Starting phenix.real_space_refine on Mon Apr 6 18:12:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihh_52871/04_2026/9ihh_52871.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihh_52871/04_2026/9ihh_52871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ihh_52871/04_2026/9ihh_52871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihh_52871/04_2026/9ihh_52871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ihh_52871/04_2026/9ihh_52871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihh_52871/04_2026/9ihh_52871.map" } resolution = 2.1 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= 0.002 sd= 0.010 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 13166 2.51 5 N 3248 2.21 5 O 4717 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Residue "A GLU 29": not complete - not flipped Residue "B GLU 29": not complete - not flipped Residue "C GLU 29": not complete - not flipped Residue "D GLU 29": not complete - not flipped Residue "E GLU 29": not complete - not flipped Residue "F GLU 29": not complete - not flipped Residue "G GLU 29": not complete - not flipped Residue "H GLU 29": not complete - not flipped Residue "I GLU 29": not complete - not flipped Residue "J GLU 29": not complete - not flipped Residue "K GLU 29": not complete - not flipped Residue "L GLU 29": not complete - not flipped Residue "M GLU 29": not complete - not flipped Residue "N GLU 29": not complete - not flipped Residue "O GLU 29": not complete - not flipped Residue "a GLU 29": not complete - not flipped Residue "b GLU 29": not complete - not flipped Residue "c GLU 29": not complete - not flipped Residue "d GLU 29": not complete - not flipped Residue "e GLU 29": not complete - not flipped Residue "f GLU 29": not complete - not flipped Residue "g GLU 29": not complete - not flipped Residue "h GLU 29": not complete - not flipped Residue "i GLU 29": not complete - not flipped Residue "j GLU 29": not complete - not flipped Residue "k GLU 29": not complete - not flipped Residue "l GLU 29": not complete - not flipped Residue "m GLU 29": not complete - not flipped Residue "n GLU 29": not complete - not flipped Time to flip 174 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21189 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "M" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "O" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "a" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "i" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "l" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "m" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 710 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "H" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "I" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "J" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "K" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "L" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "N" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "O" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "a" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "b" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "c" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "d" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "e" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "f" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "g" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "h" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "i" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "j" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "k" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "l" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "m" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "n" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Time building chain proxies: 4.24, per 1000 atoms: 0.20 Number of scatterers: 21189 At special positions: 0 Unit cell: (90.388, 89.622, 221.374, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 4717 8.00 N 3248 7.00 C 13166 6.00 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=128, symmetry=0 Number of additional bonds: simple=128, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 926.0 milliseconds 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5104 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 0 sheets defined 85.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 66 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN B 93 " --> pdb=" O LYS B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 95 removed outlier: 4.303A pdb=" N ASN C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER C 66 " --> pdb=" O ALA C 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 80 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C 92 " --> pdb=" O ALA C 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN C 93 " --> pdb=" O LYS C 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 80 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 52 removed outlier: 3.544A pdb=" N GLY E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR E 73 " --> pdb=" O GLN E 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 80 " --> pdb=" O LYS E 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 95 removed outlier: 4.305A pdb=" N ASN F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 66 " --> pdb=" O ALA F 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 73 " --> pdb=" O GLN F 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 80 " --> pdb=" O LYS F 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR G 73 " --> pdb=" O GLN G 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 80 " --> pdb=" O LYS G 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE G 92 " --> pdb=" O ALA G 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN G 93 " --> pdb=" O LYS G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER H 66 " --> pdb=" O ALA H 62 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 73 " --> pdb=" O GLN H 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 80 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN H 93 " --> pdb=" O LYS H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR I 73 " --> pdb=" O GLN I 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU I 80 " --> pdb=" O LYS I 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE I 92 " --> pdb=" O ALA I 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN I 93 " --> pdb=" O LYS I 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 73 " --> pdb=" O GLN J 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU J 80 " --> pdb=" O LYS J 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE J 92 " --> pdb=" O ALA J 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN J 93 " --> pdb=" O LYS J 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 52 removed outlier: 3.546A pdb=" N GLY K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 95 removed outlier: 4.305A pdb=" N ASN K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER K 66 " --> pdb=" O ALA K 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR K 73 " --> pdb=" O GLN K 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU K 80 " --> pdb=" O LYS K 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE K 92 " --> pdb=" O ALA K 88 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN K 93 " --> pdb=" O LYS K 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN L 64 " --> pdb=" O LEU L 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU L 65 " --> pdb=" O LEU L 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR L 73 " --> pdb=" O GLN L 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU L 80 " --> pdb=" O LYS L 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN M 64 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU M 65 " --> pdb=" O LEU M 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR M 73 " --> pdb=" O GLN M 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU M 80 " --> pdb=" O LYS M 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE M 92 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN M 93 " --> pdb=" O LYS M 89 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY N 26 " --> pdb=" O LEU N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN N 64 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER N 66 " --> pdb=" O ALA N 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR N 73 " --> pdb=" O GLN N 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU N 80 " --> pdb=" O LYS N 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE N 92 " --> pdb=" O ALA N 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN N 93 " --> pdb=" O LYS N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU O 65 " --> pdb=" O LEU O 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER O 66 " --> pdb=" O ALA O 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR O 73 " --> pdb=" O GLN O 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE O 92 " --> pdb=" O ALA O 88 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN O 93 " --> pdb=" O LYS O 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY a 26 " --> pdb=" O LEU a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN a 64 " --> pdb=" O LEU a 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU a 65 " --> pdb=" O LEU a 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER a 66 " --> pdb=" O ALA a 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR a 73 " --> pdb=" O GLN a 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU a 80 " --> pdb=" O LYS a 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE a 92 " --> pdb=" O ALA a 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN a 93 " --> pdb=" O LYS a 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 52 removed outlier: 3.546A pdb=" N GLY b 26 " --> pdb=" O LEU b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU b 65 " --> pdb=" O LEU b 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER b 66 " --> pdb=" O ALA b 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR b 73 " --> pdb=" O GLN b 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU b 80 " --> pdb=" O LYS b 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE b 92 " --> pdb=" O ALA b 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN b 93 " --> pdb=" O LYS b 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY c 26 " --> pdb=" O LEU c 22 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN c 64 " --> pdb=" O LEU c 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU c 65 " --> pdb=" O LEU c 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER c 66 " --> pdb=" O ALA c 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR c 73 " --> pdb=" O GLN c 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU c 80 " --> pdb=" O LYS c 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE c 92 " --> pdb=" O ALA c 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY d 26 " --> pdb=" O LEU d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN d 64 " --> pdb=" O LEU d 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU d 65 " --> pdb=" O LEU d 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER d 66 " --> pdb=" O ALA d 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR d 73 " --> pdb=" O GLN d 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU d 80 " --> pdb=" O LYS d 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE d 92 " --> pdb=" O ALA d 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN d 93 " --> pdb=" O LYS d 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY e 26 " --> pdb=" O LEU e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN e 64 " --> pdb=" O LEU e 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU e 65 " --> pdb=" O LEU e 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER e 66 " --> pdb=" O ALA e 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR e 73 " --> pdb=" O GLN e 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU e 80 " --> pdb=" O LYS e 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE e 92 " --> pdb=" O ALA e 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN e 93 " --> pdb=" O LYS e 89 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 52 removed outlier: 3.544A pdb=" N GLY f 26 " --> pdb=" O LEU f 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 95 removed outlier: 4.305A pdb=" N ASN f 64 " --> pdb=" O LEU f 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU f 65 " --> pdb=" O LEU f 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER f 66 " --> pdb=" O ALA f 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR f 73 " --> pdb=" O GLN f 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU f 80 " --> pdb=" O LYS f 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE f 92 " --> pdb=" O ALA f 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN f 93 " --> pdb=" O LYS f 89 " (cutoff:3.500A) Processing helix chain 'g' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY g 26 " --> pdb=" O LEU g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN g 64 " --> pdb=" O LEU g 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU g 65 " --> pdb=" O LEU g 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER g 66 " --> pdb=" O ALA g 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR g 73 " --> pdb=" O GLN g 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU g 80 " --> pdb=" O LYS g 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE g 92 " --> pdb=" O ALA g 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN g 93 " --> pdb=" O LYS g 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY h 26 " --> pdb=" O LEU h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN h 64 " --> pdb=" O LEU h 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU h 65 " --> pdb=" O LEU h 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER h 66 " --> pdb=" O ALA h 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR h 73 " --> pdb=" O GLN h 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU h 80 " --> pdb=" O LYS h 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE h 92 " --> pdb=" O ALA h 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN h 93 " --> pdb=" O LYS h 89 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 52 removed outlier: 3.546A pdb=" N GLY i 26 " --> pdb=" O LEU i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN i 64 " --> pdb=" O LEU i 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU i 65 " --> pdb=" O LEU i 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER i 66 " --> pdb=" O ALA i 62 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR i 73 " --> pdb=" O GLN i 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU i 80 " --> pdb=" O LYS i 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE i 92 " --> pdb=" O ALA i 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN i 93 " --> pdb=" O LYS i 89 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 52 removed outlier: 3.544A pdb=" N GLY j 26 " --> pdb=" O LEU j 22 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN j 64 " --> pdb=" O LEU j 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU j 65 " --> pdb=" O LEU j 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR j 73 " --> pdb=" O GLN j 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU j 80 " --> pdb=" O LYS j 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE j 92 " --> pdb=" O ALA j 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN j 93 " --> pdb=" O LYS j 89 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY k 26 " --> pdb=" O LEU k 22 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN k 64 " --> pdb=" O LEU k 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU k 65 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER k 66 " --> pdb=" O ALA k 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR k 73 " --> pdb=" O GLN k 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU k 80 " --> pdb=" O LYS k 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE k 92 " --> pdb=" O ALA k 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN k 93 " --> pdb=" O LYS k 89 " (cutoff:3.500A) Processing helix chain 'l' and resid 13 through 52 removed outlier: 3.546A pdb=" N GLY l 26 " --> pdb=" O LEU l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN l 64 " --> pdb=" O LEU l 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU l 65 " --> pdb=" O LEU l 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER l 66 " --> pdb=" O ALA l 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR l 73 " --> pdb=" O GLN l 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU l 80 " --> pdb=" O LYS l 76 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE l 92 " --> pdb=" O ALA l 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN l 93 " --> pdb=" O LYS l 89 " (cutoff:3.500A) Processing helix chain 'm' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY m 26 " --> pdb=" O LEU m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 95 removed outlier: 4.304A pdb=" N ASN m 64 " --> pdb=" O LEU m 60 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU m 65 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR m 73 " --> pdb=" O GLN m 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU m 80 " --> pdb=" O LYS m 76 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE m 92 " --> pdb=" O ALA m 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN m 93 " --> pdb=" O LYS m 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 52 removed outlier: 3.545A pdb=" N GLY n 26 " --> pdb=" O LEU n 22 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 95 removed outlier: 4.303A pdb=" N ASN n 64 " --> pdb=" O LEU n 60 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU n 65 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER n 66 " --> pdb=" O ALA n 62 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU n 80 " --> pdb=" O LYS n 76 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE n 92 " --> pdb=" O ALA n 88 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN n 93 " --> pdb=" O LYS n 89 " (cutoff:3.500A) 1856 hydrogen bonds defined for protein. 5568 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: 3.18 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6644 1.34 - 1.45: 1301 1.45 - 1.57: 12674 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 20735 Sorted by residual: bond pdb=" C MET k 3 " pdb=" O MET k 3 " ideal model delta sigma weight residual 1.235 1.218 0.017 1.35e-02 5.49e+03 1.53e+00 bond pdb=" C MET E 3 " pdb=" O MET E 3 " ideal model delta sigma weight residual 1.235 1.219 0.016 1.35e-02 5.49e+03 1.36e+00 bond pdb=" C MET B 3 " pdb=" O MET B 3 " ideal model delta sigma weight residual 1.235 1.220 0.016 1.35e-02 5.49e+03 1.34e+00 bond pdb=" C MET F 3 " pdb=" O MET F 3 " ideal model delta sigma weight residual 1.235 1.220 0.015 1.35e-02 5.49e+03 1.31e+00 bond pdb=" C MET g 3 " pdb=" O MET g 3 " ideal model delta sigma weight residual 1.235 1.220 0.015 1.35e-02 5.49e+03 1.30e+00 ... (remaining 20730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 26535 0.93 - 1.85: 990 1.85 - 2.78: 140 2.78 - 3.70: 117 3.70 - 4.63: 116 Bond angle restraints: 27898 Sorted by residual: angle pdb=" C MET B 3 " pdb=" N PRO B 4 " pdb=" CA PRO B 4 " ideal model delta sigma weight residual 119.85 122.62 -2.77 1.01e+00 9.80e-01 7.55e+00 angle pdb=" CB GLN m 93 " pdb=" CG GLN m 93 " pdb=" CD GLN m 93 " ideal model delta sigma weight residual 112.60 117.02 -4.42 1.70e+00 3.46e-01 6.77e+00 angle pdb=" CB GLN D 93 " pdb=" CG GLN D 93 " pdb=" CD GLN D 93 " ideal model delta sigma weight residual 112.60 117.01 -4.41 1.70e+00 3.46e-01 6.74e+00 angle pdb=" CB GLN N 93 " pdb=" CG GLN N 93 " pdb=" CD GLN N 93 " ideal model delta sigma weight residual 112.60 117.01 -4.41 1.70e+00 3.46e-01 6.73e+00 angle pdb=" CB GLN f 93 " pdb=" CG GLN f 93 " pdb=" CD GLN f 93 " ideal model delta sigma weight residual 112.60 117.01 -4.41 1.70e+00 3.46e-01 6.73e+00 ... (remaining 27893 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 12497 34.70 - 69.40: 379 69.40 - 104.09: 58 104.09 - 138.79: 0 138.79 - 173.49: 29 Dihedral angle restraints: 12963 sinusoidal: 5162 harmonic: 7801 Sorted by residual: dihedral pdb=" CB GLU K 29 " pdb=" CG GLU K 29 " pdb=" CD GLU K 29 " pdb=" OE1 GLU K 29 " ideal model delta sinusoidal sigma weight residual 0.00 -173.49 173.49 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB GLU k 29 " pdb=" CG GLU k 29 " pdb=" CD GLU k 29 " pdb=" OE1 GLU k 29 " ideal model delta sinusoidal sigma weight residual 0.00 -173.48 173.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" CB GLU n 29 " pdb=" CG GLU n 29 " pdb=" CD GLU n 29 " pdb=" OE1 GLU n 29 " ideal model delta sinusoidal sigma weight residual 0.00 -173.48 173.48 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 2586 0.025 - 0.051: 484 0.051 - 0.076: 439 0.076 - 0.102: 50 0.102 - 0.127: 37 Chirality restraints: 3596 Sorted by residual: chirality pdb=" CA ILE g 6 " pdb=" N ILE g 6 " pdb=" C ILE g 6 " pdb=" CB ILE g 6 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE i 6 " pdb=" N ILE i 6 " pdb=" C ILE i 6 " pdb=" CB ILE i 6 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE K 6 " pdb=" N ILE K 6 " pdb=" C ILE K 6 " pdb=" CB ILE K 6 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 3593 not shown) Planarity restraints: 3422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 2 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C GLY B 2 " 0.025 2.00e-02 2.50e+03 pdb=" O GLY B 2 " -0.009 2.00e-02 2.50e+03 pdb=" N MET B 3 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 2 " -0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C GLY O 2 " 0.023 2.00e-02 2.50e+03 pdb=" O GLY O 2 " -0.009 2.00e-02 2.50e+03 pdb=" N MET O 3 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 2 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C GLY C 2 " 0.022 2.00e-02 2.50e+03 pdb=" O GLY C 2 " -0.008 2.00e-02 2.50e+03 pdb=" N MET C 3 " -0.007 2.00e-02 2.50e+03 ... (remaining 3419 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4202 2.78 - 3.31: 22496 3.31 - 3.84: 32665 3.84 - 4.37: 42454 4.37 - 4.90: 67999 Nonbonded interactions: 169816 Sorted by model distance: nonbonded pdb=" O SER k 95 " pdb=" OG SER k 95 " model vdw 2.249 3.040 nonbonded pdb=" O SER j 95 " pdb=" OG SER j 95 " model vdw 2.249 3.040 nonbonded pdb=" O SER I 95 " pdb=" OG SER I 95 " model vdw 2.249 3.040 nonbonded pdb=" O SER K 95 " pdb=" OG SER K 95 " model vdw 2.249 3.040 nonbonded pdb=" O SER b 95 " pdb=" OG SER b 95 " model vdw 2.249 3.040 ... (remaining 169811 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: 0.06 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' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = 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' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } 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: 1.730 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: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 18.290 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.178 20863 Z= 0.644 Angle : 0.515 4.626 27898 Z= 0.292 Chirality : 0.033 0.127 3596 Planarity : 0.002 0.017 3422 Dihedral : 19.604 173.490 7859 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.13 % Allowed : 15.22 % Favored : 84.66 % 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: 3.61 (0.14), residues: 2668 helix: 2.51 (0.09), residues: 2320 sheet: None (None), residues: 0 loop : 1.66 (0.39), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG g 14 PHE 0.002 0.000 PHE M 50 HIS 0.001 0.000 HIS k 34 Details of bonding type rmsd covalent geometry : bond 0.00276 (20735) covalent geometry : angle 0.51528 (27898) hydrogen bonds : bond 0.29812 ( 1856) hydrogen bonds : angle 5.98624 ( 5568) Misc. bond : bond 0.08071 ( 128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 348 time to evaluate : 0.894 Fit side-chains REVERT: B 11 ASP cc_start: 0.9147 (m-30) cc_final: 0.8601 (p0) REVERT: C 11 ASP cc_start: 0.9153 (m-30) cc_final: 0.8605 (p0) REVERT: D 11 ASP cc_start: 0.9164 (m-30) cc_final: 0.8773 (p0) REVERT: E 11 ASP cc_start: 0.9151 (m-30) cc_final: 0.8722 (p0) REVERT: F 11 ASP cc_start: 0.9138 (m-30) cc_final: 0.8680 (p0) REVERT: G 11 ASP cc_start: 0.9127 (m-30) cc_final: 0.8701 (p0) REVERT: H 11 ASP cc_start: 0.9115 (m-30) cc_final: 0.8670 (p0) REVERT: I 11 ASP cc_start: 0.9132 (m-30) cc_final: 0.8688 (p0) REVERT: J 11 ASP cc_start: 0.9114 (m-30) cc_final: 0.8736 (p0) REVERT: K 11 ASP cc_start: 0.9104 (m-30) cc_final: 0.8584 (p0) REVERT: L 11 ASP cc_start: 0.9107 (m-30) cc_final: 0.8601 (p0) REVERT: M 11 ASP cc_start: 0.9123 (m-30) cc_final: 0.8763 (p0) REVERT: N 11 ASP cc_start: 0.9095 (m-30) cc_final: 0.8654 (p0) REVERT: O 11 ASP cc_start: 0.9105 (m-30) cc_final: 0.8679 (p0) REVERT: a 11 ASP cc_start: 0.9134 (m-30) cc_final: 0.8697 (p0) REVERT: b 11 ASP cc_start: 0.9101 (m-30) cc_final: 0.8746 (p0) REVERT: c 11 ASP cc_start: 0.9118 (m-30) cc_final: 0.8672 (p0) REVERT: d 11 ASP cc_start: 0.9124 (m-30) cc_final: 0.8680 (p0) REVERT: e 11 ASP cc_start: 0.9140 (m-30) cc_final: 0.8755 (p0) REVERT: f 11 ASP cc_start: 0.9145 (m-30) cc_final: 0.8635 (p0) REVERT: g 11 ASP cc_start: 0.9107 (m-30) cc_final: 0.8712 (p0) REVERT: h 11 ASP cc_start: 0.9122 (m-30) cc_final: 0.8687 (p0) REVERT: i 11 ASP cc_start: 0.9093 (m-30) cc_final: 0.8677 (p0) REVERT: j 11 ASP cc_start: 0.9105 (m-30) cc_final: 0.8631 (p0) REVERT: k 11 ASP cc_start: 0.9098 (m-30) cc_final: 0.8761 (p0) REVERT: l 11 ASP cc_start: 0.9145 (m-30) cc_final: 0.8718 (p0) REVERT: m 11 ASP cc_start: 0.9124 (m-30) cc_final: 0.8608 (p0) REVERT: n 11 ASP cc_start: 0.9126 (m-30) cc_final: 0.8696 (p0) outliers start: 3 outliers final: 0 residues processed: 349 average time/residue: 1.0331 time to fit residues: 389.2972 Evaluate side-chains 272 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 258 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 93 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN E 93 GLN F 93 GLN G 93 GLN ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 GLN b 93 GLN c 93 GLN ** d 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 93 GLN f 93 GLN ** g 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 93 GLN i 93 GLN ** j 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 93 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.050638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.039137 restraints weight = 62917.858| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.39 r_work: 0.2666 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 20863 Z= 0.240 Angle : 0.518 5.213 27898 Z= 0.297 Chirality : 0.036 0.119 3596 Planarity : 0.003 0.020 3422 Dihedral : 2.643 9.101 2726 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 0.99 % Allowed : 15.43 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 6.03 (0.14), residues: 2668 helix: 4.28 (0.09), residues: 2320 sheet: None (None), residues: 0 loop : 1.22 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG i 14 PHE 0.009 0.002 PHE N 57 HIS 0.002 0.001 HIS d 34 Details of bonding type rmsd covalent geometry : bond 0.00463 (20735) covalent geometry : angle 0.51773 (27898) hydrogen bonds : bond 0.13210 ( 1856) hydrogen bonds : angle 4.68897 ( 5568) Misc. bond : bond 0.00123 ( 128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 389 time to evaluate : 0.827 Fit side-chains REVERT: B 11 ASP cc_start: 0.9103 (m-30) cc_final: 0.8625 (p0) REVERT: C 11 ASP cc_start: 0.9197 (m-30) cc_final: 0.8643 (p0) REVERT: D 11 ASP cc_start: 0.9146 (m-30) cc_final: 0.8751 (p0) REVERT: E 11 ASP cc_start: 0.9112 (m-30) cc_final: 0.8717 (p0) REVERT: F 11 ASP cc_start: 0.9122 (m-30) cc_final: 0.8708 (p0) REVERT: G 11 ASP cc_start: 0.9130 (m-30) cc_final: 0.8730 (p0) REVERT: H 11 ASP cc_start: 0.9187 (m-30) cc_final: 0.8766 (p0) REVERT: I 11 ASP cc_start: 0.9184 (m-30) cc_final: 0.8807 (p0) REVERT: J 11 ASP cc_start: 0.8990 (m-30) cc_final: 0.8679 (p0) REVERT: K 11 ASP cc_start: 0.9063 (m-30) cc_final: 0.8660 (p0) REVERT: L 11 ASP cc_start: 0.9124 (m-30) cc_final: 0.8680 (p0) REVERT: M 11 ASP cc_start: 0.9143 (m-30) cc_final: 0.8759 (p0) REVERT: N 11 ASP cc_start: 0.9123 (m-30) cc_final: 0.8772 (p0) REVERT: O 11 ASP cc_start: 0.9174 (m-30) cc_final: 0.8708 (p0) REVERT: a 11 ASP cc_start: 0.9209 (m-30) cc_final: 0.8736 (p0) REVERT: b 11 ASP cc_start: 0.9173 (m-30) cc_final: 0.8695 (p0) REVERT: c 11 ASP cc_start: 0.9083 (m-30) cc_final: 0.8629 (p0) REVERT: d 11 ASP cc_start: 0.9137 (m-30) cc_final: 0.8708 (p0) REVERT: e 11 ASP cc_start: 0.9110 (m-30) cc_final: 0.8735 (p0) REVERT: f 8 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8686 (mp0) REVERT: f 11 ASP cc_start: 0.9080 (m-30) cc_final: 0.8676 (p0) REVERT: g 11 ASP cc_start: 0.9125 (m-30) cc_final: 0.8780 (p0) REVERT: h 11 ASP cc_start: 0.9078 (m-30) cc_final: 0.8676 (p0) REVERT: i 11 ASP cc_start: 0.9153 (m-30) cc_final: 0.8735 (p0) REVERT: j 11 ASP cc_start: 0.9012 (m-30) cc_final: 0.8616 (p0) REVERT: k 11 ASP cc_start: 0.9025 (m-30) cc_final: 0.8709 (p0) REVERT: l 11 ASP cc_start: 0.9069 (m-30) cc_final: 0.8692 (p0) REVERT: m 11 ASP cc_start: 0.9143 (m-30) cc_final: 0.8826 (p0) REVERT: n 11 ASP cc_start: 0.9158 (m-30) cc_final: 0.8685 (p0) outliers start: 23 outliers final: 1 residues processed: 391 average time/residue: 0.9918 time to fit residues: 419.7725 Evaluate side-chains 300 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 298 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 MET Chi-restraints excluded: chain f residue 8 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 156 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 90 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 208 optimal weight: 4.9990 chunk 172 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 145 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN D 93 GLN F 93 GLN ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.050590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.038852 restraints weight = 63315.130| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.45 r_work: 0.2656 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2526 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9189 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 20863 Z= 0.247 Angle : 0.526 5.950 27898 Z= 0.298 Chirality : 0.036 0.121 3596 Planarity : 0.003 0.022 3422 Dihedral : 2.559 7.155 2726 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.91 % Allowed : 13.45 % Favored : 85.65 % 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: 6.08 (0.14), residues: 2668 helix: 4.34 (0.09), residues: 2320 sheet: None (None), residues: 0 loop : 1.04 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG i 14 PHE 0.009 0.001 PHE N 57 HIS 0.001 0.000 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00499 (20735) covalent geometry : angle 0.52581 (27898) hydrogen bonds : bond 0.13168 ( 1856) hydrogen bonds : angle 4.69366 ( 5568) Misc. bond : bond 0.00134 ( 128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 306 time to evaluate : 0.788 Fit side-chains REVERT: B 11 ASP cc_start: 0.9121 (m-30) cc_final: 0.8664 (p0) REVERT: C 11 ASP cc_start: 0.9165 (m-30) cc_final: 0.8668 (p0) REVERT: D 11 ASP cc_start: 0.9173 (m-30) cc_final: 0.8763 (p0) REVERT: E 11 ASP cc_start: 0.9208 (m-30) cc_final: 0.8753 (p0) REVERT: F 11 ASP cc_start: 0.9225 (m-30) cc_final: 0.8727 (p0) REVERT: G 11 ASP cc_start: 0.9192 (m-30) cc_final: 0.8761 (p0) REVERT: H 11 ASP cc_start: 0.9214 (m-30) cc_final: 0.8754 (p0) REVERT: I 11 ASP cc_start: 0.9244 (m-30) cc_final: 0.8833 (p0) REVERT: J 11 ASP cc_start: 0.9048 (m-30) cc_final: 0.8727 (p0) REVERT: K 11 ASP cc_start: 0.9118 (m-30) cc_final: 0.8731 (p0) REVERT: L 11 ASP cc_start: 0.9193 (m-30) cc_final: 0.8715 (p0) REVERT: M 11 ASP cc_start: 0.9158 (m-30) cc_final: 0.8758 (p0) REVERT: N 11 ASP cc_start: 0.9152 (m-30) cc_final: 0.8800 (p0) REVERT: O 11 ASP cc_start: 0.9244 (m-30) cc_final: 0.8732 (p0) REVERT: a 11 ASP cc_start: 0.9222 (m-30) cc_final: 0.8701 (p0) REVERT: b 11 ASP cc_start: 0.9216 (m-30) cc_final: 0.8790 (p0) REVERT: c 11 ASP cc_start: 0.9140 (m-30) cc_final: 0.8606 (p0) REVERT: d 11 ASP cc_start: 0.9150 (m-30) cc_final: 0.8710 (p0) REVERT: e 11 ASP cc_start: 0.9151 (m-30) cc_final: 0.8732 (p0) REVERT: f 8 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8690 (mp0) REVERT: f 11 ASP cc_start: 0.9165 (m-30) cc_final: 0.8729 (p0) REVERT: g 11 ASP cc_start: 0.9142 (m-30) cc_final: 0.8771 (p0) REVERT: h 11 ASP cc_start: 0.9146 (m-30) cc_final: 0.8699 (p0) REVERT: h 52 LYS cc_start: 0.8274 (ttpp) cc_final: 0.8072 (ttpp) REVERT: h 93 GLN cc_start: 0.8394 (mm-40) cc_final: 0.7557 (mp10) REVERT: i 11 ASP cc_start: 0.9181 (m-30) cc_final: 0.8795 (p0) REVERT: j 11 ASP cc_start: 0.9080 (m-30) cc_final: 0.8613 (p0) REVERT: k 11 ASP cc_start: 0.9072 (m-30) cc_final: 0.8728 (p0) REVERT: l 11 ASP cc_start: 0.9182 (m-30) cc_final: 0.8767 (p0) REVERT: m 11 ASP cc_start: 0.9138 (m-30) cc_final: 0.8824 (p0) REVERT: n 11 ASP cc_start: 0.9220 (m-30) cc_final: 0.8703 (p0) outliers start: 21 outliers final: 6 residues processed: 325 average time/residue: 0.9699 time to fit residues: 342.0326 Evaluate side-chains 295 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 289 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 94 SER Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain e residue 94 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 194 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 223 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN D 93 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.051604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.039822 restraints weight = 63271.071| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.46 r_work: 0.2713 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9158 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 20863 Z= 0.224 Angle : 0.505 4.138 27898 Z= 0.286 Chirality : 0.035 0.119 3596 Planarity : 0.003 0.022 3422 Dihedral : 2.545 6.506 2726 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 1.08 % Allowed : 13.41 % Favored : 85.52 % 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: 6.22 (0.14), residues: 2668 helix: 4.46 (0.09), residues: 2320 sheet: None (None), residues: 0 loop : 0.84 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG i 14 PHE 0.008 0.001 PHE N 57 HIS 0.001 0.000 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00428 (20735) covalent geometry : angle 0.50520 (27898) hydrogen bonds : bond 0.11920 ( 1856) hydrogen bonds : angle 4.50722 ( 5568) Misc. bond : bond 0.00117 ( 128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 299 time to evaluate : 0.967 Fit side-chains REVERT: B 11 ASP cc_start: 0.9090 (m-30) cc_final: 0.8666 (p0) REVERT: C 11 ASP cc_start: 0.9147 (m-30) cc_final: 0.8630 (p0) REVERT: D 11 ASP cc_start: 0.9159 (m-30) cc_final: 0.8740 (p0) REVERT: E 11 ASP cc_start: 0.9232 (m-30) cc_final: 0.8751 (p0) REVERT: F 11 ASP cc_start: 0.9222 (m-30) cc_final: 0.8729 (p0) REVERT: G 11 ASP cc_start: 0.9143 (m-30) cc_final: 0.8748 (p0) REVERT: H 11 ASP cc_start: 0.9211 (m-30) cc_final: 0.8753 (p0) REVERT: I 11 ASP cc_start: 0.9207 (m-30) cc_final: 0.8811 (p0) REVERT: J 11 ASP cc_start: 0.9116 (m-30) cc_final: 0.8767 (p0) REVERT: K 11 ASP cc_start: 0.9123 (m-30) cc_final: 0.8773 (p0) REVERT: L 11 ASP cc_start: 0.9183 (m-30) cc_final: 0.8718 (p0) REVERT: M 11 ASP cc_start: 0.9159 (m-30) cc_final: 0.8763 (p0) REVERT: N 11 ASP cc_start: 0.9123 (m-30) cc_final: 0.8785 (p0) REVERT: O 11 ASP cc_start: 0.9242 (m-30) cc_final: 0.8756 (p0) REVERT: a 11 ASP cc_start: 0.9242 (m-30) cc_final: 0.8835 (p0) REVERT: b 11 ASP cc_start: 0.9210 (m-30) cc_final: 0.8759 (p0) REVERT: c 11 ASP cc_start: 0.9181 (m-30) cc_final: 0.8737 (p0) REVERT: d 11 ASP cc_start: 0.9141 (m-30) cc_final: 0.8698 (p0) REVERT: e 11 ASP cc_start: 0.9210 (m-30) cc_final: 0.8748 (p0) REVERT: f 11 ASP cc_start: 0.9172 (m-30) cc_final: 0.8726 (p0) REVERT: g 11 ASP cc_start: 0.9128 (m-30) cc_final: 0.8776 (p0) REVERT: h 11 ASP cc_start: 0.9162 (m-30) cc_final: 0.8725 (p0) REVERT: i 11 ASP cc_start: 0.9184 (m-30) cc_final: 0.8816 (p0) REVERT: j 11 ASP cc_start: 0.9101 (m-30) cc_final: 0.8614 (p0) REVERT: k 11 ASP cc_start: 0.9018 (m-30) cc_final: 0.8709 (p0) REVERT: l 11 ASP cc_start: 0.9154 (m-30) cc_final: 0.8756 (p0) REVERT: m 11 ASP cc_start: 0.9140 (m-30) cc_final: 0.8831 (p0) REVERT: n 11 ASP cc_start: 0.9200 (m-30) cc_final: 0.8666 (p0) outliers start: 25 outliers final: 13 residues processed: 322 average time/residue: 0.9654 time to fit residues: 337.5269 Evaluate side-chains 300 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 287 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain F residue 3 MET Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 94 SER Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain e residue 51 GLU Chi-restraints excluded: chain e residue 94 SER Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain j residue 51 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 19 optimal weight: 8.9990 chunk 240 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 190 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.048829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.037268 restraints weight = 63755.594| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.47 r_work: 0.2614 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9242 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 20863 Z= 0.272 Angle : 0.570 6.924 27898 Z= 0.320 Chirality : 0.037 0.124 3596 Planarity : 0.003 0.022 3422 Dihedral : 2.501 6.661 2726 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 2.24 % Allowed : 14.22 % Favored : 83.53 % 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: 5.94 (0.14), residues: 2668 helix: 4.29 (0.08), residues: 2320 sheet: None (None), residues: 0 loop : 0.67 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG i 14 PHE 0.009 0.002 PHE N 57 HIS 0.001 0.000 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00591 (20735) covalent geometry : angle 0.57010 (27898) hydrogen bonds : bond 0.13759 ( 1856) hydrogen bonds : angle 4.74459 ( 5568) Misc. bond : bond 0.00149 ( 128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 0.801 Fit side-chains REVERT: A 11 ASP cc_start: 0.9120 (m-30) cc_final: 0.8586 (p0) REVERT: B 11 ASP cc_start: 0.9087 (m-30) cc_final: 0.8703 (p0) REVERT: C 11 ASP cc_start: 0.9149 (m-30) cc_final: 0.8664 (p0) REVERT: D 11 ASP cc_start: 0.9133 (m-30) cc_final: 0.8767 (p0) REVERT: E 11 ASP cc_start: 0.9228 (m-30) cc_final: 0.8755 (p0) REVERT: F 11 ASP cc_start: 0.9227 (m-30) cc_final: 0.8746 (p0) REVERT: G 11 ASP cc_start: 0.9126 (m-30) cc_final: 0.8773 (p0) REVERT: H 11 ASP cc_start: 0.9189 (m-30) cc_final: 0.8835 (p0) REVERT: I 11 ASP cc_start: 0.9234 (m-30) cc_final: 0.8849 (p0) REVERT: J 11 ASP cc_start: 0.9141 (m-30) cc_final: 0.8807 (p0) REVERT: K 11 ASP cc_start: 0.9081 (m-30) cc_final: 0.8774 (p0) REVERT: L 11 ASP cc_start: 0.9121 (m-30) cc_final: 0.8725 (p0) REVERT: M 11 ASP cc_start: 0.9179 (m-30) cc_final: 0.8804 (p0) REVERT: N 11 ASP cc_start: 0.9115 (m-30) cc_final: 0.8820 (p0) REVERT: O 11 ASP cc_start: 0.9215 (m-30) cc_final: 0.8775 (p0) REVERT: a 11 ASP cc_start: 0.9182 (m-30) cc_final: 0.8709 (p0) REVERT: b 11 ASP cc_start: 0.9158 (m-30) cc_final: 0.8740 (p0) REVERT: b 15 ASP cc_start: 0.8562 (m-30) cc_final: 0.8318 (m-30) REVERT: c 11 ASP cc_start: 0.9169 (m-30) cc_final: 0.8653 (p0) REVERT: c 51 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8309 (mt-10) REVERT: d 11 ASP cc_start: 0.9156 (m-30) cc_final: 0.8694 (p0) REVERT: e 11 ASP cc_start: 0.9236 (m-30) cc_final: 0.8800 (p0) REVERT: f 11 ASP cc_start: 0.9207 (m-30) cc_final: 0.8758 (p0) REVERT: g 11 ASP cc_start: 0.9050 (m-30) cc_final: 0.8751 (p0) REVERT: h 11 ASP cc_start: 0.9189 (m-30) cc_final: 0.8758 (p0) REVERT: i 11 ASP cc_start: 0.9189 (m-30) cc_final: 0.8864 (p0) REVERT: j 11 ASP cc_start: 0.9127 (m-30) cc_final: 0.8658 (p0) REVERT: k 11 ASP cc_start: 0.9067 (m-30) cc_final: 0.8744 (p0) REVERT: l 11 ASP cc_start: 0.9165 (m-30) cc_final: 0.8770 (p0) REVERT: m 11 ASP cc_start: 0.9165 (m-30) cc_final: 0.8891 (p0) REVERT: n 11 ASP cc_start: 0.9183 (m-30) cc_final: 0.8677 (p0) outliers start: 52 outliers final: 20 residues processed: 324 average time/residue: 0.9312 time to fit residues: 328.5354 Evaluate side-chains 308 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 287 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 51 GLU Chi-restraints excluded: chain c residue 94 SER Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain e residue 94 SER Chi-restraints excluded: chain f residue 51 GLU Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain m residue 53 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 48 optimal weight: 9.9990 chunk 108 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.051463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.039764 restraints weight = 62995.288| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.45 r_work: 0.2700 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 20863 Z= 0.228 Angle : 0.536 4.949 27898 Z= 0.301 Chirality : 0.035 0.121 3596 Planarity : 0.003 0.022 3422 Dihedral : 2.528 6.517 2726 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.04 % Favored : 99.96 % Rotamer: Outliers : 1.25 % Allowed : 16.03 % Favored : 82.72 % 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: 6.19 (0.14), residues: 2668 helix: 4.48 (0.08), residues: 2320 sheet: None (None), residues: 0 loop : 0.50 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 14 PHE 0.008 0.001 PHE N 57 HIS 0.001 0.000 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00442 (20735) covalent geometry : angle 0.53551 (27898) hydrogen bonds : bond 0.11924 ( 1856) hydrogen bonds : angle 4.47424 ( 5568) Misc. bond : bond 0.00116 ( 128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 0.867 Fit side-chains REVERT: A 11 ASP cc_start: 0.9168 (m-30) cc_final: 0.8614 (p0) REVERT: B 11 ASP cc_start: 0.9128 (m-30) cc_final: 0.8713 (p0) REVERT: C 11 ASP cc_start: 0.9183 (m-30) cc_final: 0.8690 (p0) REVERT: D 11 ASP cc_start: 0.9183 (m-30) cc_final: 0.8784 (p0) REVERT: E 11 ASP cc_start: 0.9250 (m-30) cc_final: 0.8763 (p0) REVERT: F 11 ASP cc_start: 0.9231 (m-30) cc_final: 0.8762 (p0) REVERT: G 11 ASP cc_start: 0.9142 (m-30) cc_final: 0.8783 (p0) REVERT: H 11 ASP cc_start: 0.9212 (m-30) cc_final: 0.8846 (p0) REVERT: I 11 ASP cc_start: 0.9261 (m-30) cc_final: 0.8851 (p0) REVERT: J 11 ASP cc_start: 0.9163 (m-30) cc_final: 0.8824 (p0) REVERT: K 11 ASP cc_start: 0.9101 (m-30) cc_final: 0.8814 (p0) REVERT: L 11 ASP cc_start: 0.9151 (m-30) cc_final: 0.8733 (p0) REVERT: M 11 ASP cc_start: 0.9212 (m-30) cc_final: 0.8816 (p0) REVERT: N 11 ASP cc_start: 0.9123 (m-30) cc_final: 0.8817 (p0) REVERT: O 11 ASP cc_start: 0.9253 (m-30) cc_final: 0.8801 (p0) REVERT: a 11 ASP cc_start: 0.9278 (m-30) cc_final: 0.8781 (p0) REVERT: b 11 ASP cc_start: 0.9186 (m-30) cc_final: 0.8744 (p0) REVERT: c 11 ASP cc_start: 0.9219 (m-30) cc_final: 0.8667 (p0) REVERT: d 11 ASP cc_start: 0.9182 (m-30) cc_final: 0.8718 (p0) REVERT: e 11 ASP cc_start: 0.9237 (m-30) cc_final: 0.8799 (p0) REVERT: f 11 ASP cc_start: 0.9262 (m-30) cc_final: 0.8799 (p0) REVERT: g 11 ASP cc_start: 0.9108 (m-30) cc_final: 0.8778 (p0) REVERT: h 11 ASP cc_start: 0.9240 (m-30) cc_final: 0.8794 (p0) REVERT: i 11 ASP cc_start: 0.9177 (m-30) cc_final: 0.8854 (p0) REVERT: j 11 ASP cc_start: 0.9166 (m-30) cc_final: 0.8674 (p0) REVERT: k 11 ASP cc_start: 0.9049 (m-30) cc_final: 0.8733 (p0) REVERT: l 11 ASP cc_start: 0.9195 (m-30) cc_final: 0.8788 (p0) REVERT: m 11 ASP cc_start: 0.9193 (m-30) cc_final: 0.8885 (p0) REVERT: n 11 ASP cc_start: 0.9181 (m-30) cc_final: 0.8684 (p0) outliers start: 29 outliers final: 12 residues processed: 320 average time/residue: 0.9453 time to fit residues: 329.4640 Evaluate side-chains 296 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 284 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain O residue 94 SER Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 94 SER Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain e residue 94 SER Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 94 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 209 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 239 optimal weight: 0.7980 chunk 241 optimal weight: 8.9990 chunk 126 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.055204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.043391 restraints weight = 62429.207| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.45 r_work: 0.2812 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9094 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20863 Z= 0.201 Angle : 0.527 5.552 27898 Z= 0.293 Chirality : 0.034 0.118 3596 Planarity : 0.002 0.021 3422 Dihedral : 2.605 7.371 2726 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 0.69 % Allowed : 17.46 % Favored : 81.85 % 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: 6.48 (0.14), residues: 2668 helix: 4.69 (0.09), residues: 2320 sheet: None (None), residues: 0 loop : 0.48 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG d 14 PHE 0.006 0.001 PHE N 57 HIS 0.000 0.000 HIS b 34 Details of bonding type rmsd covalent geometry : bond 0.00374 (20735) covalent geometry : angle 0.52680 (27898) hydrogen bonds : bond 0.10086 ( 1856) hydrogen bonds : angle 4.16841 ( 5568) Misc. bond : bond 0.00103 ( 128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 295 time to evaluate : 0.853 Fit side-chains REVERT: B 11 ASP cc_start: 0.9087 (m-30) cc_final: 0.8684 (p0) REVERT: D 11 ASP cc_start: 0.9200 (m-30) cc_final: 0.8766 (p0) REVERT: F 11 ASP cc_start: 0.9190 (m-30) cc_final: 0.8684 (p0) REVERT: G 11 ASP cc_start: 0.9143 (m-30) cc_final: 0.8760 (p0) REVERT: H 11 ASP cc_start: 0.9228 (m-30) cc_final: 0.8756 (p0) REVERT: J 11 ASP cc_start: 0.9123 (m-30) cc_final: 0.8783 (p0) REVERT: K 11 ASP cc_start: 0.9070 (m-30) cc_final: 0.8759 (p0) REVERT: L 11 ASP cc_start: 0.9156 (m-30) cc_final: 0.8722 (p0) REVERT: N 11 ASP cc_start: 0.9124 (m-30) cc_final: 0.8788 (p0) REVERT: O 11 ASP cc_start: 0.9259 (m-30) cc_final: 0.8778 (p0) REVERT: d 11 ASP cc_start: 0.9198 (m-30) cc_final: 0.8767 (p0) REVERT: e 11 ASP cc_start: 0.9210 (m-30) cc_final: 0.8762 (p0) REVERT: f 11 ASP cc_start: 0.9242 (m-30) cc_final: 0.8746 (p0) REVERT: g 11 ASP cc_start: 0.9094 (m-30) cc_final: 0.8734 (p0) REVERT: h 11 ASP cc_start: 0.9183 (m-30) cc_final: 0.8749 (p0) REVERT: i 11 ASP cc_start: 0.9189 (m-30) cc_final: 0.8829 (p0) REVERT: m 11 ASP cc_start: 0.9184 (m-30) cc_final: 0.8862 (p0) outliers start: 16 outliers final: 10 residues processed: 310 average time/residue: 1.0074 time to fit residues: 338.3108 Evaluate side-chains 264 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 254 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain F residue 3 MET Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain e residue 94 SER Chi-restraints excluded: chain g residue 94 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 119 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.048296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.036774 restraints weight = 63777.338| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 2.47 r_work: 0.2602 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9257 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 20863 Z= 0.287 Angle : 0.622 7.064 27898 Z= 0.345 Chirality : 0.038 0.130 3596 Planarity : 0.003 0.029 3422 Dihedral : 2.510 8.089 2726 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Rotamer: Outliers : 1.51 % Allowed : 18.28 % Favored : 80.22 % 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: 5.87 (0.14), residues: 2668 helix: 4.28 (0.08), residues: 2320 sheet: None (None), residues: 0 loop : 0.29 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 14 PHE 0.008 0.002 PHE F 57 HIS 0.001 0.000 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00648 (20735) covalent geometry : angle 0.62235 (27898) hydrogen bonds : bond 0.13994 ( 1856) hydrogen bonds : angle 4.72158 ( 5568) Misc. bond : bond 0.00156 ( 128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 289 time to evaluate : 0.861 Fit side-chains REVERT: A 11 ASP cc_start: 0.9178 (m-30) cc_final: 0.8636 (p0) REVERT: B 11 ASP cc_start: 0.9157 (m-30) cc_final: 0.8771 (p0) REVERT: C 11 ASP cc_start: 0.9180 (m-30) cc_final: 0.8595 (p0) REVERT: C 15 ASP cc_start: 0.8675 (m-30) cc_final: 0.8414 (m-30) REVERT: D 11 ASP cc_start: 0.9199 (m-30) cc_final: 0.8800 (p0) REVERT: D 15 ASP cc_start: 0.8625 (m-30) cc_final: 0.8417 (m-30) REVERT: E 11 ASP cc_start: 0.9196 (m-30) cc_final: 0.8760 (p0) REVERT: F 11 ASP cc_start: 0.9267 (m-30) cc_final: 0.8753 (p0) REVERT: G 11 ASP cc_start: 0.9161 (m-30) cc_final: 0.8804 (p0) REVERT: H 11 ASP cc_start: 0.9211 (m-30) cc_final: 0.8861 (p0) REVERT: I 11 ASP cc_start: 0.9209 (m-30) cc_final: 0.8702 (p0) REVERT: J 11 ASP cc_start: 0.9193 (m-30) cc_final: 0.8810 (p0) REVERT: K 11 ASP cc_start: 0.9142 (m-30) cc_final: 0.8809 (p0) REVERT: L 11 ASP cc_start: 0.9182 (m-30) cc_final: 0.8755 (p0) REVERT: M 11 ASP cc_start: 0.9174 (m-30) cc_final: 0.8733 (p0) REVERT: N 11 ASP cc_start: 0.9159 (m-30) cc_final: 0.8847 (p0) REVERT: O 11 ASP cc_start: 0.9248 (m-30) cc_final: 0.8802 (p0) REVERT: a 11 ASP cc_start: 0.9157 (m-30) cc_final: 0.8638 (p0) REVERT: b 11 ASP cc_start: 0.9215 (m-30) cc_final: 0.8735 (p0) REVERT: b 15 ASP cc_start: 0.8629 (m-30) cc_final: 0.8388 (m-30) REVERT: c 11 ASP cc_start: 0.9189 (OUTLIER) cc_final: 0.8673 (p0) REVERT: d 11 ASP cc_start: 0.9171 (m-30) cc_final: 0.8712 (p0) REVERT: e 11 ASP cc_start: 0.9260 (m-30) cc_final: 0.8813 (p0) REVERT: f 11 ASP cc_start: 0.9263 (m-30) cc_final: 0.8776 (p0) REVERT: g 11 ASP cc_start: 0.9128 (m-30) cc_final: 0.8787 (p0) REVERT: h 11 ASP cc_start: 0.9239 (m-30) cc_final: 0.8802 (p0) REVERT: i 8 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8606 (mp0) REVERT: i 11 ASP cc_start: 0.9227 (m-30) cc_final: 0.8877 (p0) REVERT: j 11 ASP cc_start: 0.9147 (m-30) cc_final: 0.8611 (p0) REVERT: k 11 ASP cc_start: 0.9125 (m-30) cc_final: 0.8744 (p0) REVERT: l 11 ASP cc_start: 0.9200 (m-30) cc_final: 0.8701 (p0) REVERT: m 11 ASP cc_start: 0.9210 (m-30) cc_final: 0.8895 (p0) REVERT: n 11 ASP cc_start: 0.9134 (m-30) cc_final: 0.8589 (p0) outliers start: 35 outliers final: 19 residues processed: 304 average time/residue: 0.9582 time to fit residues: 316.7987 Evaluate side-chains 303 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 283 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 11 ASP Chi-restraints excluded: chain d residue 3 MET Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain e residue 53 GLU Chi-restraints excluded: chain e residue 94 SER Chi-restraints excluded: chain f residue 51 GLU Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain j residue 53 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 202 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 197 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.050644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.039084 restraints weight = 63295.349| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.45 r_work: 0.2677 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9201 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20863 Z= 0.239 Angle : 0.596 7.073 27898 Z= 0.331 Chirality : 0.036 0.126 3596 Planarity : 0.003 0.022 3422 Dihedral : 2.525 7.371 2726 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.86 % Allowed : 18.79 % Favored : 80.34 % 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: 6.05 (0.14), residues: 2668 helix: 4.41 (0.08), residues: 2320 sheet: None (None), residues: 0 loop : 0.32 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 14 PHE 0.007 0.001 PHE N 57 HIS 0.001 0.000 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00483 (20735) covalent geometry : angle 0.59579 (27898) hydrogen bonds : bond 0.12311 ( 1856) hydrogen bonds : angle 4.50608 ( 5568) Misc. bond : bond 0.00120 ( 128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 283 time to evaluate : 0.896 Fit side-chains REVERT: A 11 ASP cc_start: 0.9172 (m-30) cc_final: 0.8646 (p0) REVERT: B 11 ASP cc_start: 0.9132 (m-30) cc_final: 0.8767 (p0) REVERT: C 11 ASP cc_start: 0.9190 (m-30) cc_final: 0.8616 (p0) REVERT: D 11 ASP cc_start: 0.9192 (m-30) cc_final: 0.8805 (p0) REVERT: E 11 ASP cc_start: 0.9169 (m-30) cc_final: 0.8750 (p0) REVERT: F 11 ASP cc_start: 0.9230 (m-30) cc_final: 0.8780 (p0) REVERT: G 11 ASP cc_start: 0.9144 (m-30) cc_final: 0.8793 (p0) REVERT: H 11 ASP cc_start: 0.9207 (m-30) cc_final: 0.8858 (p0) REVERT: I 11 ASP cc_start: 0.9201 (m-30) cc_final: 0.8701 (p0) REVERT: J 11 ASP cc_start: 0.9133 (m-30) cc_final: 0.8790 (p0) REVERT: K 11 ASP cc_start: 0.9135 (m-30) cc_final: 0.8850 (p0) REVERT: L 11 ASP cc_start: 0.9193 (m-30) cc_final: 0.8770 (p0) REVERT: M 11 ASP cc_start: 0.9178 (m-30) cc_final: 0.8736 (p0) REVERT: N 11 ASP cc_start: 0.9126 (m-30) cc_final: 0.8838 (p0) REVERT: O 11 ASP cc_start: 0.9247 (m-30) cc_final: 0.8802 (p0) REVERT: a 11 ASP cc_start: 0.9167 (m-30) cc_final: 0.8645 (p0) REVERT: b 11 ASP cc_start: 0.9222 (m-30) cc_final: 0.8739 (p0) REVERT: c 11 ASP cc_start: 0.9205 (OUTLIER) cc_final: 0.8698 (p0) REVERT: d 11 ASP cc_start: 0.9169 (m-30) cc_final: 0.8692 (p0) REVERT: e 11 ASP cc_start: 0.9247 (m-30) cc_final: 0.8789 (p0) REVERT: f 11 ASP cc_start: 0.9282 (m-30) cc_final: 0.8814 (p0) REVERT: g 11 ASP cc_start: 0.9107 (m-30) cc_final: 0.8788 (p0) REVERT: h 11 ASP cc_start: 0.9244 (m-30) cc_final: 0.8800 (p0) REVERT: i 11 ASP cc_start: 0.9209 (m-30) cc_final: 0.8866 (p0) REVERT: j 11 ASP cc_start: 0.9151 (m-30) cc_final: 0.8645 (p0) REVERT: k 11 ASP cc_start: 0.9084 (m-30) cc_final: 0.8739 (p0) REVERT: l 11 ASP cc_start: 0.9194 (m-30) cc_final: 0.8700 (p0) REVERT: m 11 ASP cc_start: 0.9203 (m-30) cc_final: 0.8900 (p0) REVERT: n 11 ASP cc_start: 0.9133 (m-30) cc_final: 0.8589 (p0) outliers start: 20 outliers final: 17 residues processed: 293 average time/residue: 0.9616 time to fit residues: 306.5161 Evaluate side-chains 294 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 276 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 11 ASP Chi-restraints excluded: chain c residue 94 SER Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain e residue 94 SER Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain j residue 53 GLU Chi-restraints excluded: chain k residue 53 GLU Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain m residue 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 51 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 125 optimal weight: 0.9980 chunk 252 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 GLN ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.050183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.038592 restraints weight = 63575.934| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.46 r_work: 0.2661 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9205 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20863 Z= 0.246 Angle : 0.609 7.701 27898 Z= 0.338 Chirality : 0.036 0.132 3596 Planarity : 0.003 0.024 3422 Dihedral : 2.538 9.010 2726 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.91 % Allowed : 18.62 % Favored : 80.47 % 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: 5.98 (0.14), residues: 2668 helix: 4.37 (0.08), residues: 2320 sheet: None (None), residues: 0 loop : 0.23 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG i 14 PHE 0.008 0.001 PHE N 57 HIS 0.001 0.000 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00507 (20735) covalent geometry : angle 0.60874 (27898) hydrogen bonds : bond 0.12577 ( 1856) hydrogen bonds : angle 4.53270 ( 5568) Misc. bond : bond 0.00125 ( 128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5336 Ramachandran restraints generated. 2668 Oldfield, 0 Emsley, 2668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 283 time to evaluate : 0.609 Fit side-chains REVERT: A 11 ASP cc_start: 0.9172 (m-30) cc_final: 0.8643 (p0) REVERT: B 11 ASP cc_start: 0.9155 (m-30) cc_final: 0.8779 (p0) REVERT: C 11 ASP cc_start: 0.9190 (m-30) cc_final: 0.8610 (p0) REVERT: D 11 ASP cc_start: 0.9194 (m-30) cc_final: 0.8809 (p0) REVERT: E 11 ASP cc_start: 0.9167 (m-30) cc_final: 0.8747 (p0) REVERT: F 11 ASP cc_start: 0.9235 (m-30) cc_final: 0.8750 (p0) REVERT: G 11 ASP cc_start: 0.9148 (m-30) cc_final: 0.8791 (p0) REVERT: H 11 ASP cc_start: 0.9192 (m-30) cc_final: 0.8846 (p0) REVERT: I 11 ASP cc_start: 0.9206 (m-30) cc_final: 0.8695 (p0) REVERT: J 11 ASP cc_start: 0.9160 (m-30) cc_final: 0.8803 (p0) REVERT: K 11 ASP cc_start: 0.9128 (m-30) cc_final: 0.8830 (p0) REVERT: L 11 ASP cc_start: 0.9190 (m-30) cc_final: 0.8765 (p0) REVERT: M 11 ASP cc_start: 0.9170 (m-30) cc_final: 0.8736 (p0) REVERT: N 11 ASP cc_start: 0.9134 (m-30) cc_final: 0.8844 (p0) REVERT: O 11 ASP cc_start: 0.9249 (m-30) cc_final: 0.8792 (p0) REVERT: a 11 ASP cc_start: 0.9172 (m-30) cc_final: 0.8686 (p0) REVERT: b 11 ASP cc_start: 0.9211 (m-30) cc_final: 0.8728 (p0) REVERT: c 11 ASP cc_start: 0.9198 (m-30) cc_final: 0.8689 (p0) REVERT: d 11 ASP cc_start: 0.9174 (m-30) cc_final: 0.8721 (p0) REVERT: e 11 ASP cc_start: 0.9243 (m-30) cc_final: 0.8789 (p0) REVERT: f 11 ASP cc_start: 0.9248 (m-30) cc_final: 0.8792 (p0) REVERT: g 11 ASP cc_start: 0.9118 (m-30) cc_final: 0.8794 (p0) REVERT: h 11 ASP cc_start: 0.9214 (m-30) cc_final: 0.8790 (p0) REVERT: i 11 ASP cc_start: 0.9200 (m-30) cc_final: 0.8859 (p0) REVERT: j 11 ASP cc_start: 0.9138 (m-30) cc_final: 0.8633 (p0) REVERT: k 11 ASP cc_start: 0.9104 (m-30) cc_final: 0.8736 (p0) REVERT: l 11 ASP cc_start: 0.9175 (m-30) cc_final: 0.8687 (p0) REVERT: m 11 ASP cc_start: 0.9198 (m-30) cc_final: 0.8904 (p0) REVERT: n 11 ASP cc_start: 0.9134 (m-30) cc_final: 0.8594 (p0) outliers start: 21 outliers final: 18 residues processed: 293 average time/residue: 0.9633 time to fit residues: 306.4612 Evaluate side-chains 299 residues out of total 2320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 281 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain F residue 94 SER Chi-restraints excluded: chain G residue 53 GLU Chi-restraints excluded: chain I residue 94 SER Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain K residue 53 GLU Chi-restraints excluded: chain K residue 94 SER Chi-restraints excluded: chain L residue 94 SER Chi-restraints excluded: chain M residue 53 GLU Chi-restraints excluded: chain b residue 94 SER Chi-restraints excluded: chain c residue 94 SER Chi-restraints excluded: chain d residue 94 SER Chi-restraints excluded: chain e residue 94 SER Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain j residue 53 GLU Chi-restraints excluded: chain k residue 53 GLU Chi-restraints excluded: chain l residue 53 GLU Chi-restraints excluded: chain m residue 53 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 245 optimal weight: 10.0000 chunk 246 optimal weight: 5.9990 chunk 227 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 259 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 240 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.050393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.038783 restraints weight = 63521.582| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.46 r_work: 0.2669 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9199 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20863 Z= 0.242 Angle : 0.600 7.647 27898 Z= 0.333 Chirality : 0.036 0.128 3596 Planarity : 0.003 0.022 3422 Dihedral : 2.544 8.650 2726 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.91 % Allowed : 18.58 % Favored : 80.52 % 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: 5.99 (0.14), residues: 2668 helix: 4.37 (0.08), residues: 2320 sheet: None (None), residues: 0 loop : 0.19 (0.35), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG i 14 PHE 0.008 0.001 PHE N 57 HIS 0.001 0.000 HIS I 34 Details of bonding type rmsd covalent geometry : bond 0.00493 (20735) covalent geometry : angle 0.60002 (27898) hydrogen bonds : bond 0.12444 ( 1856) hydrogen bonds : angle 4.51600 ( 5568) Misc. bond : bond 0.00122 ( 128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10930.26 seconds wall clock time: 185 minutes 28.90 seconds (11128.90 seconds total)