" N ASN D 60 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.823A pdb=" N ASP D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 232 removed outlier: 4.007A pdb=" N GLU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 250 removed outlier: 3.662A pdb=" N LYS D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 289 removed outlier: 3.626A pdb=" N TYR D 283 " --> pdb=" O THR D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'D' and resid 418 through 424 Processing helix chain 'C' and resid 11 through 16 removed outlier: 3.529A pdb=" N GLN C 15 " --> pdb=" O MET C 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 11 through 16' Processing helix chain 'C' and resid 30 through 37 removed outlier: 3.688A pdb=" N LYS C 34 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP C 35 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR C 37 " --> pdb=" O LYS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 44 Processing helix chain 'C' and resid 55 through 63 removed outlier: 3.630A pdb=" N ASN C 60 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 151 through 159 removed outlier: 3.824A pdb=" N ASP C 155 " --> pdb=" O ARG C 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 232 removed outlier: 4.007A pdb=" N GLU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 250 removed outlier: 3.661A pdb=" N LYS C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 289 removed outlier: 3.627A pdb=" N TYR C 283 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 418 through 424 168 hydrogen bonds defined for protein. 420 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: 5.88 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13140 1.04 - 1.24: 1273 1.24 - 1.43: 4663 1.43 - 1.63: 7800 1.63 - 1.83: 140 Bond restraints: 27016 Sorted by residual: bond pdb=" C MET B 328 " pdb=" O MET B 328 " ideal model delta sigma weight residual 1.234 1.174 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" C MET C 328 " pdb=" O MET C 328 " ideal model delta sigma weight residual 1.234 1.174 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" C MET A 328 " pdb=" O MET A 328 " ideal model delta sigma weight residual 1.234 1.174 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" C MET D 328 " pdb=" O MET D 328 " ideal model delta sigma weight residual 1.234 1.175 0.059 1.17e-02 7.31e+03 2.53e+01 bond pdb=" C LYS B 34 " pdb=" O LYS B 34 " ideal model delta sigma weight residual 1.242 1.192 0.050 1.00e-02 1.00e+04 2.50e+01 ... (remaining 27011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 42630 2.11 - 4.21: 5575 4.21 - 6.32: 439 6.32 - 8.43: 50 8.43 - 10.53: 10 Bond angle restraints: 48704 Sorted by residual: angle pdb=" N LEU C 36 " pdb=" CA LEU C 36 " pdb=" C LEU C 36 " ideal model delta sigma weight residual 112.54 104.08 8.46 1.22e+00 6.72e-01 4.80e+01 angle pdb=" N LEU A 36 " pdb=" CA LEU A 36 " pdb=" C LEU A 36 " ideal model delta sigma weight residual 112.54 104.09 8.45 1.22e+00 6.72e-01 4.80e+01 angle pdb=" N LEU B 36 " pdb=" CA LEU B 36 " pdb=" C LEU B 36 " ideal model delta sigma weight residual 112.54 104.13 8.41 1.22e+00 6.72e-01 4.75e+01 angle pdb=" N LEU D 36 " pdb=" CA LEU D 36 " pdb=" C LEU D 36 " ideal model delta sigma weight residual 112.54 104.13 8.41 1.22e+00 6.72e-01 4.75e+01 angle pdb=" N GLU D 229 " pdb=" CA GLU D 229 " pdb=" C GLU D 229 " ideal model delta sigma weight residual 113.28 107.15 6.13 1.22e+00 6.72e-01 2.53e+01 ... (remaining 48699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 11908 24.80 - 49.60: 692 49.60 - 74.40: 144 74.40 - 99.20: 4 99.20 - 124.00: 4 Dihedral angle restraints: 12752 sinusoidal: 6976 harmonic: 5776 Sorted by residual: dihedral pdb=" C5' AMP B 501 " pdb=" O5' AMP B 501 " pdb=" P AMP B 501 " pdb=" O3P AMP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 64.00 -124.00 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" C5' AMP D 501 " pdb=" O5' AMP D 501 " pdb=" P AMP D 501 " pdb=" O3P AMP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 63.95 -123.95 1 2.00e+01 2.50e-03 3.74e+01 dihedral pdb=" C5' AMP C 501 " pdb=" O5' AMP C 501 " pdb=" P AMP C 501 " pdb=" O3P AMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 -173.46 113.46 1 2.00e+01 2.50e-03 3.36e+01 ... (remaining 12749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1588 0.089 - 0.177: 416 0.177 - 0.266: 36 0.266 - 0.355: 4 0.355 - 0.444: 8 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA VAL D 277 " pdb=" N VAL D 277 " pdb=" C VAL D 277 " pdb=" CB VAL D 277 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA VAL A 277 " pdb=" N VAL A 277 " pdb=" C VAL A 277 " pdb=" CB VAL A 277 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA VAL C 277 " pdb=" N VAL C 277 " pdb=" C VAL C 277 " pdb=" CB VAL C 277 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 2049 not shown) Planarity restraints: 4072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 88 " -0.019 2.00e-02 2.50e+03 3.12e-02 3.89e+01 pdb=" CG TRP C 88 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP C 88 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 88 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP C 88 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 88 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 88 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 88 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 88 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP C 88 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP C 88 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP C 88 " 0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP C 88 " 0.073 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 88 " -0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 88 " -0.078 2.00e-02 2.50e+03 pdb=" HH2 TRP C 88 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 88 " 0.020 2.00e-02 2.50e+03 3.12e-02 3.88e+01 pdb=" CG TRP B 88 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 88 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 88 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP B 88 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 88 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 88 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 88 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP B 88 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP B 88 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP B 88 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP B 88 " -0.074 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 88 " 0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 88 " 0.078 2.00e-02 2.50e+03 pdb=" HH2 TRP B 88 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 88 " 0.020 2.00e-02 2.50e+03 3.12e-02 3.88e+01 pdb=" CG TRP D 88 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP D 88 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 88 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP D 88 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 88 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 88 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 88 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 88 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP D 88 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP D 88 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP D 88 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP D 88 " -0.074 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 88 " 0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 88 " 0.077 2.00e-02 2.50e+03 pdb=" HH2 TRP D 88 " -0.040 2.00e-02 2.50e+03 ... (remaining 4069 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1590 2.18 - 2.79: 53196 2.79 - 3.39: 71788 3.39 - 4.00: 101967 4.00 - 4.60: 155837 Nonbonded interactions: 384378 Sorted by model distance: nonbonded pdb=" HE1 TYR B 145 " pdb=" HH TYR B 149 " model vdw 1.576 2.100 nonbonded pdb=" HE1 TYR D 145 " pdb=" HH TYR D 149 " model vdw 1.577 2.100 nonbonded pdb=" HE1 TYR A 145 " pdb=" HH TYR A 149 " model vdw 1.577 2.100 nonbonded pdb=" HE1 TYR C 145 " pdb=" HH TYR C 149 " model vdw 1.577 2.100 nonbonded pdb=" OD1 ASP B 276 " pdb=" H ASP B 276 " model vdw 1.651 2.450 ... (remaining 384373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.43 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: 0.590 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: 0.150 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 28.820 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 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 : 0.011 0.069 13840 Z= 0.630 Angle : 1.306 10.533 18776 Z= 0.788 Chirality : 0.078 0.444 2052 Planarity : 0.011 0.092 2448 Dihedral : 15.159 124.001 5188 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.60 % Allowed : 9.14 % Favored : 87.26 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.30 (0.17), residues: 1708 helix: -3.76 (0.16), residues: 384 sheet: -1.79 (0.36), residues: 184 loop : -1.75 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.005 ARG C 107 TYR 0.020 0.006 TYR C 222 PHE 0.033 0.005 PHE C 259 TRP 0.033 0.008 TRP D 284 HIS 0.017 0.006 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.01140 (13840) covalent geometry : angle 1.30557 (18776) hydrogen bonds : bond 0.27787 ( 168) hydrogen bonds : angle 10.58058 ( 420) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 351 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 0.755 Fit side-chains REVERT: A 39 LYS cc_start: 0.8089 (mttt) cc_final: 0.7538 (mtmt) REVERT: A 115 ARG cc_start: 0.6426 (mpt180) cc_final: 0.6204 (mmt180) REVERT: A 123 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7252 (mm-40) REVERT: A 148 ASP cc_start: 0.7818 (t0) cc_final: 0.7606 (t0) REVERT: A 186 ASN cc_start: 0.7395 (m-40) cc_final: 0.7119 (m-40) REVERT: A 191 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 198 ASN cc_start: 0.8102 (t0) cc_final: 0.7888 (p0) REVERT: A 229 GLU cc_start: 0.8369 (tt0) cc_final: 0.8105 (tt0) REVERT: A 232 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7387 (mtm-85) REVERT: A 237 SER cc_start: 0.9001 (m) cc_final: 0.8766 (p) REVERT: A 328 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7004 (mtp) REVERT: A 355 ARG cc_start: 0.6686 (mmt90) cc_final: 0.5805 (tpt-90) REVERT: A 380 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.6488 (mtp85) REVERT: A 406 ARG cc_start: 0.7509 (OUTLIER) cc_final: 0.6896 (mtt180) REVERT: A 428 LYS cc_start: 0.8165 (tttt) cc_final: 0.7857 (mtpp) REVERT: B 11 MET cc_start: 0.8189 (mmm) cc_final: 0.7918 (tpp) REVERT: B 39 LYS cc_start: 0.8101 (mttt) cc_final: 0.7566 (mtmt) REVERT: B 92 ASN cc_start: 0.7427 (m-40) cc_final: 0.7179 (m-40) REVERT: B 123 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: B 148 ASP cc_start: 0.7859 (t0) cc_final: 0.7620 (t0) REVERT: B 186 ASN cc_start: 0.7405 (m-40) cc_final: 0.7193 (m110) REVERT: B 191 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 198 ASN cc_start: 0.8061 (t0) cc_final: 0.7846 (p0) REVERT: B 229 GLU cc_start: 0.8375 (tt0) cc_final: 0.8145 (tt0) REVERT: B 232 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7424 (mtm-85) REVERT: B 237 SER cc_start: 0.9009 (m) cc_final: 0.8773 (p) REVERT: B 311 GLU cc_start: 0.8290 (tt0) cc_final: 0.8081 (tt0) REVERT: B 355 ARG cc_start: 0.6777 (mmt90) cc_final: 0.5880 (tpt-90) REVERT: B 380 ARG cc_start: 0.7088 (ttp-170) cc_final: 0.6623 (mtp85) REVERT: B 406 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6873 (mtp180) REVERT: B 428 LYS cc_start: 0.8315 (tttt) cc_final: 0.7928 (mtpp) REVERT: D 11 MET cc_start: 0.8117 (mmm) cc_final: 0.7814 (tpp) REVERT: D 39 LYS cc_start: 0.8170 (mttt) cc_final: 0.7626 (mtmt) REVERT: D 115 ARG cc_start: 0.6436 (mpt180) cc_final: 0.6119 (mmt180) REVERT: D 123 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.6020 (mp10) REVERT: D 148 ASP cc_start: 0.7843 (t0) cc_final: 0.7613 (t0) REVERT: D 186 ASN cc_start: 0.7408 (m-40) cc_final: 0.7141 (m-40) REVERT: D 191 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7161 (mm-30) REVERT: D 229 GLU cc_start: 0.8327 (tt0) cc_final: 0.8105 (tt0) REVERT: D 232 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7382 (mtm-85) REVERT: D 237 SER cc_start: 0.8999 (m) cc_final: 0.8755 (p) REVERT: D 311 GLU cc_start: 0.8304 (tt0) cc_final: 0.8087 (tt0) REVERT: D 328 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7146 (mtp) REVERT: D 355 ARG cc_start: 0.6784 (mmt90) cc_final: 0.5884 (tpt-90) REVERT: D 380 ARG cc_start: 0.7058 (ttp-170) cc_final: 0.6583 (mtp85) REVERT: D 406 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.6931 (mtp180) REVERT: D 428 LYS cc_start: 0.8315 (tttt) cc_final: 0.7956 (mtpp) REVERT: C 11 MET cc_start: 0.8176 (mmm) cc_final: 0.7959 (tpp) REVERT: C 39 LYS cc_start: 0.8195 (mttt) cc_final: 0.7657 (mtmt) REVERT: C 123 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7322 (mm-40) REVERT: C 148 ASP cc_start: 0.7814 (t0) cc_final: 0.7584 (t0) REVERT: C 186 ASN cc_start: 0.7428 (m-40) cc_final: 0.7202 (m110) REVERT: C 191 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7150 (mm-30) REVERT: C 229 GLU cc_start: 0.8390 (tt0) cc_final: 0.8159 (tt0) REVERT: C 232 ARG cc_start: 0.7825 (mtt90) cc_final: 0.7393 (mtm-85) REVERT: C 237 SER cc_start: 0.8993 (m) cc_final: 0.8766 (p) REVERT: C 311 GLU cc_start: 0.8326 (tt0) cc_final: 0.8082 (tt0) REVERT: C 355 ARG cc_start: 0.6781 (mmt90) cc_final: 0.5877 (tpt-90) REVERT: C 380 ARG cc_start: 0.6980 (ttp-170) cc_final: 0.6498 (mtp85) REVERT: C 406 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6929 (mtp180) REVERT: C 428 LYS cc_start: 0.8326 (tttt) cc_final: 0.7931 (mtpp) outliers start: 48 outliers final: 8 residues processed: 327 average time/residue: 1.4125 time to fit residues: 500.2723 Evaluate side-chains 232 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 406 ARG Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 406 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 235 ASN A 429 GLN B 147 GLN B 235 ASN D 147 GLN D 235 ASN C 147 GLN C 235 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.129584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099602 restraints weight = 89189.702| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.33 r_work: 0.3039 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13840 Z= 0.138 Angle : 0.662 7.353 18776 Z= 0.332 Chirality : 0.048 0.145 2052 Planarity : 0.005 0.044 2448 Dihedral : 8.746 88.269 1994 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.66 % Allowed : 16.76 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.19), residues: 1708 helix: -2.12 (0.22), residues: 392 sheet: -1.70 (0.36), residues: 188 loop : -1.36 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 115 TYR 0.012 0.001 TYR A 114 PHE 0.013 0.001 PHE D 259 TRP 0.014 0.001 TRP D 284 HIS 0.012 0.002 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00304 (13840) covalent geometry : angle 0.66163 (18776) hydrogen bonds : bond 0.04688 ( 168) hydrogen bonds : angle 6.05380 ( 420) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 266 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.632 Fit side-chains REVERT: A 39 LYS cc_start: 0.8798 (mttt) cc_final: 0.8398 (mtmt) REVERT: A 106 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.6995 (mp10) REVERT: A 115 ARG cc_start: 0.7381 (mpt180) cc_final: 0.7094 (mmt-90) REVERT: A 123 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: A 126 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7328 (p0) REVERT: A 155 ASP cc_start: 0.8510 (t70) cc_final: 0.7823 (t0) REVERT: A 186 ASN cc_start: 0.7713 (m-40) cc_final: 0.7489 (m-40) REVERT: A 243 ASP cc_start: 0.6704 (m-30) cc_final: 0.6245 (m-30) REVERT: A 279 THR cc_start: 0.9074 (p) cc_final: 0.8776 (t) REVERT: A 302 ARG cc_start: 0.8628 (mmm-85) cc_final: 0.8406 (mpt-90) REVERT: A 355 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7496 (tpt-90) REVERT: A 380 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7781 (mtp85) REVERT: A 428 LYS cc_start: 0.8607 (tttt) cc_final: 0.8377 (mtpp) REVERT: B 11 MET cc_start: 0.8528 (mmm) cc_final: 0.8314 (tpp) REVERT: B 39 LYS cc_start: 0.8728 (mttt) cc_final: 0.8344 (mtmt) REVERT: B 106 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6874 (mp10) REVERT: B 123 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7008 (mp10) REVERT: B 155 ASP cc_start: 0.8583 (t70) cc_final: 0.7886 (t0) REVERT: B 267 ASP cc_start: 0.6934 (p0) cc_final: 0.6717 (p0) REVERT: B 279 THR cc_start: 0.9082 (p) cc_final: 0.8770 (t) REVERT: B 302 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8469 (mpt-90) REVERT: B 355 ARG cc_start: 0.7938 (mmt90) cc_final: 0.7517 (tpt-90) REVERT: B 375 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7775 (ttm110) REVERT: B 380 ARG cc_start: 0.8066 (ttp-170) cc_final: 0.7826 (mtp85) REVERT: B 428 LYS cc_start: 0.8595 (tttt) cc_final: 0.8385 (mtpp) REVERT: D 39 LYS cc_start: 0.8791 (mttt) cc_final: 0.8395 (mtmt) REVERT: D 106 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: D 115 ARG cc_start: 0.7372 (mpt180) cc_final: 0.6961 (mmt-90) REVERT: D 123 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.6960 (mp10) REVERT: D 126 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7296 (p0) REVERT: D 134 GLU cc_start: 0.8219 (mt-10) cc_final: 0.8007 (tt0) REVERT: D 155 ASP cc_start: 0.8530 (t70) cc_final: 0.7830 (t0) REVERT: D 237 SER cc_start: 0.9158 (m) cc_final: 0.8955 (p) REVERT: D 302 ARG cc_start: 0.8646 (mmm-85) cc_final: 0.8424 (mpt-90) REVERT: D 355 ARG cc_start: 0.7905 (mmt90) cc_final: 0.7496 (tpt-90) REVERT: D 375 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7744 (ttm110) REVERT: D 380 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7774 (mtp85) REVERT: D 428 LYS cc_start: 0.8585 (tttt) cc_final: 0.8335 (mtpp) REVERT: C 39 LYS cc_start: 0.8794 (mttt) cc_final: 0.8406 (mtmt) REVERT: C 106 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.6896 (mp10) REVERT: C 123 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7004 (mp10) REVERT: C 126 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7276 (p0) REVERT: C 134 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8023 (tt0) REVERT: C 155 ASP cc_start: 0.8615 (t70) cc_final: 0.7840 (t0) REVERT: C 229 GLU cc_start: 0.8593 (tt0) cc_final: 0.8386 (tt0) REVERT: C 243 ASP cc_start: 0.6731 (m-30) cc_final: 0.6291 (m-30) REVERT: C 279 THR cc_start: 0.9097 (p) cc_final: 0.8784 (t) REVERT: C 302 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8430 (mpt-90) REVERT: C 355 ARG cc_start: 0.7906 (mmt90) cc_final: 0.7496 (tpt-90) REVERT: C 380 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7730 (mtp85) outliers start: 20 outliers final: 2 residues processed: 258 average time/residue: 1.4304 time to fit residues: 399.1862 Evaluate side-chains 208 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 195 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 154 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 399 ASN D 310 ASN D 399 ASN C 347 GLN C 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.102710 restraints weight = 88454.914| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.31 r_work: 0.3014 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 13840 Z= 0.176 Angle : 0.620 6.756 18776 Z= 0.310 Chirality : 0.048 0.142 2052 Planarity : 0.005 0.042 2448 Dihedral : 7.372 78.698 1956 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.59 % Allowed : 16.55 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.19), residues: 1708 helix: -1.48 (0.25), residues: 392 sheet: -1.57 (0.35), residues: 188 loop : -1.21 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 162 TYR 0.011 0.001 TYR B 309 PHE 0.011 0.001 PHE C 259 TRP 0.012 0.001 TRP D 284 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00408 (13840) covalent geometry : angle 0.62025 (18776) hydrogen bonds : bond 0.03819 ( 168) hydrogen bonds : angle 5.43128 ( 420) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 226 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 207 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8793 (mttt) cc_final: 0.8348 (mtmt) REVERT: A 106 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.6733 (mp10) REVERT: A 115 ARG cc_start: 0.7375 (mpt180) cc_final: 0.7108 (mmt90) REVERT: A 123 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.6471 (mp10) REVERT: A 126 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 155 ASP cc_start: 0.8598 (t70) cc_final: 0.7826 (t0) REVERT: A 186 ASN cc_start: 0.7713 (m-40) cc_final: 0.7454 (m-40) REVERT: A 228 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7935 (mt-10) REVERT: A 243 ASP cc_start: 0.6642 (m-30) cc_final: 0.6404 (m-30) REVERT: A 355 ARG cc_start: 0.7921 (mmt90) cc_final: 0.7421 (tpt90) REVERT: A 380 ARG cc_start: 0.8013 (ttp-170) cc_final: 0.7739 (mtp85) REVERT: A 428 LYS cc_start: 0.8657 (tttt) cc_final: 0.8421 (mtpp) REVERT: B 11 MET cc_start: 0.8511 (mmm) cc_final: 0.8206 (tpp) REVERT: B 39 LYS cc_start: 0.8819 (mttt) cc_final: 0.8369 (mtmt) REVERT: B 123 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.6788 (mp10) REVERT: B 126 ASP cc_start: 0.7793 (m-30) cc_final: 0.7302 (p0) REVERT: B 155 ASP cc_start: 0.8540 (t70) cc_final: 0.7571 (t0) REVERT: B 355 ARG cc_start: 0.7938 (mmt90) cc_final: 0.7422 (tpt90) REVERT: B 380 ARG cc_start: 0.8048 (ttp-170) cc_final: 0.7739 (mtp85) REVERT: B 428 LYS cc_start: 0.8662 (tttt) cc_final: 0.8407 (mtpp) REVERT: D 39 LYS cc_start: 0.8828 (mttt) cc_final: 0.8378 (mtmt) REVERT: D 106 GLN cc_start: 0.7650 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: D 115 ARG cc_start: 0.7333 (mpt180) cc_final: 0.7052 (mmt90) REVERT: D 123 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.6602 (mp10) REVERT: D 126 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7248 (p0) REVERT: D 134 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8006 (tt0) REVERT: D 155 ASP cc_start: 0.8524 (t70) cc_final: 0.7765 (t0) REVERT: D 186 ASN cc_start: 0.7657 (m-40) cc_final: 0.7389 (m-40) REVERT: D 228 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7818 (mt-10) REVERT: D 237 SER cc_start: 0.9182 (m) cc_final: 0.8960 (p) REVERT: D 355 ARG cc_start: 0.7931 (mmt90) cc_final: 0.7430 (tpt90) REVERT: D 380 ARG cc_start: 0.8032 (ttp-170) cc_final: 0.7726 (mtp85) REVERT: D 428 LYS cc_start: 0.8619 (tttt) cc_final: 0.8394 (mtpp) REVERT: C 39 LYS cc_start: 0.8856 (mttt) cc_final: 0.8397 (mtmt) REVERT: C 123 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.6503 (mp10) REVERT: C 126 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7270 (p0) REVERT: C 134 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7832 (tt0) REVERT: C 155 ASP cc_start: 0.8581 (t70) cc_final: 0.7725 (t0) REVERT: C 228 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7996 (mt-10) REVERT: C 243 ASP cc_start: 0.6642 (m-30) cc_final: 0.6382 (m-30) REVERT: C 355 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7411 (tpt90) REVERT: C 380 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.7729 (mtp85) outliers start: 19 outliers final: 4 residues processed: 221 average time/residue: 1.3802 time to fit residues: 331.9756 Evaluate side-chains 202 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 189 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 289 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.130264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.099907 restraints weight = 81002.887| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.28 r_work: 0.3022 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13840 Z= 0.103 Angle : 0.573 6.354 18776 Z= 0.281 Chirality : 0.046 0.141 2052 Planarity : 0.004 0.035 2448 Dihedral : 6.861 67.485 1956 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.62 % Allowed : 18.84 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.20), residues: 1708 helix: -0.99 (0.27), residues: 392 sheet: -1.66 (0.34), residues: 204 loop : -1.07 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 162 TYR 0.007 0.001 TYR C 309 PHE 0.010 0.001 PHE D 178 TRP 0.008 0.001 TRP B 284 HIS 0.002 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00234 (13840) covalent geometry : angle 0.57310 (18776) hydrogen bonds : bond 0.02931 ( 168) hydrogen bonds : angle 5.07027 ( 420) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 205 time to evaluate : 0.685 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8842 (mttt) cc_final: 0.8387 (mtmt) REVERT: A 115 ARG cc_start: 0.7360 (mpt180) cc_final: 0.7079 (mmt90) REVERT: A 123 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.6348 (mp10) REVERT: A 126 ASP cc_start: 0.7701 (m-30) cc_final: 0.7277 (p0) REVERT: A 155 ASP cc_start: 0.8585 (t70) cc_final: 0.7816 (t0) REVERT: A 228 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8011 (mt-10) REVERT: A 355 ARG cc_start: 0.7850 (mmt90) cc_final: 0.7173 (tpt-90) REVERT: A 380 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.7722 (mtp85) REVERT: A 428 LYS cc_start: 0.8649 (tttt) cc_final: 0.8391 (mtpp) REVERT: B 11 MET cc_start: 0.8470 (mmm) cc_final: 0.8224 (tpp) REVERT: B 39 LYS cc_start: 0.8806 (mttt) cc_final: 0.8359 (mtmt) REVERT: B 123 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: B 126 ASP cc_start: 0.7761 (m-30) cc_final: 0.7266 (p0) REVERT: B 155 ASP cc_start: 0.8648 (t70) cc_final: 0.7781 (t0) REVERT: B 328 MET cc_start: 0.7723 (mtp) cc_final: 0.7229 (mmt) REVERT: B 355 ARG cc_start: 0.7881 (mmt90) cc_final: 0.7315 (tpt90) REVERT: B 380 ARG cc_start: 0.8032 (ttp-170) cc_final: 0.7759 (mtp85) REVERT: B 428 LYS cc_start: 0.8651 (tttt) cc_final: 0.8413 (mtpp) REVERT: D 39 LYS cc_start: 0.8830 (mttt) cc_final: 0.8382 (mtmt) REVERT: D 112 ASN cc_start: 0.7667 (t0) cc_final: 0.7380 (t0) REVERT: D 115 ARG cc_start: 0.7372 (mpt180) cc_final: 0.7096 (mmt90) REVERT: D 123 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.6380 (mp10) REVERT: D 126 ASP cc_start: 0.7660 (m-30) cc_final: 0.7245 (p0) REVERT: D 134 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7960 (tt0) REVERT: D 155 ASP cc_start: 0.8501 (t70) cc_final: 0.7752 (t0) REVERT: D 228 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7955 (mt-10) REVERT: D 243 ASP cc_start: 0.6794 (m-30) cc_final: 0.6578 (m-30) REVERT: D 328 MET cc_start: 0.7825 (mmm) cc_final: 0.7199 (mmt) REVERT: D 355 ARG cc_start: 0.7886 (mmt90) cc_final: 0.7288 (tpt90) REVERT: D 380 ARG cc_start: 0.8039 (ttp-170) cc_final: 0.7754 (mtp85) REVERT: D 428 LYS cc_start: 0.8628 (tttt) cc_final: 0.8388 (mtpp) REVERT: C 39 LYS cc_start: 0.8841 (mttt) cc_final: 0.8380 (mtmt) REVERT: C 123 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.6372 (mp10) REVERT: C 126 ASP cc_start: 0.7738 (m-30) cc_final: 0.7276 (p0) REVERT: C 134 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7783 (tt0) REVERT: C 155 ASP cc_start: 0.8626 (t70) cc_final: 0.7794 (t0) REVERT: C 228 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8038 (mt-10) REVERT: C 355 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7259 (tpt90) REVERT: C 380 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7727 (mtp85) outliers start: 5 outliers final: 1 residues processed: 209 average time/residue: 1.3075 time to fit residues: 298.1898 Evaluate side-chains 194 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 189 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain C residue 123 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 0.4980 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 114 optimal weight: 0.0970 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 310 ASN B 186 ASN D 186 ASN C 186 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.133333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102328 restraints weight = 91800.867| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.39 r_work: 0.2989 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13840 Z= 0.139 Angle : 0.573 6.276 18776 Z= 0.281 Chirality : 0.046 0.140 2052 Planarity : 0.004 0.034 2448 Dihedral : 6.694 62.246 1956 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.59 % Allowed : 18.70 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.20), residues: 1708 helix: -0.81 (0.27), residues: 392 sheet: -1.66 (0.34), residues: 204 loop : -1.05 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 162 TYR 0.008 0.001 TYR B 309 PHE 0.008 0.001 PHE D 178 TRP 0.009 0.001 TRP B 284 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00322 (13840) covalent geometry : angle 0.57281 (18776) hydrogen bonds : bond 0.02863 ( 168) hydrogen bonds : angle 4.82830 ( 420) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.662 Fit side-chains REVERT: A 39 LYS cc_start: 0.8833 (mttt) cc_final: 0.8412 (mtmt) REVERT: A 106 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.6667 (mp10) REVERT: A 115 ARG cc_start: 0.7450 (mpt180) cc_final: 0.7172 (mmt90) REVERT: A 123 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.6316 (mp10) REVERT: A 126 ASP cc_start: 0.7740 (m-30) cc_final: 0.7322 (p0) REVERT: A 155 ASP cc_start: 0.8666 (t70) cc_final: 0.7865 (t0) REVERT: A 228 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8067 (mt-10) REVERT: A 302 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7976 (mpt-90) REVERT: A 321 ASP cc_start: 0.8390 (p0) cc_final: 0.8155 (p0) REVERT: A 355 ARG cc_start: 0.7895 (mmt90) cc_final: 0.7321 (mtp180) REVERT: A 380 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7781 (mtp85) REVERT: A 428 LYS cc_start: 0.8670 (tttt) cc_final: 0.8417 (mtpp) REVERT: B 11 MET cc_start: 0.8501 (mmm) cc_final: 0.8180 (tpp) REVERT: B 39 LYS cc_start: 0.8843 (mttt) cc_final: 0.8428 (mtmt) REVERT: B 123 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.6564 (mp10) REVERT: B 126 ASP cc_start: 0.7825 (m-30) cc_final: 0.7331 (p0) REVERT: B 155 ASP cc_start: 0.8682 (t70) cc_final: 0.7893 (t0) REVERT: B 302 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7987 (mpt-90) REVERT: B 355 ARG cc_start: 0.7901 (mmt90) cc_final: 0.7268 (tpt-90) REVERT: B 380 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7787 (mtp85) REVERT: B 428 LYS cc_start: 0.8651 (tttt) cc_final: 0.8415 (mtpp) REVERT: D 39 LYS cc_start: 0.8866 (mttt) cc_final: 0.8450 (mtmt) REVERT: D 106 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.6561 (mp10) REVERT: D 115 ARG cc_start: 0.7445 (mpt180) cc_final: 0.7161 (mmt90) REVERT: D 123 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.6353 (mp10) REVERT: D 126 ASP cc_start: 0.7708 (m-30) cc_final: 0.7348 (p0) REVERT: D 134 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8020 (tt0) REVERT: D 155 ASP cc_start: 0.8665 (t70) cc_final: 0.7914 (t0) REVERT: D 228 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7887 (mt-10) REVERT: D 302 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8042 (mpt-90) REVERT: D 328 MET cc_start: 0.7855 (mmm) cc_final: 0.7218 (mmt) REVERT: D 355 ARG cc_start: 0.7939 (mmt90) cc_final: 0.7278 (tpt-90) REVERT: D 380 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7786 (mtp85) REVERT: D 428 LYS cc_start: 0.8645 (tttt) cc_final: 0.8408 (mtpp) REVERT: C 39 LYS cc_start: 0.8882 (mttt) cc_final: 0.8462 (mtmt) REVERT: C 123 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.6257 (mp10) REVERT: C 126 ASP cc_start: 0.7800 (m-30) cc_final: 0.7356 (p0) REVERT: C 134 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7845 (tt0) REVERT: C 155 ASP cc_start: 0.8653 (t70) cc_final: 0.7831 (t0) REVERT: C 228 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8084 (mt-10) REVERT: C 302 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8048 (mpt-90) REVERT: C 355 ARG cc_start: 0.7916 (mmt90) cc_final: 0.7328 (mtp180) REVERT: C 380 ARG cc_start: 0.8014 (ttp-170) cc_final: 0.7751 (mtp85) outliers start: 19 outliers final: 7 residues processed: 206 average time/residue: 1.4109 time to fit residues: 316.2137 Evaluate side-chains 203 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 302 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.130607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099380 restraints weight = 96143.369| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.52 r_work: 0.3004 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13840 Z= 0.103 Angle : 0.554 6.246 18776 Z= 0.271 Chirality : 0.046 0.137 2052 Planarity : 0.004 0.037 2448 Dihedral : 6.464 58.311 1956 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.66 % Allowed : 18.98 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.20), residues: 1708 helix: -0.51 (0.28), residues: 396 sheet: -1.71 (0.34), residues: 208 loop : -0.96 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.008 0.001 TYR B 309 PHE 0.009 0.001 PHE C 240 TRP 0.008 0.001 TRP B 284 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00241 (13840) covalent geometry : angle 0.55367 (18776) hydrogen bonds : bond 0.02627 ( 168) hydrogen bonds : angle 4.58921 ( 420) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.615 Fit side-chains REVERT: A 39 LYS cc_start: 0.8842 (mttt) cc_final: 0.8423 (mtmt) REVERT: A 115 ARG cc_start: 0.7384 (mpt180) cc_final: 0.7123 (mmt90) REVERT: A 123 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8040 (mm-40) REVERT: A 126 ASP cc_start: 0.7757 (m-30) cc_final: 0.7387 (p0) REVERT: A 155 ASP cc_start: 0.8654 (t70) cc_final: 0.7845 (t0) REVERT: A 302 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7985 (mpt-90) REVERT: A 355 ARG cc_start: 0.7857 (mmt90) cc_final: 0.7282 (mtp180) REVERT: A 380 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7764 (mtp85) REVERT: A 428 LYS cc_start: 0.8662 (tttt) cc_final: 0.8418 (mtpp) REVERT: B 39 LYS cc_start: 0.8806 (mttt) cc_final: 0.8391 (mtmt) REVERT: B 123 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: B 126 ASP cc_start: 0.7736 (m-30) cc_final: 0.7345 (p0) REVERT: B 155 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.7813 (t0) REVERT: B 302 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8020 (mpt-90) REVERT: B 355 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7282 (mtp180) REVERT: B 380 ARG cc_start: 0.8073 (ttp-170) cc_final: 0.7808 (mtp85) REVERT: B 428 LYS cc_start: 0.8659 (tttt) cc_final: 0.8435 (mtpp) REVERT: D 39 LYS cc_start: 0.8823 (mttt) cc_final: 0.8408 (mtmt) REVERT: D 115 ARG cc_start: 0.7369 (mpt180) cc_final: 0.7110 (mmt90) REVERT: D 123 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: D 126 ASP cc_start: 0.7721 (m-30) cc_final: 0.7337 (p0) REVERT: D 134 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8032 (tt0) REVERT: D 155 ASP cc_start: 0.8662 (t70) cc_final: 0.7916 (t0) REVERT: D 302 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8031 (mpt-90) REVERT: D 328 MET cc_start: 0.7891 (mmm) cc_final: 0.7245 (mmt) REVERT: D 355 ARG cc_start: 0.7837 (mmt90) cc_final: 0.7292 (mtp180) REVERT: D 380 ARG cc_start: 0.8067 (ttp-170) cc_final: 0.7806 (mtp85) REVERT: D 428 LYS cc_start: 0.8646 (tttt) cc_final: 0.8414 (mtpp) REVERT: C 39 LYS cc_start: 0.8875 (mttt) cc_final: 0.8460 (mtmt) REVERT: C 123 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7987 (mm-40) REVERT: C 126 ASP cc_start: 0.7813 (m-30) cc_final: 0.7367 (p0) REVERT: C 134 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7871 (tt0) REVERT: C 155 ASP cc_start: 0.8649 (t70) cc_final: 0.7842 (t0) REVERT: C 228 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8098 (mt-10) REVERT: C 302 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8050 (mpt-90) REVERT: C 355 ARG cc_start: 0.7828 (mmt90) cc_final: 0.7284 (mtp180) REVERT: C 380 ARG cc_start: 0.8064 (ttp-170) cc_final: 0.7786 (mtp85) outliers start: 20 outliers final: 10 residues processed: 209 average time/residue: 1.3157 time to fit residues: 301.0157 Evaluate side-chains 207 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 302 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 chunk 145 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.127703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.097390 restraints weight = 92515.360| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 3.37 r_work: 0.3004 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 13840 Z= 0.120 Angle : 0.555 6.150 18776 Z= 0.270 Chirality : 0.046 0.138 2052 Planarity : 0.004 0.038 2448 Dihedral : 6.349 55.580 1956 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.80 % Allowed : 19.32 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.20), residues: 1708 helix: -0.36 (0.28), residues: 396 sheet: -1.66 (0.34), residues: 208 loop : -0.96 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 162 TYR 0.008 0.001 TYR B 309 PHE 0.008 0.001 PHE B 178 TRP 0.008 0.001 TRP B 284 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00285 (13840) covalent geometry : angle 0.55463 (18776) hydrogen bonds : bond 0.02629 ( 168) hydrogen bonds : angle 4.46682 ( 420) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.748 Fit side-chains REVERT: A 39 LYS cc_start: 0.8858 (mttt) cc_final: 0.8450 (mtmt) REVERT: A 115 ARG cc_start: 0.7389 (mpt180) cc_final: 0.7090 (mmt90) REVERT: A 123 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: A 126 ASP cc_start: 0.7787 (m-30) cc_final: 0.7427 (p0) REVERT: A 155 ASP cc_start: 0.8677 (t70) cc_final: 0.7903 (t0) REVERT: A 302 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7973 (mpt-90) REVERT: A 328 MET cc_start: 0.7960 (mmm) cc_final: 0.7428 (mmt) REVERT: A 355 ARG cc_start: 0.7848 (mmt90) cc_final: 0.7328 (mtp180) REVERT: A 380 ARG cc_start: 0.8023 (ttp-170) cc_final: 0.7792 (mtp85) REVERT: A 428 LYS cc_start: 0.8672 (tttt) cc_final: 0.8442 (mtpp) REVERT: B 39 LYS cc_start: 0.8835 (mttt) cc_final: 0.8434 (mtmt) REVERT: B 123 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.7884 (mt0) REVERT: B 126 ASP cc_start: 0.7753 (m-30) cc_final: 0.7394 (p0) REVERT: B 155 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.7771 (t0) REVERT: B 302 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7990 (mpt-90) REVERT: B 355 ARG cc_start: 0.7854 (mmt90) cc_final: 0.7342 (mtp180) REVERT: B 380 ARG cc_start: 0.8095 (ttp-170) cc_final: 0.7840 (mtp85) REVERT: B 428 LYS cc_start: 0.8657 (tttt) cc_final: 0.8444 (mtpp) REVERT: D 39 LYS cc_start: 0.8865 (mttt) cc_final: 0.8458 (mtmt) REVERT: D 115 ARG cc_start: 0.7390 (mpt180) cc_final: 0.7122 (mmt90) REVERT: D 123 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: D 126 ASP cc_start: 0.7730 (m-30) cc_final: 0.7385 (p0) REVERT: D 134 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8061 (tt0) REVERT: D 155 ASP cc_start: 0.8696 (t70) cc_final: 0.7970 (t0) REVERT: D 302 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8015 (mpt-90) REVERT: D 328 MET cc_start: 0.7947 (mmm) cc_final: 0.7317 (mmt) REVERT: D 355 ARG cc_start: 0.7835 (mmt90) cc_final: 0.7336 (mtp180) REVERT: D 380 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7833 (mtp85) REVERT: D 428 LYS cc_start: 0.8646 (tttt) cc_final: 0.8431 (mtpp) REVERT: C 39 LYS cc_start: 0.8866 (mttt) cc_final: 0.8457 (mtmt) REVERT: C 123 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.8046 (mm-40) REVERT: C 126 ASP cc_start: 0.7804 (m-30) cc_final: 0.7436 (p0) REVERT: C 134 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7983 (tt0) REVERT: C 155 ASP cc_start: 0.8628 (t70) cc_final: 0.7863 (t0) REVERT: C 302 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8059 (mpt-90) REVERT: C 355 ARG cc_start: 0.7849 (mmt90) cc_final: 0.7333 (mtp180) REVERT: C 380 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7816 (mtp85) outliers start: 22 outliers final: 11 residues processed: 202 average time/residue: 1.4032 time to fit residues: 309.4307 Evaluate side-chains 203 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 108 MET Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 302 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 145 optimal weight: 0.2980 chunk 56 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.102961 restraints weight = 89170.440| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.36 r_work: 0.2990 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2999 r_free = 0.2999 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13840 Z= 0.130 Angle : 0.557 6.098 18776 Z= 0.273 Chirality : 0.046 0.138 2052 Planarity : 0.004 0.040 2448 Dihedral : 6.310 55.857 1956 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.73 % Allowed : 19.46 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.20), residues: 1708 helix: -0.24 (0.28), residues: 396 sheet: -1.63 (0.34), residues: 208 loop : -0.94 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.009 0.001 TYR B 309 PHE 0.010 0.001 PHE A 178 TRP 0.008 0.001 TRP B 284 HIS 0.004 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00306 (13840) covalent geometry : angle 0.55701 (18776) hydrogen bonds : bond 0.02700 ( 168) hydrogen bonds : angle 4.43198 ( 420) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.653 Fit side-chains REVERT: A 39 LYS cc_start: 0.8860 (mttt) cc_final: 0.8421 (mtmt) REVERT: A 115 ARG cc_start: 0.7267 (mpt180) cc_final: 0.6970 (mmt90) REVERT: A 123 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7843 (mt0) REVERT: A 126 ASP cc_start: 0.7779 (m-30) cc_final: 0.7406 (p0) REVERT: A 155 ASP cc_start: 0.8660 (t70) cc_final: 0.7841 (t0) REVERT: A 168 MET cc_start: 0.8268 (ttp) cc_final: 0.7958 (ttp) REVERT: A 302 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7997 (mpt-90) REVERT: A 328 MET cc_start: 0.7852 (mmm) cc_final: 0.7364 (mmt) REVERT: A 355 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7280 (mtp180) REVERT: A 380 ARG cc_start: 0.8055 (ttp-170) cc_final: 0.7760 (mtp85) REVERT: A 428 LYS cc_start: 0.8649 (tttt) cc_final: 0.8418 (mtpp) REVERT: B 39 LYS cc_start: 0.8835 (mttt) cc_final: 0.8412 (mtmt) REVERT: B 123 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: B 126 ASP cc_start: 0.7746 (m-30) cc_final: 0.7385 (p0) REVERT: B 155 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.7790 (t0) REVERT: B 302 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8018 (mpt-90) REVERT: B 355 ARG cc_start: 0.7843 (mmt90) cc_final: 0.7283 (mtp180) REVERT: B 380 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7795 (mtp85) REVERT: B 428 LYS cc_start: 0.8654 (tttt) cc_final: 0.8430 (mtpp) REVERT: D 39 LYS cc_start: 0.8854 (mttt) cc_final: 0.8434 (mtmt) REVERT: D 115 ARG cc_start: 0.7265 (mpt180) cc_final: 0.6968 (mmt90) REVERT: D 123 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7822 (mt0) REVERT: D 126 ASP cc_start: 0.7738 (m-30) cc_final: 0.7363 (p0) REVERT: D 134 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8052 (tt0) REVERT: D 155 ASP cc_start: 0.8693 (t70) cc_final: 0.7940 (t0) REVERT: D 302 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8046 (mpt-90) REVERT: D 328 MET cc_start: 0.7936 (mmm) cc_final: 0.7309 (mmt) REVERT: D 355 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7312 (mtp180) REVERT: D 380 ARG cc_start: 0.8066 (ttp-170) cc_final: 0.7788 (mtp85) REVERT: D 428 LYS cc_start: 0.8631 (tttt) cc_final: 0.8405 (mtpp) REVERT: C 39 LYS cc_start: 0.8849 (mttt) cc_final: 0.8424 (mtmt) REVERT: C 123 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: C 126 ASP cc_start: 0.7812 (m-30) cc_final: 0.7435 (p0) REVERT: C 134 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7984 (tt0) REVERT: C 155 ASP cc_start: 0.8717 (t70) cc_final: 0.7845 (t0) REVERT: C 302 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8061 (mpt-90) REVERT: C 355 ARG cc_start: 0.7894 (mmt90) cc_final: 0.7290 (mtp180) REVERT: C 380 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7776 (mtp85) outliers start: 21 outliers final: 7 residues processed: 203 average time/residue: 1.2880 time to fit residues: 285.0739 Evaluate side-chains 198 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 302 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 167 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 141 optimal weight: 0.0970 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.130204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098985 restraints weight = 95825.738| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.55 r_work: 0.2983 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13840 Z= 0.120 Angle : 0.555 6.130 18776 Z= 0.271 Chirality : 0.046 0.138 2052 Planarity : 0.004 0.040 2448 Dihedral : 6.263 55.543 1956 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.45 % Allowed : 19.74 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.20), residues: 1708 helix: -0.14 (0.28), residues: 400 sheet: -1.61 (0.34), residues: 208 loop : -0.91 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.008 0.001 TYR D 309 PHE 0.011 0.001 PHE B 178 TRP 0.008 0.001 TRP C 284 HIS 0.002 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00286 (13840) covalent geometry : angle 0.55544 (18776) hydrogen bonds : bond 0.02699 ( 168) hydrogen bonds : angle 4.38294 ( 420) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 0.697 Fit side-chains REVERT: A 39 LYS cc_start: 0.8825 (mttt) cc_final: 0.8354 (mtmt) REVERT: A 115 ARG cc_start: 0.7153 (mpt180) cc_final: 0.6843 (mmt90) REVERT: A 123 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: A 126 ASP cc_start: 0.7751 (m-30) cc_final: 0.7354 (p0) REVERT: A 155 ASP cc_start: 0.8646 (t70) cc_final: 0.7786 (t0) REVERT: A 328 MET cc_start: 0.7827 (mmm) cc_final: 0.7340 (mmt) REVERT: A 355 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7157 (mtp180) REVERT: A 380 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7663 (mtp85) REVERT: A 428 LYS cc_start: 0.8661 (tttt) cc_final: 0.8397 (mtpp) REVERT: B 39 LYS cc_start: 0.8803 (mttt) cc_final: 0.8345 (mtmt) REVERT: B 123 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7785 (mt0) REVERT: B 126 ASP cc_start: 0.7730 (m-30) cc_final: 0.7340 (p0) REVERT: B 155 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.7717 (t0) REVERT: B 168 MET cc_start: 0.7953 (ttp) cc_final: 0.7697 (ttp) REVERT: B 302 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8045 (mpt-90) REVERT: B 355 ARG cc_start: 0.7819 (mmt90) cc_final: 0.7157 (mtp180) REVERT: B 380 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7678 (mtp85) REVERT: B 428 LYS cc_start: 0.8639 (tttt) cc_final: 0.8396 (mtpp) REVERT: D 39 LYS cc_start: 0.8822 (mttt) cc_final: 0.8370 (mtmt) REVERT: D 115 ARG cc_start: 0.7152 (mpt180) cc_final: 0.6842 (mmt90) REVERT: D 123 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: D 126 ASP cc_start: 0.7715 (m-30) cc_final: 0.7321 (p0) REVERT: D 134 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7998 (tt0) REVERT: D 155 ASP cc_start: 0.8662 (t70) cc_final: 0.7866 (t0) REVERT: D 302 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8024 (mpt-90) REVERT: D 328 MET cc_start: 0.7891 (mmm) cc_final: 0.7259 (mmt) REVERT: D 355 ARG cc_start: 0.7870 (mmt90) cc_final: 0.7163 (mtp180) REVERT: D 380 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7677 (mtp85) REVERT: D 428 LYS cc_start: 0.8619 (tttt) cc_final: 0.8372 (mtpp) REVERT: C 39 LYS cc_start: 0.8821 (mttt) cc_final: 0.8351 (mtmt) REVERT: C 123 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7772 (mt0) REVERT: C 126 ASP cc_start: 0.7754 (m-30) cc_final: 0.7354 (p0) REVERT: C 134 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7921 (tt0) REVERT: C 155 ASP cc_start: 0.8684 (t70) cc_final: 0.7751 (t0) REVERT: C 168 MET cc_start: 0.7930 (ttp) cc_final: 0.7675 (ttp) REVERT: C 302 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8037 (mpt-90) REVERT: C 355 ARG cc_start: 0.7866 (mmt90) cc_final: 0.7157 (mtp180) REVERT: C 380 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7674 (mtp85) outliers start: 17 outliers final: 7 residues processed: 198 average time/residue: 1.4079 time to fit residues: 302.9340 Evaluate side-chains 196 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 181 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 302 ARG Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 302 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 93 optimal weight: 0.0670 chunk 142 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 138 optimal weight: 0.0970 chunk 131 optimal weight: 0.6980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.129665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099123 restraints weight = 91927.742| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.41 r_work: 0.3029 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13840 Z= 0.089 Angle : 0.544 6.123 18776 Z= 0.265 Chirality : 0.045 0.137 2052 Planarity : 0.004 0.041 2448 Dihedral : 6.098 50.080 1956 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.62 % Allowed : 20.29 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.20), residues: 1708 helix: 0.13 (0.28), residues: 400 sheet: -1.67 (0.34), residues: 216 loop : -0.82 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.005 0.001 TYR D 309 PHE 0.011 0.001 PHE B 178 TRP 0.009 0.001 TRP D 274 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd covalent geometry : bond 0.00208 (13840) covalent geometry : angle 0.54390 (18776) hydrogen bonds : bond 0.02589 ( 168) hydrogen bonds : angle 4.26608 ( 420) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 192 time to evaluate : 0.669 Fit side-chains REVERT: A 39 LYS cc_start: 0.8888 (mttt) cc_final: 0.8483 (mtmt) REVERT: A 115 ARG cc_start: 0.7189 (mpt180) cc_final: 0.6932 (mmt90) REVERT: A 123 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: A 126 ASP cc_start: 0.7793 (m-30) cc_final: 0.7446 (p0) REVERT: A 155 ASP cc_start: 0.8665 (t70) cc_final: 0.7864 (t0) REVERT: A 168 MET cc_start: 0.8288 (ttp) cc_final: 0.7964 (ttp) REVERT: A 328 MET cc_start: 0.7868 (mmm) cc_final: 0.7375 (mmt) REVERT: A 355 ARG cc_start: 0.7771 (mmt90) cc_final: 0.7264 (mtp180) REVERT: A 380 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7794 (mtp85) REVERT: A 428 LYS cc_start: 0.8649 (tttt) cc_final: 0.8430 (mtpp) REVERT: B 39 LYS cc_start: 0.8842 (mttt) cc_final: 0.8439 (mtmt) REVERT: B 123 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: B 126 ASP cc_start: 0.7745 (m-30) cc_final: 0.7412 (p0) REVERT: B 155 ASP cc_start: 0.8765 (t70) cc_final: 0.7837 (t0) REVERT: B 168 MET cc_start: 0.7992 (ttp) cc_final: 0.7782 (ttp) REVERT: B 355 ARG cc_start: 0.7801 (mmt90) cc_final: 0.7288 (mtp180) REVERT: B 380 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7806 (mtp85) REVERT: B 428 LYS cc_start: 0.8646 (tttt) cc_final: 0.8440 (mtpp) REVERT: D 39 LYS cc_start: 0.8865 (mttt) cc_final: 0.8465 (mtmt) REVERT: D 115 ARG cc_start: 0.7144 (mpt180) cc_final: 0.6886 (mmt90) REVERT: D 123 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: D 126 ASP cc_start: 0.7773 (m-30) cc_final: 0.7436 (p0) REVERT: D 134 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8071 (tt0) REVERT: D 155 ASP cc_start: 0.8680 (t70) cc_final: 0.7937 (t0) REVERT: D 168 MET cc_start: 0.7777 (ttp) cc_final: 0.7517 (ttp) REVERT: D 328 MET cc_start: 0.7937 (mmm) cc_final: 0.7326 (mmt) REVERT: D 355 ARG cc_start: 0.7775 (mmt90) cc_final: 0.7272 (mtp180) REVERT: D 380 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7789 (mtp85) REVERT: D 428 LYS cc_start: 0.8618 (tttt) cc_final: 0.8413 (mtpp) REVERT: C 39 LYS cc_start: 0.8854 (mttt) cc_final: 0.8456 (mtmt) REVERT: C 123 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: C 126 ASP cc_start: 0.7787 (m-30) cc_final: 0.7437 (p0) REVERT: C 134 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7946 (tt0) REVERT: C 155 ASP cc_start: 0.8684 (t70) cc_final: 0.7774 (t0) REVERT: C 168 MET cc_start: 0.7971 (ttp) cc_final: 0.7762 (ttp) REVERT: C 355 ARG cc_start: 0.7784 (mmt90) cc_final: 0.7269 (mtp180) REVERT: C 380 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7791 (mtp85) outliers start: 5 outliers final: 5 residues processed: 197 average time/residue: 1.3710 time to fit residues: 295.0249 Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 321 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 160 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 110 optimal weight: 0.0770 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.130598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099504 restraints weight = 88952.014| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.46 r_work: 0.3003 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3016 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13840 Z= 0.132 Angle : 0.558 6.076 18776 Z= 0.271 Chirality : 0.046 0.136 2052 Planarity : 0.004 0.043 2448 Dihedral : 6.120 52.068 1956 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.04 % Allowed : 19.81 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.20), residues: 1708 helix: 0.05 (0.28), residues: 404 sheet: -1.68 (0.34), residues: 216 loop : -0.79 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 162 TYR 0.008 0.001 TYR B 309 PHE 0.009 0.001 PHE B 178 TRP 0.008 0.001 TRP A 284 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00315 (13840) covalent geometry : angle 0.55756 (18776) hydrogen bonds : bond 0.02699 ( 168) hydrogen bonds : angle 4.28786 ( 420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7835.62 seconds wall clock time: 133 minutes 2.35 seconds (7982.35 seconds total)