Starting phenix.real_space_refine on Sun Sep 13 23:36:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r8u_4761/09_2026/6r8u_4761_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r8u_4761/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6r8u_4761/09_2026/6r8u_4761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r8u_4761/09_2026/6r8u_4761.map" model { file = "/net/cci-nas-00/data/ceres_data/6r8u_4761/09_2026/6r8u_4761_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r8u_4761/09_2026/6r8u_4761_trim.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.72, 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: 2.48 Conformation dependent library (CDL) restraints added in 1.3 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: 0.36 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: 5.38 Time building geometry restraints manager: 3.35 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 - 2.07: 42543 2.07 - 4.14: 5644 4.14 - 6.22: 461 6.22 - 8.29: 48 8.29 - 10.36: 8 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: 1592 0.089 - 0.177: 416 0.177 - 0.266: 32 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: 0.03 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.570 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 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= 0.628 Angle : 1.282 10.360 18776 Z= 0.785 Chirality : 0.078 0.444 2052 Planarity : 0.011 0.092 2448 Dihedral : 15.140 124.001 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/Z covalent geometry : bond 0.01137 / 0.63 (13840) covalent geometry : angle 1.28245 / 0.78 (18776) hydrogen bonds : bond 0.27787 / 18.68 ( 168) hydrogen bonds : angle 10.58058 / 7.38 ( 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 : 0.743 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: 1.3126 time to fit residues: 470.0708 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 : 0.655 ------------------------------------------------------------------------------- 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... 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 = 0.129599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099507 restraints weight = 89223.641| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.34 r_work: 0.3038 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3047 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3047 r_free = 0.3047 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 = 0.3047 r_free = 0.3047 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3047 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13840 Z= 0.145 Angle : 0.643 6.377 18776 Z= 0.330 Chirality : 0.048 0.144 2052 Planarity : 0.006 0.044 2448 Dihedral : 9.132 96.031 1994 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.66 % Allowed : 16.62 % Favored : 81.72 % 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: -2.40 (0.19), residues: 1708 helix: -2.17 (0.22), residues: 392 sheet: -1.71 (0.36), residues: 188 loop : -1.37 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 115 TYR 0.011 0.001 TYR A 114 PHE 0.013 0.001 PHE D 259 TRP 0.015 0.001 TRP D 284 HIS 0.013 0.002 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (13840) covalent geometry : angle 0.64283 / 0.33 (18776) hydrogen bonds : bond 0.05059 / 3.49 ( 168) hydrogen bonds : angle 6.07490 / 4.09 ( 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 261 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8813 (mttt) cc_final: 0.8416 (mtmt) REVERT: A 106 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.6818 (mp10) REVERT: A 123 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: A 126 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7334 (p0) REVERT: A 134 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7996 (tt0) REVERT: A 155 ASP cc_start: 0.8496 (t70) cc_final: 0.7776 (t0) REVERT: A 186 ASN cc_start: 0.7714 (m-40) cc_final: 0.7493 (m-40) REVERT: A 279 THR cc_start: 0.9083 (p) cc_final: 0.8788 (t) REVERT: A 302 ARG cc_start: 0.8654 (mmm-85) cc_final: 0.8432 (mpt-90) REVERT: A 355 ARG cc_start: 0.7898 (mmt90) cc_final: 0.7496 (tpt-90) REVERT: A 380 ARG cc_start: 0.8031 (ttp-170) cc_final: 0.7776 (mtp85) REVERT: A 428 LYS cc_start: 0.8611 (tttt) cc_final: 0.8374 (mtpp) REVERT: B 11 MET cc_start: 0.8526 (mmm) cc_final: 0.8310 (tpp) REVERT: B 39 LYS cc_start: 0.8744 (mttt) cc_final: 0.8361 (mtmt) REVERT: B 106 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: B 123 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: B 155 ASP cc_start: 0.8566 (t70) cc_final: 0.7883 (t0) REVERT: B 267 ASP cc_start: 0.6948 (p0) cc_final: 0.6712 (p0) REVERT: B 279 THR cc_start: 0.9095 (p) cc_final: 0.8786 (t) REVERT: B 302 ARG cc_start: 0.8696 (mmm-85) cc_final: 0.8481 (mpt-90) REVERT: B 355 ARG cc_start: 0.7943 (mmt90) cc_final: 0.7513 (tpt-90) REVERT: B 375 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7770 (ttm110) REVERT: B 380 ARG cc_start: 0.8067 (ttp-170) cc_final: 0.7810 (mtp85) REVERT: B 428 LYS cc_start: 0.8597 (tttt) cc_final: 0.8379 (mtpp) REVERT: D 39 LYS cc_start: 0.8808 (mttt) cc_final: 0.8413 (mtmt) REVERT: D 106 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6784 (mp10) REVERT: D 123 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: D 126 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7305 (p0) REVERT: D 134 GLU cc_start: 0.8224 (mt-10) cc_final: 0.8024 (tt0) REVERT: D 155 ASP cc_start: 0.8526 (t70) cc_final: 0.7832 (t0) REVERT: D 302 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8458 (mpt-90) REVERT: D 355 ARG cc_start: 0.7937 (mmt90) cc_final: 0.7496 (tpt-90) REVERT: D 375 ARG cc_start: 0.8159 (mtm110) cc_final: 0.7739 (ttm110) REVERT: D 380 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7752 (mtp85) REVERT: D 428 LYS cc_start: 0.8562 (tttt) cc_final: 0.8326 (mtpp) REVERT: C 39 LYS cc_start: 0.8807 (mttt) cc_final: 0.8425 (mtmt) REVERT: C 106 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6778 (mp10) REVERT: C 123 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.6976 (mp10) REVERT: C 126 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.7271 (p0) REVERT: C 134 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8018 (tt0) REVERT: C 155 ASP cc_start: 0.8615 (t70) cc_final: 0.7901 (t0) REVERT: C 229 GLU cc_start: 0.8612 (tt0) cc_final: 0.8398 (tt0) REVERT: C 243 ASP cc_start: 0.6720 (m-30) cc_final: 0.6260 (m-30) REVERT: C 279 THR cc_start: 0.9109 (p) cc_final: 0.8801 (t) REVERT: C 302 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8444 (mpt-90) REVERT: C 355 ARG cc_start: 0.7914 (mmt90) cc_final: 0.7499 (tpt-90) REVERT: C 375 ARG cc_start: 0.8142 (mtm110) cc_final: 0.7716 (ttm110) REVERT: C 380 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7736 (mtp85) REVERT: C 428 LYS cc_start: 0.8590 (tttt) cc_final: 0.8389 (mtpp) outliers start: 20 outliers final: 3 residues processed: 253 average time/residue: 1.4349 time to fit residues: 396.3466 Evaluate side-chains 214 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 321 ASP Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 321 ASP 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 321 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 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: 0.9980 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3579 r_free = 0.3579 target = 0.132833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.102306 restraints weight = 88629.050| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.32 r_work: 0.3011 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3020 r_free = 0.3020 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 = 0.3020 r_free = 0.3020 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13840 Z= 0.193 Angle : 0.606 6.790 18776 Z= 0.307 Chirality : 0.047 0.140 2052 Planarity : 0.005 0.041 2448 Dihedral : 7.900 83.682 1956 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.45 % Allowed : 17.04 % Favored : 81.51 % 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: -2.09 (0.19), residues: 1708 helix: -1.63 (0.25), residues: 396 sheet: -1.62 (0.35), residues: 188 loop : -1.26 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 162 TYR 0.009 0.001 TYR D 309 PHE 0.010 0.001 PHE B 259 TRP 0.013 0.001 TRP D 284 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.19 (13840) covalent geometry : angle 0.60645 / 0.31 (18776) hydrogen bonds : bond 0.03779 / 2.59 ( 168) hydrogen bonds : angle 5.61101 / 3.77 ( 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 225 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8802 (mttt) cc_final: 0.8367 (mtmt) REVERT: A 106 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6683 (mp10) REVERT: A 115 ARG cc_start: 0.7352 (mpt180) cc_final: 0.7073 (mmt90) REVERT: A 123 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.6633 (mp10) REVERT: A 126 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7312 (p0) REVERT: A 134 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7981 (tt0) REVERT: A 155 ASP cc_start: 0.8566 (t70) cc_final: 0.7829 (t0) REVERT: A 186 ASN cc_start: 0.7663 (m-40) cc_final: 0.7400 (m-40) REVERT: A 228 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 243 ASP cc_start: 0.6596 (m-30) cc_final: 0.6348 (m-30) REVERT: A 279 THR cc_start: 0.8975 (p) cc_final: 0.8624 (t) REVERT: A 355 ARG cc_start: 0.7905 (mmt90) cc_final: 0.7418 (tpt90) REVERT: A 380 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7731 (mtp85) REVERT: A 428 LYS cc_start: 0.8648 (tttt) cc_final: 0.8413 (mtpp) REVERT: B 11 MET cc_start: 0.8542 (mmm) cc_final: 0.8274 (tpp) REVERT: B 39 LYS cc_start: 0.8829 (mttt) cc_final: 0.8383 (mtmt) REVERT: B 106 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6632 (mp10) REVERT: B 123 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.6664 (mp10) REVERT: B 126 ASP cc_start: 0.7800 (m-30) cc_final: 0.7303 (p0) REVERT: B 155 ASP cc_start: 0.8670 (t70) cc_final: 0.7893 (t0) REVERT: B 279 THR cc_start: 0.8957 (p) cc_final: 0.8620 (t) REVERT: B 355 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7436 (tpt90) REVERT: B 380 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7749 (mtp85) REVERT: B 428 LYS cc_start: 0.8654 (tttt) cc_final: 0.8404 (mtpp) REVERT: D 39 LYS cc_start: 0.8836 (mttt) cc_final: 0.8391 (mtmt) REVERT: D 106 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6675 (mp10) REVERT: D 115 ARG cc_start: 0.7368 (mpt180) cc_final: 0.7056 (mmt-90) REVERT: D 123 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.6647 (mp10) REVERT: D 126 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7298 (p0) REVERT: D 134 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8004 (tt0) REVERT: D 155 ASP cc_start: 0.8608 (t70) cc_final: 0.7829 (t0) REVERT: D 186 ASN cc_start: 0.7661 (m-40) cc_final: 0.7408 (m-40) REVERT: D 228 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7791 (mt-10) REVERT: D 243 ASP cc_start: 0.6514 (m-30) cc_final: 0.6285 (m-30) REVERT: D 355 ARG cc_start: 0.7943 (mmt90) cc_final: 0.7433 (tpt90) REVERT: D 380 ARG cc_start: 0.8036 (ttp-170) cc_final: 0.7712 (mtp85) REVERT: D 428 LYS cc_start: 0.8616 (tttt) cc_final: 0.8393 (mtpp) REVERT: C 39 LYS cc_start: 0.8859 (mttt) cc_final: 0.8409 (mtmt) REVERT: C 106 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: C 123 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.6503 (mp10) REVERT: C 126 ASP cc_start: 0.7725 (OUTLIER) cc_final: 0.7259 (p0) REVERT: C 134 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7786 (tt0) REVERT: C 155 ASP cc_start: 0.8676 (t70) cc_final: 0.7877 (t0) REVERT: C 228 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7859 (mt-10) REVERT: C 243 ASP cc_start: 0.6570 (m-30) cc_final: 0.6343 (m-30) REVERT: C 355 ARG cc_start: 0.7942 (mmt90) cc_final: 0.7423 (tpt90) REVERT: C 380 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7735 (mtp85) REVERT: C 428 LYS cc_start: 0.8637 (tttt) cc_final: 0.8406 (mtpp) outliers start: 17 outliers final: 3 residues processed: 219 average time/residue: 1.3414 time to fit residues: 322.6252 Evaluate side-chains 201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 106 GLN 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 106 GLN Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 126 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 164 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN B 399 ASN D 310 ASN D 347 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.131054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100750 restraints weight = 81393.733| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.21 r_work: 0.2962 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13840 Z= 0.188 Angle : 0.589 6.264 18776 Z= 0.296 Chirality : 0.047 0.138 2052 Planarity : 0.004 0.038 2448 Dihedral : 7.626 78.999 1956 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.52 % Allowed : 18.21 % Favored : 80.26 % 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: -1.96 (0.19), residues: 1708 helix: -1.38 (0.25), residues: 392 sheet: -1.71 (0.34), residues: 204 loop : -1.19 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 162 TYR 0.011 0.001 TYR B 309 PHE 0.013 0.001 PHE D 178 TRP 0.011 0.001 TRP A 284 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (13840) covalent geometry : angle 0.58858 / 0.30 (18776) hydrogen bonds : bond 0.03138 / 2.15 ( 168) hydrogen bonds : angle 5.39504 / 3.63 ( 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 218 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8853 (mttt) cc_final: 0.8437 (mtmt) REVERT: A 106 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.6704 (mp10) REVERT: A 112 ASN cc_start: 0.7741 (t0) cc_final: 0.7397 (t0) REVERT: A 115 ARG cc_start: 0.7458 (mpt180) cc_final: 0.7220 (mmt90) REVERT: A 123 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.6462 (mp10) REVERT: A 126 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7393 (p0) REVERT: A 134 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7974 (tt0) REVERT: A 155 ASP cc_start: 0.8663 (t70) cc_final: 0.7905 (t0) REVERT: A 302 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8137 (mpt-90) REVERT: A 355 ARG cc_start: 0.7969 (mmt90) cc_final: 0.7240 (tpt-90) REVERT: A 380 ARG cc_start: 0.8048 (ttp-170) cc_final: 0.7768 (mtp85) REVERT: A 428 LYS cc_start: 0.8644 (tttt) cc_final: 0.8406 (mtpp) REVERT: B 11 MET cc_start: 0.8542 (mmm) cc_final: 0.8341 (tpp) REVERT: B 39 LYS cc_start: 0.8869 (mttt) cc_final: 0.8454 (mtmt) REVERT: B 123 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.6486 (mp10) REVERT: B 126 ASP cc_start: 0.7841 (m-30) cc_final: 0.7363 (p0) REVERT: B 155 ASP cc_start: 0.8687 (t70) cc_final: 0.7931 (t0) REVERT: B 302 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8203 (mpt-90) REVERT: B 355 ARG cc_start: 0.7983 (mmt90) cc_final: 0.7368 (tpt90) REVERT: B 380 ARG cc_start: 0.8083 (ttp-170) cc_final: 0.7771 (mtp85) REVERT: D 39 LYS cc_start: 0.8834 (mttt) cc_final: 0.8434 (mtmt) REVERT: D 106 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: D 112 ASN cc_start: 0.7720 (t0) cc_final: 0.7265 (t0) REVERT: D 115 ARG cc_start: 0.7454 (mpt180) cc_final: 0.7220 (mmt90) REVERT: D 123 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.6441 (mp10) REVERT: D 126 ASP cc_start: 0.7771 (m-30) cc_final: 0.7410 (p0) REVERT: D 134 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8040 (tt0) REVERT: D 155 ASP cc_start: 0.8678 (t70) cc_final: 0.7918 (t0) REVERT: D 243 ASP cc_start: 0.6632 (m-30) cc_final: 0.6419 (m-30) REVERT: D 302 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8097 (mpt-90) REVERT: D 328 MET cc_start: 0.7481 (mtp) cc_final: 0.7158 (mmt) REVERT: D 355 ARG cc_start: 0.7974 (mmt90) cc_final: 0.7357 (tpt90) REVERT: D 380 ARG cc_start: 0.8077 (ttp-170) cc_final: 0.7768 (mtp85) REVERT: D 428 LYS cc_start: 0.8652 (tttt) cc_final: 0.8400 (mtpp) REVERT: C 39 LYS cc_start: 0.8853 (mttt) cc_final: 0.8448 (mtmt) REVERT: C 123 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.6482 (mp10) REVERT: C 126 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7323 (p0) REVERT: C 134 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7889 (tt0) REVERT: C 155 ASP cc_start: 0.8680 (t70) cc_final: 0.7907 (t0) REVERT: C 243 ASP cc_start: 0.6598 (m-30) cc_final: 0.6391 (m-30) REVERT: C 302 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8074 (mpt-90) REVERT: C 328 MET cc_start: 0.7477 (mtp) cc_final: 0.7211 (mtm) REVERT: C 355 ARG cc_start: 0.7977 (mmt90) cc_final: 0.7329 (tpt90) REVERT: C 380 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7770 (mtp85) REVERT: C 428 LYS cc_start: 0.8678 (tttt) cc_final: 0.8464 (mtpp) outliers start: 18 outliers final: 5 residues processed: 209 average time/residue: 1.2447 time to fit residues: 287.4730 Evaluate side-chains 201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 126 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 302 ARG Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 123 GLN 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 126 ASP Chi-restraints excluded: chain C residue 302 ARG 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: 0.7980 chunk 103 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 0.0030 chunk 14 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 186 ASN A 310 ASN B 186 ASN D 186 ASN D 310 ASN C 186 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.128107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097348 restraints weight = 93173.561| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 3.44 r_work: 0.2967 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2971 r_free = 0.2971 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13840 Z= 0.133 Angle : 0.562 6.258 18776 Z= 0.280 Chirality : 0.046 0.140 2052 Planarity : 0.004 0.035 2448 Dihedral : 7.368 75.958 1956 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.45 % Allowed : 18.91 % Favored : 79.64 % 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: -1.79 (0.19), residues: 1708 helix: -1.06 (0.26), residues: 396 sheet: -1.72 (0.34), residues: 204 loop : -1.12 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.008 0.001 TYR A 309 PHE 0.011 0.001 PHE D 178 TRP 0.009 0.001 TRP B 284 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (13840) covalent geometry : angle 0.56167 / 0.28 (18776) hydrogen bonds : bond 0.02846 / 1.97 ( 168) hydrogen bonds : angle 5.12503 / 3.45 ( 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 205 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8797 (mttt) cc_final: 0.8361 (mtmt) REVERT: A 112 ASN cc_start: 0.7751 (t0) cc_final: 0.7426 (t0) REVERT: A 115 ARG cc_start: 0.7385 (mpt180) cc_final: 0.7158 (mmt90) REVERT: A 123 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.6404 (mp10) REVERT: A 126 ASP cc_start: 0.7786 (m-30) cc_final: 0.7378 (p0) REVERT: A 134 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7986 (tt0) REVERT: A 155 ASP cc_start: 0.8679 (t70) cc_final: 0.7898 (t0) REVERT: A 302 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8012 (mpt-90) REVERT: A 355 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7269 (mtp180) REVERT: A 380 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7732 (mtp85) REVERT: A 428 LYS cc_start: 0.8657 (tttt) cc_final: 0.8394 (mtpp) REVERT: B 39 LYS cc_start: 0.8862 (mttt) cc_final: 0.8433 (mtmt) REVERT: B 123 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.6362 (mp10) REVERT: B 126 ASP cc_start: 0.7797 (m-30) cc_final: 0.7338 (p0) REVERT: B 155 ASP cc_start: 0.8681 (t70) cc_final: 0.7896 (t0) REVERT: B 302 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8045 (mpt-90) REVERT: B 355 ARG cc_start: 0.7962 (mmt90) cc_final: 0.7292 (mtp180) REVERT: B 380 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7719 (mtp85) REVERT: D 39 LYS cc_start: 0.8831 (mttt) cc_final: 0.8418 (mtmt) REVERT: D 112 ASN cc_start: 0.7731 (t0) cc_final: 0.7420 (t0) REVERT: D 115 ARG cc_start: 0.7401 (mpt180) cc_final: 0.7164 (mmt90) REVERT: D 123 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.6431 (mp10) REVERT: D 126 ASP cc_start: 0.7782 (m-30) cc_final: 0.7386 (p0) REVERT: D 134 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8002 (tt0) REVERT: D 155 ASP cc_start: 0.8677 (t70) cc_final: 0.7910 (t0) REVERT: D 243 ASP cc_start: 0.6678 (m-30) cc_final: 0.6460 (m-30) REVERT: D 302 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8023 (mpt-90) REVERT: D 328 MET cc_start: 0.7604 (mtp) cc_final: 0.7143 (mmt) REVERT: D 355 ARG cc_start: 0.7963 (mmt90) cc_final: 0.7285 (mtp180) REVERT: D 380 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7722 (mtp85) REVERT: D 428 LYS cc_start: 0.8640 (tttt) cc_final: 0.8386 (mtpp) REVERT: C 39 LYS cc_start: 0.8851 (mttt) cc_final: 0.8429 (mtmt) REVERT: C 123 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.6425 (mp10) REVERT: C 126 ASP cc_start: 0.7793 (m-30) cc_final: 0.7327 (p0) REVERT: C 134 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7902 (tt0) REVERT: C 155 ASP cc_start: 0.8676 (t70) cc_final: 0.7884 (t0) REVERT: C 302 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8024 (mpt-90) REVERT: C 321 ASP cc_start: 0.8376 (p0) cc_final: 0.8116 (p0) REVERT: C 355 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7278 (mtp180) REVERT: C 380 ARG cc_start: 0.8047 (ttp-170) cc_final: 0.7713 (mtp85) REVERT: C 428 LYS cc_start: 0.8661 (tttt) cc_final: 0.8440 (mtpp) outliers start: 17 outliers final: 9 residues processed: 199 average time/residue: 1.2660 time to fit residues: 277.4249 Evaluate side-chains 199 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 182 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 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 123 GLN Chi-restraints excluded: chain C residue 289 ASP 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: 4.9990 chunk 136 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN D 310 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.097564 restraints weight = 96569.518| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.55 r_work: 0.2965 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 13840 Z= 0.116 Angle : 0.545 6.318 18776 Z= 0.269 Chirality : 0.045 0.138 2052 Planarity : 0.004 0.035 2448 Dihedral : 7.179 72.034 1956 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.52 % Allowed : 19.18 % Favored : 79.29 % 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: -1.54 (0.20), residues: 1708 helix: -0.76 (0.27), residues: 400 sheet: -1.68 (0.34), residues: 204 loop : -0.98 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 162 TYR 0.007 0.001 TYR D 309 PHE 0.010 0.001 PHE A 178 TRP 0.008 0.001 TRP B 284 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13840) covalent geometry : angle 0.54457 / 0.27 (18776) hydrogen bonds : bond 0.02705 / 1.89 ( 168) hydrogen bonds : angle 4.90386 / 3.32 ( 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 214 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8793 (mttt) cc_final: 0.8345 (mtmt) REVERT: A 115 ARG cc_start: 0.7282 (mpt180) cc_final: 0.7052 (mmt90) REVERT: A 126 ASP cc_start: 0.7792 (m-30) cc_final: 0.7367 (p0) REVERT: A 134 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8009 (tt0) REVERT: A 155 ASP cc_start: 0.8654 (t70) cc_final: 0.7859 (t0) REVERT: A 355 ARG cc_start: 0.7888 (mmt90) cc_final: 0.7183 (mtp180) REVERT: A 380 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.7689 (mtp85) REVERT: A 428 LYS cc_start: 0.8662 (tttt) cc_final: 0.8393 (mtpp) REVERT: B 39 LYS cc_start: 0.8808 (mttt) cc_final: 0.8357 (mtmt) REVERT: B 126 ASP cc_start: 0.7753 (m-30) cc_final: 0.7327 (p0) REVERT: B 155 ASP cc_start: 0.8670 (t70) cc_final: 0.7870 (t0) REVERT: B 355 ARG cc_start: 0.7930 (mmt90) cc_final: 0.7232 (mtp180) REVERT: B 380 ARG cc_start: 0.8053 (ttp-170) cc_final: 0.7713 (mtp85) REVERT: D 39 LYS cc_start: 0.8822 (mttt) cc_final: 0.8375 (mtmt) REVERT: D 115 ARG cc_start: 0.7307 (mpt180) cc_final: 0.7074 (mmt90) REVERT: D 126 ASP cc_start: 0.7783 (m-30) cc_final: 0.7368 (p0) REVERT: D 134 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8024 (tt0) REVERT: D 155 ASP cc_start: 0.8667 (t70) cc_final: 0.7880 (t0) REVERT: D 328 MET cc_start: 0.7653 (mtp) cc_final: 0.7214 (mmt) REVERT: D 355 ARG cc_start: 0.7900 (mmt90) cc_final: 0.7197 (mtp180) REVERT: D 380 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7678 (mtp85) REVERT: D 428 LYS cc_start: 0.8637 (tttt) cc_final: 0.8381 (mtpp) REVERT: C 39 LYS cc_start: 0.8795 (mttt) cc_final: 0.8354 (mtmt) REVERT: C 126 ASP cc_start: 0.7792 (m-30) cc_final: 0.7361 (p0) REVERT: C 134 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7898 (tt0) REVERT: C 155 ASP cc_start: 0.8673 (t70) cc_final: 0.7872 (t0) REVERT: C 355 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7187 (mtp180) REVERT: C 380 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7674 (mtp85) REVERT: C 428 LYS cc_start: 0.8655 (tttt) cc_final: 0.8432 (mtpp) outliers start: 18 outliers final: 15 residues processed: 211 average time/residue: 1.3392 time to fit residues: 310.7742 Evaluate side-chains 201 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 186 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 289 ASP 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 289 ASP Chi-restraints excluded: chain B residue 321 ASP 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 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 289 ASP 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: 3.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.131481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.100005 restraints weight = 90669.829| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.41 r_work: 0.2965 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2968 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2968 r_free = 0.2968 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2968 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13840 Z= 0.140 Angle : 0.550 6.225 18776 Z= 0.273 Chirality : 0.046 0.137 2052 Planarity : 0.004 0.035 2448 Dihedral : 7.151 69.989 1956 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.59 % Allowed : 19.53 % 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: -1.51 (0.20), residues: 1708 helix: -0.52 (0.27), residues: 396 sheet: -1.71 (0.34), residues: 208 loop : -1.04 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 162 TYR 0.009 0.001 TYR B 309 PHE 0.010 0.001 PHE C 240 TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (13840) covalent geometry : angle 0.54992 / 0.27 (18776) hydrogen bonds : bond 0.02809 / 1.95 ( 168) hydrogen bonds : angle 4.85104 / 3.29 ( 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 207 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8815 (mttt) cc_final: 0.8387 (mtmt) REVERT: A 115 ARG cc_start: 0.7248 (mpt180) cc_final: 0.7017 (mmt90) REVERT: A 126 ASP cc_start: 0.7813 (m-30) cc_final: 0.7411 (p0) REVERT: A 134 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8048 (tt0) REVERT: A 155 ASP cc_start: 0.8671 (t70) cc_final: 0.7895 (t0) REVERT: A 302 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8021 (mpt-90) REVERT: A 355 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7262 (mtp180) REVERT: A 380 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7718 (mtp85) REVERT: A 428 LYS cc_start: 0.8667 (tttt) cc_final: 0.8409 (mtpp) REVERT: B 39 LYS cc_start: 0.8830 (mttt) cc_final: 0.8396 (mtmt) REVERT: B 126 ASP cc_start: 0.7760 (m-30) cc_final: 0.7377 (p0) REVERT: B 155 ASP cc_start: 0.8673 (t70) cc_final: 0.7880 (t0) REVERT: B 302 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8034 (mpt-90) REVERT: B 355 ARG cc_start: 0.7920 (mmt90) cc_final: 0.7281 (mtp180) REVERT: B 380 ARG cc_start: 0.8084 (ttp-170) cc_final: 0.7765 (mtp85) REVERT: D 39 LYS cc_start: 0.8873 (mttt) cc_final: 0.8453 (mtmt) REVERT: D 115 ARG cc_start: 0.7267 (mpt180) cc_final: 0.7028 (mmt90) REVERT: D 126 ASP cc_start: 0.7761 (m-30) cc_final: 0.7367 (p0) REVERT: D 134 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8038 (tt0) REVERT: D 155 ASP cc_start: 0.8675 (t70) cc_final: 0.7900 (t0) REVERT: D 302 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8037 (mpt-90) REVERT: D 355 ARG cc_start: 0.7908 (mmt90) cc_final: 0.7274 (mtp180) REVERT: D 380 ARG cc_start: 0.8070 (ttp-170) cc_final: 0.7757 (mtp85) REVERT: D 428 LYS cc_start: 0.8640 (tttt) cc_final: 0.8393 (mtpp) REVERT: C 39 LYS cc_start: 0.8820 (mttt) cc_final: 0.8387 (mtmt) REVERT: C 126 ASP cc_start: 0.7811 (m-30) cc_final: 0.7407 (p0) REVERT: C 134 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7946 (tt0) REVERT: C 155 ASP cc_start: 0.8681 (t70) cc_final: 0.7900 (t0) REVERT: C 302 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.8023 (mpt-90) REVERT: C 355 ARG cc_start: 0.7898 (mmt90) cc_final: 0.7239 (mtp180) REVERT: C 380 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7721 (mtp85) REVERT: C 428 LYS cc_start: 0.8642 (tttt) cc_final: 0.8436 (mtpp) outliers start: 19 outliers final: 16 residues processed: 199 average time/residue: 1.3030 time to fit residues: 286.1715 Evaluate side-chains 207 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 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 289 ASP Chi-restraints excluded: chain B residue 302 ARG Chi-restraints excluded: chain B residue 321 ASP 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 289 ASP 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: 1.9990 chunk 76 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 310 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.132868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.101792 restraints weight = 89044.540| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.35 r_work: 0.2980 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3066 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= 0.117 Angle : 0.539 6.256 18776 Z= 0.267 Chirality : 0.045 0.137 2052 Planarity : 0.004 0.040 2448 Dihedral : 7.061 66.434 1956 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.39 % Allowed : 19.39 % Favored : 79.22 % 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: -1.39 (0.20), residues: 1708 helix: -0.34 (0.27), residues: 400 sheet: -1.66 (0.34), residues: 208 loop : -0.98 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 162 TYR 0.007 0.001 TYR C 309 PHE 0.012 0.001 PHE C 178 TRP 0.008 0.001 TRP A 274 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (13840) covalent geometry : angle 0.53869 / 0.27 (18776) hydrogen bonds : bond 0.02691 / 1.88 ( 168) hydrogen bonds : angle 4.64940 / 3.15 ( 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 208 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8872 (mttt) cc_final: 0.8459 (mtmt) REVERT: A 115 ARG cc_start: 0.7195 (mpt180) cc_final: 0.6920 (mmt90) REVERT: A 123 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: A 126 ASP cc_start: 0.7792 (m-30) cc_final: 0.7418 (p0) REVERT: A 134 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8043 (tt0) REVERT: A 155 ASP cc_start: 0.8642 (t70) cc_final: 0.7828 (t0) REVERT: A 168 MET cc_start: 0.7944 (ttp) cc_final: 0.7678 (ttp) REVERT: A 302 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8016 (mpt-90) REVERT: A 355 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7282 (mtp180) REVERT: A 380 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7778 (mtp85) REVERT: A 428 LYS cc_start: 0.8661 (tttt) cc_final: 0.8422 (mtpp) REVERT: B 39 LYS cc_start: 0.8853 (mttt) cc_final: 0.8435 (mtmt) REVERT: B 123 GLN cc_start: 0.8219 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: B 126 ASP cc_start: 0.7789 (m-30) cc_final: 0.7427 (p0) REVERT: B 155 ASP cc_start: 0.8653 (t70) cc_final: 0.7839 (t0) REVERT: B 355 ARG cc_start: 0.7901 (mmt90) cc_final: 0.7303 (mtp180) REVERT: B 380 ARG cc_start: 0.8085 (ttp-170) cc_final: 0.7772 (mtp85) REVERT: D 39 LYS cc_start: 0.8879 (mttt) cc_final: 0.8474 (mtmt) REVERT: D 115 ARG cc_start: 0.7275 (mpt180) cc_final: 0.6993 (mmt90) REVERT: D 123 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: D 126 ASP cc_start: 0.7782 (m-30) cc_final: 0.7411 (p0) REVERT: D 134 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8049 (tt0) REVERT: D 155 ASP cc_start: 0.8682 (t70) cc_final: 0.7919 (t0) REVERT: D 355 ARG cc_start: 0.7878 (mmt90) cc_final: 0.7280 (mtp180) REVERT: D 380 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7785 (mtp85) REVERT: D 428 LYS cc_start: 0.8628 (tttt) cc_final: 0.8403 (mtpp) REVERT: C 39 LYS cc_start: 0.8875 (mttt) cc_final: 0.8450 (mtmt) REVERT: C 126 ASP cc_start: 0.7778 (m-30) cc_final: 0.7418 (p0) REVERT: C 134 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7977 (tt0) REVERT: C 155 ASP cc_start: 0.8694 (t70) cc_final: 0.7871 (t0) REVERT: C 355 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7274 (mtp180) REVERT: C 380 ARG cc_start: 0.8094 (ttp-170) cc_final: 0.7784 (mtp85) outliers start: 16 outliers final: 8 residues processed: 203 average time/residue: 1.2823 time to fit residues: 286.5579 Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN 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 348 SER Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 289 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 167 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 162 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 165 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.133175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101667 restraints weight = 94700.418| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.46 r_work: 0.2975 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13840 Z= 0.118 Angle : 0.542 6.250 18776 Z= 0.267 Chirality : 0.045 0.136 2052 Planarity : 0.004 0.041 2448 Dihedral : 7.018 63.473 1956 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.11 % Allowed : 19.53 % 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: -1.29 (0.20), residues: 1708 helix: -0.23 (0.28), residues: 400 sheet: -1.50 (0.35), residues: 204 loop : -0.96 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.007 0.001 TYR C 309 PHE 0.011 0.001 PHE A 178 TRP 0.009 0.001 TRP B 284 HIS 0.002 0.001 HIS D 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13840) covalent geometry : angle 0.54199 / 0.27 (18776) hydrogen bonds : bond 0.02691 / 1.88 ( 168) hydrogen bonds : angle 4.60774 / 3.11 ( 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 200 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7659 (mt0) REVERT: A 39 LYS cc_start: 0.8878 (mttt) cc_final: 0.8460 (mtmt) REVERT: A 115 ARG cc_start: 0.7233 (mpt180) cc_final: 0.6954 (mmt90) REVERT: A 123 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: A 126 ASP cc_start: 0.7808 (m-30) cc_final: 0.7432 (p0) REVERT: A 134 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8045 (tt0) REVERT: A 155 ASP cc_start: 0.8595 (t70) cc_final: 0.7841 (t0) REVERT: A 355 ARG cc_start: 0.7892 (mmt90) cc_final: 0.7266 (mtp180) REVERT: A 380 ARG cc_start: 0.8089 (ttp-170) cc_final: 0.7769 (mtp85) REVERT: A 428 LYS cc_start: 0.8663 (tttt) cc_final: 0.8419 (mtpp) REVERT: B 15 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7687 (mt0) REVERT: B 39 LYS cc_start: 0.8879 (mttt) cc_final: 0.8474 (mtmt) REVERT: B 123 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: B 126 ASP cc_start: 0.7800 (m-30) cc_final: 0.7429 (p0) REVERT: B 155 ASP cc_start: 0.8658 (t70) cc_final: 0.7810 (t0) REVERT: B 355 ARG cc_start: 0.7899 (mmt90) cc_final: 0.7291 (mtp180) REVERT: B 380 ARG cc_start: 0.8073 (ttp-170) cc_final: 0.7751 (mtp85) REVERT: D 39 LYS cc_start: 0.8888 (mttt) cc_final: 0.8475 (mtmt) REVERT: D 115 ARG cc_start: 0.7246 (mpt180) cc_final: 0.6967 (mmt90) REVERT: D 123 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: D 126 ASP cc_start: 0.7791 (m-30) cc_final: 0.7431 (p0) REVERT: D 134 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8055 (tt0) REVERT: D 155 ASP cc_start: 0.8688 (t70) cc_final: 0.7916 (t0) REVERT: D 168 MET cc_start: 0.7996 (ttp) cc_final: 0.7770 (ttp) REVERT: D 355 ARG cc_start: 0.7876 (mmt90) cc_final: 0.7272 (mtp180) REVERT: D 380 ARG cc_start: 0.8059 (ttp-170) cc_final: 0.7750 (mtp85) REVERT: D 428 LYS cc_start: 0.8635 (tttt) cc_final: 0.8404 (mtpp) REVERT: C 39 LYS cc_start: 0.8879 (mttt) cc_final: 0.8462 (mtmt) REVERT: C 126 ASP cc_start: 0.7785 (m-30) cc_final: 0.7416 (p0) REVERT: C 134 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7985 (tt0) REVERT: C 155 ASP cc_start: 0.8696 (t70) cc_final: 0.7926 (t0) REVERT: C 168 MET cc_start: 0.7833 (ttp) cc_final: 0.7583 (ttp) REVERT: C 302 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8052 (mpt-90) REVERT: C 355 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7268 (mtp180) REVERT: C 380 ARG cc_start: 0.8078 (ttp-170) cc_final: 0.7774 (mtp85) outliers start: 12 outliers final: 8 residues processed: 199 average time/residue: 1.2822 time to fit residues: 281.5056 Evaluate side-chains 195 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN 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 289 ASP 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 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 289 ASP 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: 2.9990 chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 142 optimal weight: 0.0030 chunk 161 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 131 optimal weight: 0.5980 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.129791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.098575 restraints weight = 92016.893| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.50 r_work: 0.2983 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13840 Z= 0.109 Angle : 0.536 6.233 18776 Z= 0.264 Chirality : 0.045 0.136 2052 Planarity : 0.004 0.044 2448 Dihedral : 6.935 58.348 1956 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.18 % Allowed : 19.25 % Favored : 79.57 % 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: -1.20 (0.20), residues: 1708 helix: -0.06 (0.28), residues: 400 sheet: -1.59 (0.34), residues: 212 loop : -0.90 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 162 TYR 0.007 0.001 TYR B 309 PHE 0.011 0.001 PHE A 178 TRP 0.009 0.001 TRP D 274 HIS 0.002 0.001 HIS C 326 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (13840) covalent geometry : angle 0.53612 / 0.26 (18776) hydrogen bonds : bond 0.02693 / 1.88 ( 168) hydrogen bonds : angle 4.55141 / 3.08 ( 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 200 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.721 Fit side-chains REVERT: A 15 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7531 (mt0) REVERT: A 39 LYS cc_start: 0.8851 (mttt) cc_final: 0.8402 (mtmt) REVERT: A 115 ARG cc_start: 0.7137 (mpt180) cc_final: 0.6874 (mmt90) REVERT: A 123 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7734 (mt0) REVERT: A 126 ASP cc_start: 0.7772 (m-30) cc_final: 0.7373 (p0) REVERT: A 134 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7980 (tt0) REVERT: A 155 ASP cc_start: 0.8556 (t70) cc_final: 0.7767 (t0) REVERT: A 355 ARG cc_start: 0.7866 (mmt90) cc_final: 0.7135 (mtp180) REVERT: A 380 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7652 (mtp85) REVERT: A 428 LYS cc_start: 0.8657 (tttt) cc_final: 0.8391 (mtpp) REVERT: B 15 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7552 (mt0) REVERT: B 39 LYS cc_start: 0.8843 (mttt) cc_final: 0.8405 (mtmt) REVERT: B 123 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: B 126 ASP cc_start: 0.7766 (m-30) cc_final: 0.7379 (p0) REVERT: B 155 ASP cc_start: 0.8634 (t70) cc_final: 0.7756 (t0) REVERT: B 168 MET cc_start: 0.7706 (ttp) cc_final: 0.7504 (ttp) REVERT: B 355 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7144 (mtp180) REVERT: B 380 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7663 (mtp85) REVERT: D 39 LYS cc_start: 0.8850 (mttt) cc_final: 0.8406 (mtmt) REVERT: D 115 ARG cc_start: 0.7134 (mpt180) cc_final: 0.6873 (mmt90) REVERT: D 123 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: D 126 ASP cc_start: 0.7749 (m-30) cc_final: 0.7357 (p0) REVERT: D 134 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7976 (tt0) REVERT: D 155 ASP cc_start: 0.8650 (t70) cc_final: 0.7838 (t0) REVERT: D 168 MET cc_start: 0.7777 (ttp) cc_final: 0.7566 (ttp) REVERT: D 355 ARG cc_start: 0.7828 (mmt90) cc_final: 0.7123 (mtp180) REVERT: D 380 ARG cc_start: 0.8001 (ttp-170) cc_final: 0.7643 (mtp85) REVERT: D 428 LYS cc_start: 0.8629 (tttt) cc_final: 0.8374 (mtpp) REVERT: C 39 LYS cc_start: 0.8855 (mttt) cc_final: 0.8405 (mtmt) REVERT: C 123 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7758 (mt0) REVERT: C 126 ASP cc_start: 0.7753 (m-30) cc_final: 0.7362 (p0) REVERT: C 134 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7969 (tt0) REVERT: C 155 ASP cc_start: 0.8652 (t70) cc_final: 0.7848 (t0) REVERT: C 168 MET cc_start: 0.7902 (ttp) cc_final: 0.7612 (ttp) REVERT: C 302 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8051 (mpt-90) REVERT: C 380 ARG cc_start: 0.8017 (ttp-170) cc_final: 0.7652 (mtp85) REVERT: C 428 LYS cc_start: 0.8626 (tttt) cc_final: 0.8367 (mtpp) outliers start: 13 outliers final: 8 residues processed: 198 average time/residue: 1.2747 time to fit residues: 278.3105 Evaluate side-chains 193 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN 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 289 ASP 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 348 SER Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 289 ASP 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 160 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 110 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 99 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.129976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.099199 restraints weight = 88739.790| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.39 r_work: 0.3007 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3252 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= 0.095 Angle : 0.532 6.197 18776 Z= 0.262 Chirality : 0.045 0.136 2052 Planarity : 0.004 0.043 2448 Dihedral : 6.825 57.057 1956 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.18 % Allowed : 19.04 % Favored : 79.78 % 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: -1.11 (0.20), residues: 1708 helix: 0.08 (0.28), residues: 404 sheet: -1.63 (0.34), residues: 212 loop : -0.84 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 162 TYR 0.006 0.001 TYR B 309 PHE 0.013 0.001 PHE B 178 TRP 0.009 0.001 TRP B 274 HIS 0.003 0.001 HIS C 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (13840) covalent geometry : angle 0.53222 / 0.26 (18776) hydrogen bonds : bond 0.02658 / 1.86 ( 168) hydrogen bonds : angle 4.48647 / 3.04 ( 420) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8135.91 seconds wall clock time: 138 minutes 15.96 seconds (8295.96 seconds total)