Starting phenix.real_space_refine on Fri Oct 30 23:18:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pn9_71747/10_2026/9pn9_71747_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pn9_71747/10_2026/9pn9_71747.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pn9_71747/10_2026/9pn9_71747_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pn9_71747/10_2026/9pn9_71747_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pn9_71747/10_2026/9pn9_71747.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pn9_71747/10_2026/9pn9_71747.map" } resolution = 2.68 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= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 81 5.16 5 C 12132 2.51 5 N 3357 2.21 5 O 3672 1.98 5 H 19225 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38467 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "B" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "E" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "F" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "H" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "I" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 436 Classifications: {'peptide': 30} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 27} Chain: "J" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "K" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "L" Number of atoms: 3839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3839 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "M" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "N" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "O" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "P" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "Q" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Chain: "R" Number of atoms: 3838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 3838 Classifications: {'peptide': 246} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 233} Chain breaks: 1 Time building chain proxies: 6.25, per 1000 atoms: 0.16 Number of scatterers: 38467 At special positions: 0 Unit cell: (132.606, 133.44, 110.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 81 16.00 O 3672 8.00 N 3357 7.00 C 12132 6.00 H 19225 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: 3.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4590 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 1 sheets defined 35.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 18 through 28 Processing helix chain 'B' and resid 9 through 13 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 18 through 28 Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 18 through 28 Processing helix chain 'D' and resid 9 through 13 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 18 through 28 Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 18 through 28 Processing helix chain 'F' and resid 9 through 13 Processing helix chain 'F' and resid 15 through 17 No H-bonds generated for 'chain 'F' and resid 15 through 17' Processing helix chain 'F' and resid 18 through 28 Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 18 through 28 Processing helix chain 'H' and resid 9 through 13 Processing helix chain 'H' and resid 15 through 17 No H-bonds generated for 'chain 'H' and resid 15 through 17' Processing helix chain 'H' and resid 18 through 28 Processing helix chain 'I' and resid 9 through 13 Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 18 through 28 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 75 Processing helix chain 'J' and resid 85 through 99 Processing helix chain 'J' and resid 211 through 235 Processing helix chain 'J' and resid 241 through 246 removed outlier: 4.024A pdb=" N GLN J 246 " --> pdb=" O ALA J 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 256 Processing helix chain 'K' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 75 Processing helix chain 'K' and resid 85 through 99 Processing helix chain 'K' and resid 211 through 235 Processing helix chain 'K' and resid 241 through 246 removed outlier: 4.024A pdb=" N GLN K 246 " --> pdb=" O ALA K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 256 Processing helix chain 'L' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 75 Processing helix chain 'L' and resid 85 through 99 Processing helix chain 'L' and resid 211 through 235 Processing helix chain 'L' and resid 241 through 246 removed outlier: 4.023A pdb=" N GLN L 246 " --> pdb=" O ALA L 243 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 256 Processing helix chain 'M' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS M 26 " --> pdb=" O LYS M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 75 Processing helix chain 'M' and resid 85 through 99 Processing helix chain 'M' and resid 211 through 235 Processing helix chain 'M' and resid 241 through 246 removed outlier: 4.024A pdb=" N GLN M 246 " --> pdb=" O ALA M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 256 Processing helix chain 'N' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS N 26 " --> pdb=" O LYS N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 75 Processing helix chain 'N' and resid 85 through 99 Processing helix chain 'N' and resid 211 through 235 Processing helix chain 'N' and resid 241 through 246 removed outlier: 4.023A pdb=" N GLN N 246 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 247 through 256 Processing helix chain 'O' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS O 26 " --> pdb=" O LYS O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 75 Processing helix chain 'O' and resid 85 through 99 Processing helix chain 'O' and resid 211 through 235 Processing helix chain 'O' and resid 241 through 246 removed outlier: 4.024A pdb=" N GLN O 246 " --> pdb=" O ALA O 243 " (cutoff:3.500A) Processing helix chain 'O' and resid 247 through 256 Processing helix chain 'P' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS P 26 " --> pdb=" O LYS P 22 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 75 Processing helix chain 'P' and resid 85 through 99 Processing helix chain 'P' and resid 211 through 235 Processing helix chain 'P' and resid 241 through 246 removed outlier: 4.023A pdb=" N GLN P 246 " --> pdb=" O ALA P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 256 Processing helix chain 'Q' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS Q 26 " --> pdb=" O LYS Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 75 Processing helix chain 'Q' and resid 85 through 99 Processing helix chain 'Q' and resid 211 through 235 Processing helix chain 'Q' and resid 241 through 246 removed outlier: 4.024A pdb=" N GLN Q 246 " --> pdb=" O ALA Q 243 " (cutoff:3.500A) Processing helix chain 'Q' and resid 247 through 256 Processing helix chain 'R' and resid 18 through 26 removed outlier: 3.663A pdb=" N HIS R 26 " --> pdb=" O LYS R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 75 Processing helix chain 'R' and resid 85 through 99 Processing helix chain 'R' and resid 211 through 235 Processing helix chain 'R' and resid 241 through 246 removed outlier: 4.023A pdb=" N GLN R 246 " --> pdb=" O ALA R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 247 through 256 Processing sheet with id=AA1, first strand: chain 'J' and resid 13 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 13 through 14 current: chain 'J' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER J 173 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN J 165 " --> pdb=" O ILE J 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE J 171 " --> pdb=" O ASN J 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE J 194 " --> pdb=" O ARG J 198 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG J 198 " --> pdb=" O ILE J 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 198 through 209 current: chain 'K' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER K 173 " --> pdb=" O VAL K 163 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ASN K 165 " --> pdb=" O ILE K 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE K 171 " --> pdb=" O ASN K 165 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE K 194 " --> pdb=" O ARG K 198 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG K 198 " --> pdb=" O ILE K 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 198 through 209 current: chain 'L' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER L 173 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN L 165 " --> pdb=" O ILE L 171 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE L 171 " --> pdb=" O ASN L 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L 194 " --> pdb=" O ARG L 198 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG L 198 " --> pdb=" O ILE L 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 198 through 209 current: chain 'M' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER M 173 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN M 165 " --> pdb=" O ILE M 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE M 171 " --> pdb=" O ASN M 165 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE M 194 " --> pdb=" O ARG M 198 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG M 198 " --> pdb=" O ILE M 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 198 through 209 current: chain 'N' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER N 173 " --> pdb=" O VAL N 163 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN N 165 " --> pdb=" O ILE N 171 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE N 171 " --> pdb=" O ASN N 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE N 194 " --> pdb=" O ARG N 198 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG N 198 " --> pdb=" O ILE N 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 198 through 209 current: chain 'O' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER O 173 " --> pdb=" O VAL O 163 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN O 165 " --> pdb=" O ILE O 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE O 171 " --> pdb=" O ASN O 165 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE O 194 " --> pdb=" O ARG O 198 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG O 198 " --> pdb=" O ILE O 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 198 through 209 current: chain 'P' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER P 173 " --> pdb=" O VAL P 163 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN P 165 " --> pdb=" O ILE P 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE P 171 " --> pdb=" O ASN P 165 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE P 194 " --> pdb=" O ARG P 198 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ARG P 198 " --> pdb=" O ILE P 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 198 through 209 current: chain 'Q' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER Q 173 " --> pdb=" O VAL Q 163 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ASN Q 165 " --> pdb=" O ILE Q 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE Q 171 " --> pdb=" O ASN Q 165 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE Q 194 " --> pdb=" O ARG Q 198 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG Q 198 " --> pdb=" O ILE Q 194 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 198 through 209 current: chain 'R' and resid 146 through 165 removed outlier: 3.808A pdb=" N SER R 173 " --> pdb=" O VAL R 163 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN R 165 " --> pdb=" O ILE R 171 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE R 171 " --> pdb=" O ASN R 165 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE R 194 " --> pdb=" O ARG R 198 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ARG R 198 " --> pdb=" O ILE R 194 " (cutoff:3.500A) 801 hydrogen bonds defined for protein. 2295 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: 8.44 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19207 1.03 - 1.23: 56 1.23 - 1.42: 8053 1.42 - 1.62: 11349 1.62 - 1.81: 144 Bond restraints: 38809 Sorted by residual: bond pdb=" N CYS J 1 " pdb=" H1 CYS J 1 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" N CYS L 1 " pdb=" H1 CYS L 1 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N CYS K 1 " pdb=" H1 CYS K 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N CYS Q 1 " pdb=" H1 CYS Q 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N CYS N 1 " pdb=" H1 CYS N 1 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.51e+01 ... (remaining 38804 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 69359 2.25 - 4.50: 564 4.50 - 6.75: 81 6.75 - 8.99: 18 8.99 - 11.24: 27 Bond angle restraints: 70049 Sorted by residual: angle pdb=" CA MET G 3 " pdb=" CB MET G 3 " pdb=" HB2 MET G 3 " ideal model delta sigma weight residual 109.00 120.24 -11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA MET E 3 " pdb=" CB MET E 3 " pdb=" HB2 MET E 3 " ideal model delta sigma weight residual 109.00 120.21 -11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA MET F 3 " pdb=" CB MET F 3 " pdb=" HB2 MET F 3 " ideal model delta sigma weight residual 109.00 120.21 -11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA MET H 3 " pdb=" CB MET H 3 " pdb=" HB2 MET H 3 " ideal model delta sigma weight residual 109.00 120.21 -11.21 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA MET A 3 " pdb=" CB MET A 3 " pdb=" HB2 MET A 3 " ideal model delta sigma weight residual 109.00 120.19 -11.19 3.00e+00 1.11e-01 1.39e+01 ... (remaining 70044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16446 17.98 - 35.96: 1313 35.96 - 53.94: 405 53.94 - 71.91: 125 71.91 - 89.89: 27 Dihedral angle restraints: 18316 sinusoidal: 10161 harmonic: 8155 Sorted by residual: dihedral pdb=" CB LYS L 242 " pdb=" CG LYS L 242 " pdb=" CD LYS L 242 " pdb=" CE LYS L 242 " ideal model delta sinusoidal sigma weight residual 60.00 118.44 -58.44 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS Q 242 " pdb=" CG LYS Q 242 " pdb=" CD LYS Q 242 " pdb=" CE LYS Q 242 " ideal model delta sinusoidal sigma weight residual 60.00 118.43 -58.43 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS J 242 " pdb=" CG LYS J 242 " pdb=" CD LYS J 242 " pdb=" CE LYS J 242 " ideal model delta sinusoidal sigma weight residual 60.00 118.42 -58.42 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 18313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1879 0.028 - 0.056: 704 0.056 - 0.083: 204 0.083 - 0.111: 98 0.111 - 0.139: 121 Chirality restraints: 3006 Sorted by residual: chirality pdb=" CA ILE L 79 " pdb=" N ILE L 79 " pdb=" C ILE L 79 " pdb=" CB ILE L 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE N 79 " pdb=" N ILE N 79 " pdb=" C ILE N 79 " pdb=" CB ILE N 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA ILE R 79 " pdb=" N ILE R 79 " pdb=" C ILE R 79 " pdb=" CB ILE R 79 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 3003 not shown) Planarity restraints: 5832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 6 " 0.012 2.00e-02 2.50e+03 1.86e-02 5.19e+00 pdb=" CD GLN F 6 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN F 6 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN F 6 " 0.011 2.00e-02 2.50e+03 pdb="HE21 GLN F 6 " 0.000 2.00e-02 2.50e+03 pdb="HE22 GLN F 6 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN H 6 " 0.012 2.00e-02 2.50e+03 1.85e-02 5.16e+00 pdb=" CD GLN H 6 " -0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN H 6 " 0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN H 6 " 0.012 2.00e-02 2.50e+03 pdb="HE21 GLN H 6 " -0.000 2.00e-02 2.50e+03 pdb="HE22 GLN H 6 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 6 " -0.012 2.00e-02 2.50e+03 1.85e-02 5.15e+00 pdb=" CD GLN A 6 " 0.040 2.00e-02 2.50e+03 pdb=" OE1 GLN A 6 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN A 6 " -0.011 2.00e-02 2.50e+03 pdb="HE21 GLN A 6 " 0.000 2.00e-02 2.50e+03 pdb="HE22 GLN A 6 " -0.002 2.00e-02 2.50e+03 ... (remaining 5829 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.42: 18128 2.42 - 2.96: 88480 2.96 - 3.51: 101069 3.51 - 4.05: 139323 4.05 - 4.60: 207706 Nonbonded interactions: 554706 Sorted by model distance: nonbonded pdb=" H GLU K 221 " pdb=" HG2 GLU K 221 " model vdw 1.869 2.270 nonbonded pdb=" H GLU J 221 " pdb=" HG2 GLU J 221 " model vdw 1.870 2.270 nonbonded pdb=" H GLU M 221 " pdb=" HG2 GLU M 221 " model vdw 1.870 2.270 nonbonded pdb=" H GLU R 221 " pdb=" HG2 GLU R 221 " model vdw 1.870 2.270 nonbonded pdb=" H GLU P 221 " pdb=" HG2 GLU P 221 " model vdw 1.871 2.270 ... (remaining 554701 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = (chain 'L' and (resid 1 through 25 or (resid 26 and (name N or name CA or name C \ or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 \ or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name HE \ 2)) or resid 27 through 257)) selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.100 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 33.740 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9009 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 : 0.003 0.045 19584 Z= 0.117 Angle : 0.576 5.284 26550 Z= 0.318 Chirality : 0.042 0.139 3006 Planarity : 0.004 0.028 3492 Dihedral : 15.295 89.892 7263 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.43 % Allowed : 12.50 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.18), residues: 2430 helix: 2.21 (0.20), residues: 729 sheet: 0.50 (0.20), residues: 675 loop : 0.13 (0.20), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 8 TYR 0.006 0.001 TYR N 253 PHE 0.013 0.002 PHE C 12 TRP 0.002 0.000 TRP P 237 HIS 0.001 0.000 HIS L 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (19584) covalent geometry : angle 0.57618 / 0.32 (26550) hydrogen bonds : bond 0.16022 / 10.27 ( 801) hydrogen bonds : angle 6.66186 / 4.61 ( 2295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 314 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: J 230 ASP cc_start: 0.8995 (t0) cc_final: 0.8736 (OUTLIER) REVERT: K 7 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7628 (mppt) REVERT: K 82 GLU cc_start: 0.8883 (tp30) cc_final: 0.8653 (tp30) REVERT: K 149 ASP cc_start: 0.9260 (p0) cc_final: 0.9045 (p0) REVERT: K 256 MET cc_start: 0.9213 (mtp) cc_final: 0.8817 (mtp) REVERT: L 7 LYS cc_start: 0.7922 (mtpt) cc_final: 0.7707 (mppt) REVERT: L 230 ASP cc_start: 0.9010 (t0) cc_final: 0.8760 (t0) REVERT: L 256 MET cc_start: 0.9169 (mtp) cc_final: 0.8775 (mtp) REVERT: M 7 LYS cc_start: 0.7988 (mtpt) cc_final: 0.7666 (mppt) REVERT: N 7 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7684 (mppt) REVERT: N 256 MET cc_start: 0.9218 (mtp) cc_final: 0.8813 (mtp) REVERT: O 7 LYS cc_start: 0.8062 (mtpt) cc_final: 0.7754 (mppt) REVERT: P 7 LYS cc_start: 0.8040 (mtpt) cc_final: 0.7692 (mppt) REVERT: P 256 MET cc_start: 0.9207 (mtp) cc_final: 0.8883 (mtp) REVERT: Q 7 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7768 (mppt) REVERT: Q 256 MET cc_start: 0.9224 (mtp) cc_final: 0.8898 (mtp) REVERT: R 7 LYS cc_start: 0.8011 (mtpt) cc_final: 0.7778 (mppt) REVERT: R 244 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8186 (mt-10) outliers start: 9 outliers final: 1 residues processed: 314 average time/residue: 1.1717 time to fit residues: 423.7844 Evaluate side-chains 244 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [216, 98, 194, 227, 107, 10, 66, 130, 124, 103, 235] chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 6 GLN F 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.061974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.052717 restraints weight = 136363.293| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 2.39 r_work: 0.2516 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2410 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 19584 Z= 0.239 Angle : 0.580 5.429 26550 Z= 0.307 Chirality : 0.044 0.139 3006 Planarity : 0.004 0.027 3492 Dihedral : 5.141 44.205 2682 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.77 % Allowed : 11.54 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.18), residues: 2430 helix: 2.54 (0.20), residues: 756 sheet: 0.51 (0.20), residues: 684 loop : 0.12 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 162 TYR 0.013 0.001 TYR K 253 PHE 0.012 0.001 PHE H 12 TRP 0.002 0.001 TRP J 237 HIS 0.002 0.000 HIS L 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (19584) covalent geometry : angle 0.58031 / 0.31 (26550) hydrogen bonds : bond 0.03865 / 2.50 ( 801) hydrogen bonds : angle 4.56340 / 3.17 ( 2295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 209 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 LYS cc_start: 0.7937 (mtpt) cc_final: 0.7480 (mppt) REVERT: L 7 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7479 (mppt) REVERT: L 256 MET cc_start: 0.8863 (mtp) cc_final: 0.8389 (mtp) REVERT: M 7 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7621 (mppt) REVERT: N 7 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7572 (mppt) REVERT: N 256 MET cc_start: 0.8901 (mtp) cc_final: 0.8502 (mtp) REVERT: O 7 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7474 (mppt) REVERT: P 7 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7532 (mppt) REVERT: Q 7 LYS cc_start: 0.8080 (mtpt) cc_final: 0.7644 (mppt) REVERT: Q 256 MET cc_start: 0.8900 (mtp) cc_final: 0.8488 (mtp) REVERT: R 7 LYS cc_start: 0.7951 (mtpt) cc_final: 0.7487 (mppt) REVERT: R 44 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8881 (mt-10) REVERT: R 210 GLU cc_start: 0.8912 (tt0) cc_final: 0.8655 (tt0) outliers start: 16 outliers final: 4 residues processed: 215 average time/residue: 1.2920 time to fit residues: 315.8598 Evaluate side-chains 192 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 188 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain R residue 185 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [34, 21, 229, 133, 36, 41, 170, 144, 201, 15, 17] chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 11 ASN D 11 ASN E 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.062164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.052852 restraints weight = 134655.987| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 2.38 r_work: 0.2533 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2429 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19584 Z= 0.176 Angle : 0.515 4.729 26550 Z= 0.271 Chirality : 0.042 0.139 3006 Planarity : 0.003 0.031 3492 Dihedral : 4.965 45.929 2682 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.34 % Allowed : 11.78 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.60 (0.18), residues: 2430 helix: 2.73 (0.20), residues: 765 sheet: 0.75 (0.20), residues: 684 loop : -0.00 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 83 TYR 0.012 0.001 TYR K 253 PHE 0.006 0.001 PHE B 5 TRP 0.002 0.000 TRP Q 237 HIS 0.001 0.000 HIS L 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 (19584) covalent geometry : angle 0.51539 / 0.27 (26550) hydrogen bonds : bond 0.03414 / 2.20 ( 801) hydrogen bonds : angle 4.30636 / 2.99 ( 2295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7500 (mppt) REVERT: L 7 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7448 (mppt) REVERT: L 185 GLU cc_start: 0.8927 (tt0) cc_final: 0.8448 (pp20) REVERT: M 7 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7627 (mppt) REVERT: M 44 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8833 (mt-10) REVERT: M 185 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8300 (pp20) REVERT: N 7 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7547 (mppt) REVERT: O 7 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7498 (mppt) REVERT: P 7 LYS cc_start: 0.8022 (mtpt) cc_final: 0.7545 (mppt) REVERT: Q 7 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7615 (mppt) REVERT: R 7 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7499 (mppt) REVERT: R 44 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8866 (mt-10) outliers start: 7 outliers final: 4 residues processed: 201 average time/residue: 1.2877 time to fit residues: 295.1017 Evaluate side-chains 192 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain M residue 185 GLU Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain R residue 185 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [40, 173, 50, 90, 2, 61, 232, 35, 225, 31, 55] chunk 40 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 ASN F 6 GLN G 11 ASN H 11 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.061102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.051817 restraints weight = 135291.350| |-----------------------------------------------------------------------------| r_work (start): 0.2608 rms_B_bonded: 2.36 r_work: 0.2504 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2400 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19584 Z= 0.228 Angle : 0.542 5.131 26550 Z= 0.285 Chirality : 0.043 0.139 3006 Planarity : 0.004 0.030 3492 Dihedral : 5.173 52.378 2682 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.57 % Allowed : 12.45 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.67 (0.18), residues: 2430 helix: 2.79 (0.20), residues: 765 sheet: 0.83 (0.20), residues: 684 loop : -0.02 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 83 TYR 0.012 0.001 TYR K 253 PHE 0.007 0.001 PHE H 5 TRP 0.002 0.001 TRP J 237 HIS 0.001 0.000 HIS R 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (19584) covalent geometry : angle 0.54198 / 0.29 (26550) hydrogen bonds : bond 0.03496 / 2.25 ( 801) hydrogen bonds : angle 4.22550 / 2.94 ( 2295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7472 (mppt) REVERT: L 7 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7458 (mppt) REVERT: L 185 GLU cc_start: 0.8953 (tt0) cc_final: 0.8484 (pp20) REVERT: M 7 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7677 (mppt) REVERT: M 185 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8313 (pp20) REVERT: N 7 LYS cc_start: 0.8027 (mtpt) cc_final: 0.7570 (mppt) REVERT: N 201 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: O 7 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7604 (mppt) REVERT: P 7 LYS cc_start: 0.8024 (mtpt) cc_final: 0.7501 (mppt) REVERT: Q 7 LYS cc_start: 0.8098 (mtpt) cc_final: 0.7606 (mppt) REVERT: R 7 LYS cc_start: 0.7969 (mtpt) cc_final: 0.7508 (mppt) outliers start: 12 outliers final: 5 residues processed: 192 average time/residue: 1.2786 time to fit residues: 280.4917 Evaluate side-chains 185 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain M residue 185 GLU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain R residue 185 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [225, 120, 69, 164, 127, 159, 103, 106, 148, 110, 184] chunk 225 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.2824 r_free = 0.2824 target = 0.061985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.052660 restraints weight = 134354.416| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 2.38 r_work: 0.2527 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2421 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19584 Z= 0.160 Angle : 0.503 4.940 26550 Z= 0.263 Chirality : 0.042 0.139 3006 Planarity : 0.003 0.030 3492 Dihedral : 4.963 49.907 2682 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.53 % Allowed : 12.60 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.83 (0.18), residues: 2430 helix: 2.93 (0.20), residues: 765 sheet: 0.87 (0.20), residues: 684 loop : 0.13 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 83 TYR 0.010 0.001 TYR K 253 PHE 0.005 0.001 PHE B 5 TRP 0.002 0.000 TRP K 237 HIS 0.001 0.000 HIS L 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (19584) covalent geometry : angle 0.50289 / 0.26 (26550) hydrogen bonds : bond 0.03094 / 1.99 ( 801) hydrogen bonds : angle 4.06792 / 2.83 ( 2295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 185 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 213 MET cc_start: 0.9168 (ptt) cc_final: 0.8929 (ptt) REVERT: K 7 LYS cc_start: 0.7984 (mtpt) cc_final: 0.7487 (mppt) REVERT: K 201 GLU cc_start: 0.8908 (pm20) cc_final: 0.8442 (pm20) REVERT: L 7 LYS cc_start: 0.7927 (mtpt) cc_final: 0.7437 (mppt) REVERT: L 185 GLU cc_start: 0.8977 (tt0) cc_final: 0.8537 (pp20) REVERT: M 7 LYS cc_start: 0.8057 (mtpt) cc_final: 0.7661 (mppt) REVERT: M 185 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8346 (pp20) REVERT: N 7 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7545 (mppt) REVERT: N 185 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8468 (pp20) REVERT: O 7 LYS cc_start: 0.7998 (mtpt) cc_final: 0.7512 (mppt) REVERT: O 185 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8431 (pp20) REVERT: P 7 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7498 (mppt) REVERT: P 201 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: Q 7 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7636 (mppt) REVERT: Q 185 GLU cc_start: 0.8923 (tt0) cc_final: 0.8494 (pp20) REVERT: R 7 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7495 (mppt) REVERT: R 44 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8796 (mt-10) outliers start: 11 outliers final: 2 residues processed: 191 average time/residue: 1.3447 time to fit residues: 291.5890 Evaluate side-chains 187 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain M residue 185 GLU Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain O residue 185 GLU Chi-restraints excluded: chain P residue 185 GLU Chi-restraints excluded: chain P residue 201 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [134, 207, 77, 112, 191, 6, 137, 17, 194, 54, 218] chunk 134 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 218 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.2827 r_free = 0.2827 target = 0.062134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.052807 restraints weight = 134339.587| |-----------------------------------------------------------------------------| r_work (start): 0.2622 rms_B_bonded: 2.38 r_work: 0.2517 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19584 Z= 0.143 Angle : 0.494 5.131 26550 Z= 0.258 Chirality : 0.042 0.139 3006 Planarity : 0.003 0.029 3492 Dihedral : 4.833 48.178 2682 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.24 % Allowed : 12.88 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.91 (0.18), residues: 2430 helix: 3.02 (0.20), residues: 765 sheet: 0.87 (0.20), residues: 684 loop : 0.20 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 83 TYR 0.009 0.001 TYR K 253 PHE 0.005 0.001 PHE B 5 TRP 0.002 0.000 TRP Q 237 HIS 0.001 0.000 HIS L 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (19584) covalent geometry : angle 0.49418 / 0.26 (26550) hydrogen bonds : bond 0.02971 / 1.91 ( 801) hydrogen bonds : angle 3.98820 / 2.78 ( 2295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 7 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7474 (mppt) REVERT: K 201 GLU cc_start: 0.8875 (pm20) cc_final: 0.8506 (pm20) REVERT: K 217 MET cc_start: 0.9276 (tpt) cc_final: 0.9023 (tpp) REVERT: L 7 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7427 (mppt) REVERT: L 185 GLU cc_start: 0.8988 (tt0) cc_final: 0.8542 (pp20) REVERT: M 7 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7643 (mppt) REVERT: M 185 GLU cc_start: 0.8894 (tt0) cc_final: 0.8379 (pp20) REVERT: N 7 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7538 (mppt) REVERT: N 185 GLU cc_start: 0.8918 (tt0) cc_final: 0.8491 (pp20) REVERT: N 201 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8371 (pm20) REVERT: O 7 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7522 (mppt) REVERT: O 185 GLU cc_start: 0.8975 (tt0) cc_final: 0.8478 (pp20) REVERT: P 7 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7503 (mppt) REVERT: Q 7 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7622 (mppt) REVERT: R 7 LYS cc_start: 0.7983 (mtpt) cc_final: 0.7498 (mppt) REVERT: R 44 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8818 (mt-10) REVERT: R 185 GLU cc_start: 0.8993 (tt0) cc_final: 0.8517 (pp20) outliers start: 5 outliers final: 2 residues processed: 190 average time/residue: 1.3303 time to fit residues: 286.9159 Evaluate side-chains 181 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain P residue 185 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [113, 128, 100, 194, 24, 8, 87, 219, 76, 134, 187] chunk 113 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 219 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 187 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 ASN F 11 ASN I 11 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.060492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.051198 restraints weight = 135356.299| |-----------------------------------------------------------------------------| r_work (start): 0.2577 rms_B_bonded: 2.35 r_work: 0.2472 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 19584 Z= 0.244 Angle : 0.551 5.489 26550 Z= 0.289 Chirality : 0.043 0.138 3006 Planarity : 0.004 0.030 3492 Dihedral : 5.235 53.664 2682 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.86 % Allowed : 12.31 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 1.78 (0.18), residues: 2430 helix: 2.97 (0.20), residues: 765 sheet: 0.80 (0.20), residues: 684 loop : 0.06 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 83 TYR 0.011 0.001 TYR K 253 PHE 0.008 0.001 PHE C 5 TRP 0.002 0.001 TRP J 237 HIS 0.002 0.000 HIS R 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.24 (19584) covalent geometry : angle 0.55139 / 0.29 (26550) hydrogen bonds : bond 0.03530 / 2.26 ( 801) hydrogen bonds : angle 4.11134 / 2.86 ( 2295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 213 MET cc_start: 0.9180 (ptt) cc_final: 0.8768 (ptt) REVERT: K 7 LYS cc_start: 0.7997 (mtpt) cc_final: 0.7451 (mppt) REVERT: K 185 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8485 (pp20) REVERT: K 201 GLU cc_start: 0.8947 (pm20) cc_final: 0.8539 (pm20) REVERT: L 7 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7406 (mppt) REVERT: L 185 GLU cc_start: 0.8993 (tt0) cc_final: 0.8536 (pp20) REVERT: L 201 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8508 (pm20) REVERT: M 7 LYS cc_start: 0.8052 (mtpt) cc_final: 0.7641 (mppt) REVERT: M 185 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8337 (pp20) REVERT: N 7 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7528 (mppt) REVERT: N 185 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8464 (pp20) REVERT: N 201 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8458 (pm20) REVERT: O 7 LYS cc_start: 0.8131 (mtpt) cc_final: 0.7648 (mppt) REVERT: O 185 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8440 (pp20) REVERT: P 7 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7575 (mppt) REVERT: Q 7 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7607 (mppt) REVERT: Q 185 GLU cc_start: 0.8969 (tt0) cc_final: 0.8515 (pp20) REVERT: R 7 LYS cc_start: 0.8013 (mtpt) cc_final: 0.7547 (mppt) outliers start: 18 outliers final: 3 residues processed: 186 average time/residue: 1.4077 time to fit residues: 295.5566 Evaluate side-chains 185 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain M residue 185 GLU Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain O residue 185 GLU Chi-restraints excluded: chain O residue 244 GLU Chi-restraints excluded: chain P residue 185 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [60, 211, 218, 14, 104, 161, 8, 26, 111, 78, 226] chunk 60 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 218 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 chunk 161 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 226 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.2846 r_free = 0.2846 target = 0.062968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.053631 restraints weight = 132637.803| |-----------------------------------------------------------------------------| r_work (start): 0.2651 rms_B_bonded: 2.37 r_work: 0.2548 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19584 Z= 0.106 Angle : 0.481 5.525 26550 Z= 0.250 Chirality : 0.041 0.137 3006 Planarity : 0.003 0.029 3492 Dihedral : 4.709 45.792 2682 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.57 % Allowed : 12.60 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.07 (0.18), residues: 2430 helix: 3.12 (0.20), residues: 765 sheet: 0.92 (0.21), residues: 594 loop : 0.41 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 83 TYR 0.008 0.001 TYR P 253 PHE 0.005 0.001 PHE D 7 TRP 0.002 0.000 TRP K 237 HIS 0.001 0.000 HIS M 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (19584) covalent geometry : angle 0.48063 / 0.25 (26550) hydrogen bonds : bond 0.02710 / 1.74 ( 801) hydrogen bonds : angle 3.89081 / 2.72 ( 2295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 185 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8426 (pp20) REVERT: K 7 LYS cc_start: 0.7906 (mtpt) cc_final: 0.7411 (mppt) REVERT: K 185 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8532 (pp20) REVERT: K 201 GLU cc_start: 0.8922 (pm20) cc_final: 0.8528 (pm20) REVERT: L 7 LYS cc_start: 0.7868 (mtpt) cc_final: 0.7421 (mppt) REVERT: L 185 GLU cc_start: 0.8974 (tt0) cc_final: 0.8535 (pp20) REVERT: M 7 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7527 (mppt) REVERT: M 185 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8388 (pp20) REVERT: N 7 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7524 (mppt) REVERT: N 185 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8486 (pp20) REVERT: N 201 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8393 (pm20) REVERT: O 7 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7485 (mppt) REVERT: O 185 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8493 (pp20) REVERT: P 7 LYS cc_start: 0.8064 (mtpt) cc_final: 0.7493 (mppt) REVERT: Q 7 LYS cc_start: 0.8082 (mtpt) cc_final: 0.7599 (mppt) REVERT: R 7 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7483 (mppt) REVERT: R 44 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8772 (mt-10) outliers start: 12 outliers final: 0 residues processed: 198 average time/residue: 1.3674 time to fit residues: 307.2303 Evaluate side-chains 184 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 178 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain K residue 185 GLU Chi-restraints excluded: chain M residue 185 GLU Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain O residue 185 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [1, 196, 212, 214, 210, 131, 120, 135, 183, 169, 161] chunk 1 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 214 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 = 0.2817 r_free = 0.2817 target = 0.061703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.052352 restraints weight = 134886.751| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 2.37 r_work: 0.2500 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2397 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19584 Z= 0.174 Angle : 0.516 5.749 26550 Z= 0.268 Chirality : 0.042 0.136 3006 Planarity : 0.003 0.029 3492 Dihedral : 4.905 48.951 2682 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.29 % Allowed : 12.93 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.02 (0.17), residues: 2430 helix: 3.14 (0.20), residues: 765 sheet: 0.91 (0.21), residues: 594 loop : 0.31 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 83 TYR 0.009 0.001 TYR K 253 PHE 0.006 0.001 PHE B 5 TRP 0.002 0.000 TRP J 237 HIS 0.001 0.000 HIS R 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (19584) covalent geometry : angle 0.51582 / 0.27 (26550) hydrogen bonds : bond 0.03103 / 1.99 ( 801) hydrogen bonds : angle 3.97165 / 2.77 ( 2295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 185 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8398 (pp20) REVERT: J 213 MET cc_start: 0.9098 (ptt) cc_final: 0.8818 (ptt) REVERT: K 7 LYS cc_start: 0.7985 (mtpt) cc_final: 0.7494 (mppt) REVERT: K 201 GLU cc_start: 0.8926 (pm20) cc_final: 0.8535 (pm20) REVERT: L 7 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7425 (mppt) REVERT: L 185 GLU cc_start: 0.8998 (tt0) cc_final: 0.8559 (pp20) REVERT: M 7 LYS cc_start: 0.8034 (mtpt) cc_final: 0.7642 (mppt) REVERT: M 185 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8409 (pp20) REVERT: M 201 GLU cc_start: 0.8918 (pm20) cc_final: 0.8417 (pm20) REVERT: N 7 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7556 (mppt) REVERT: N 185 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8489 (pp20) REVERT: N 201 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8421 (pm20) REVERT: O 7 LYS cc_start: 0.8099 (mtpt) cc_final: 0.7642 (mppt) REVERT: O 185 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8500 (pp20) REVERT: P 7 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7599 (mppt) REVERT: Q 7 LYS cc_start: 0.8123 (mtpt) cc_final: 0.7614 (mppt) REVERT: R 7 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7519 (mppt) REVERT: R 44 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8780 (mt-10) outliers start: 6 outliers final: 0 residues processed: 185 average time/residue: 1.3501 time to fit residues: 282.9400 Evaluate side-chains 182 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 185 GLU Chi-restraints excluded: chain M residue 185 GLU Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain O residue 185 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [27, 93, 9, 197, 63, 50, 72, 109, 171, 132, 108] chunk 27 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.2842 r_free = 0.2842 target = 0.062864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.053428 restraints weight = 133614.345| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 2.41 r_work: 0.2550 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19584 Z= 0.112 Angle : 0.485 6.021 26550 Z= 0.251 Chirality : 0.041 0.137 3006 Planarity : 0.003 0.029 3492 Dihedral : 4.651 45.802 2682 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.24 % Allowed : 12.98 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.12 (0.17), residues: 2430 helix: 3.19 (0.19), residues: 765 sheet: 0.95 (0.21), residues: 594 loop : 0.41 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 83 TYR 0.008 0.001 TYR K 253 PHE 0.004 0.001 PHE D 7 TRP 0.002 0.000 TRP K 237 HIS 0.000 0.000 HIS M 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (19584) covalent geometry : angle 0.48483 / 0.25 (26550) hydrogen bonds : bond 0.02725 / 1.75 ( 801) hydrogen bonds : angle 3.88079 / 2.71 ( 2295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 190 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 213 MET cc_start: 0.9067 (ptt) cc_final: 0.8784 (ptt) REVERT: K 7 LYS cc_start: 0.7900 (mtpt) cc_final: 0.7400 (mppt) REVERT: K 201 GLU cc_start: 0.8932 (pm20) cc_final: 0.8542 (pm20) REVERT: L 7 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7373 (mppt) REVERT: L 185 GLU cc_start: 0.8990 (tt0) cc_final: 0.8533 (pp20) REVERT: L 201 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8429 (pm20) REVERT: M 7 LYS cc_start: 0.7945 (mtpt) cc_final: 0.7517 (mppt) REVERT: M 185 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8381 (pp20) REVERT: M 201 GLU cc_start: 0.8882 (pm20) cc_final: 0.8459 (pm20) REVERT: N 7 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7509 (mppt) REVERT: N 185 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8475 (pp20) REVERT: N 201 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: O 7 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7584 (mppt) REVERT: O 185 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8481 (pp20) REVERT: P 7 LYS cc_start: 0.8059 (mtpt) cc_final: 0.7488 (mppt) REVERT: Q 7 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7566 (mppt) REVERT: R 7 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7455 (mppt) REVERT: R 44 GLU cc_start: 0.9118 (mt-10) cc_final: 0.8743 (mt-10) outliers start: 5 outliers final: 0 residues processed: 192 average time/residue: 1.3922 time to fit residues: 302.5068 Evaluate side-chains 189 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 201 GLU Chi-restraints excluded: chain M residue 185 GLU Chi-restraints excluded: chain N residue 185 GLU Chi-restraints excluded: chain N residue 201 GLU Chi-restraints excluded: chain O residue 185 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: [157, 155, 23, 131, 234, 115, 196, 187, 183, 229, 3] chunk 157 optimal weight: 3.9990 chunk 155 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 131 optimal weight: 0.0970 chunk 234 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.2823 r_free = 0.2823 target = 0.061900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.052559 restraints weight = 133873.282| |-----------------------------------------------------------------------------| r_work (start): 0.2624 rms_B_bonded: 2.37 r_work: 0.2520 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 19584 Z= 0.172 Angle : 0.514 5.239 26550 Z= 0.267 Chirality : 0.042 0.136 3006 Planarity : 0.003 0.030 3492 Dihedral : 4.848 48.424 2682 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.34 % Allowed : 12.88 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 2.06 (0.17), residues: 2430 helix: 3.19 (0.19), residues: 765 sheet: 0.91 (0.21), residues: 594 loop : 0.33 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 83 TYR 0.009 0.001 TYR K 253 PHE 0.006 0.001 PHE B 5 TRP 0.002 0.000 TRP M 237 HIS 0.001 0.000 HIS R 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (19584) covalent geometry : angle 0.51377 / 0.27 (26550) hydrogen bonds : bond 0.03068 / 1.97 ( 801) hydrogen bonds : angle 3.94616 / 2.75 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9996.11 seconds wall clock time: 169 minutes 46.50 seconds (10186.50 seconds total)