Starting phenix.real_space_refine on Wed Mar 4 04:19:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ovh_20212/03_2026/6ovh_20212_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ovh_20212/03_2026/6ovh_20212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ovh_20212/03_2026/6ovh_20212_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ovh_20212/03_2026/6ovh_20212_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ovh_20212/03_2026/6ovh_20212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ovh_20212/03_2026/6ovh_20212.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 20 7.16 5 Zn 24 6.06 5 S 84 5.16 5 C 6672 2.51 5 N 1872 2.21 5 O 2223 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10895 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "B" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "C" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "D" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "E" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "F" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "G" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "H" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "I" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "J" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "K" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "L" Number of atoms: 838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} Conformer: "B" Number of residues, atoms: 106, 824 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 101} bond proxies already assigned to first conformer: 822 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {' FE': 1, ' ZN': 3, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {' FE': 2, ' ZN': 1, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {' FE': 1, ' ZN': 2, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {' FE': 1, ' ZN': 3, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 57 Unusual residues: {' FE': 1, ' ZN': 3, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {' ZN': 1, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 54 Unusual residues: {' ZN': 1, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {' FE': 1, ' ZN': 2, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 56 Unusual residues: {' FE': 1, ' ZN': 2, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 55 Unusual residues: {' ZN': 2, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 55 Unusual residues: {' ZN': 2, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 55 Unusual residues: {' ZN': 2, 'HAE': 2, 'HEC': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} 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: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "L" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Residues with excluded nonbonded symmetry interactions: 69 residue: pdb=" N GLU A 4 " occ=0.64 ... (7 atoms not shown) pdb=" OE2 GLU A 4 " occ=0.64 residue: pdb=" N ASP A 28 " occ=0.45 ... (6 atoms not shown) pdb=" OD2 ASP A 28 " occ=0.45 residue: pdb=" N GLN A 38 " occ=0.41 ... (7 atoms not shown) pdb=" NE2 GLN A 38 " occ=0.41 residue: pdb=" N ATRP A 66 " occ=0.70 ... (26 atoms not shown) pdb=" CH2BTRP A 66 " occ=0.30 residue: pdb=" N LEU A 94 " occ=0.44 ... (6 atoms not shown) pdb=" CD2 LEU A 94 " occ=0.44 residue: pdb=" N THR A 96 " occ=0.54 ... (5 atoms not shown) pdb=" CG2 THR A 96 " occ=0.54 residue: pdb=" N GLU B 18 " occ=0.66 ... (7 atoms not shown) pdb=" OE2 GLU B 18 " occ=0.66 residue: pdb=" N ASP B 28 " occ=0.52 ... (6 atoms not shown) pdb=" OD2 ASP B 28 " occ=0.52 residue: pdb=" N GLN B 38 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN B 38 " occ=0.50 residue: pdb=" N ATRP B 66 " occ=0.70 ... (26 atoms not shown) pdb=" CH2BTRP B 66 " occ=0.30 residue: pdb=" N HIS B 77 " occ=0.54 ... (8 atoms not shown) pdb=" NE2 HIS B 77 " occ=0.54 residue: pdb=" N TRP C 41 " occ=0.52 ... (12 atoms not shown) pdb=" CH2 TRP C 41 " occ=0.52 ... (remaining 57 not shown) Time building chain proxies: 4.40, per 1000 atoms: 0.40 Number of scatterers: 10895 At special positions: 0 Unit cell: (105.65, 98.8884, 95.5076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 24 29.99 Fe 20 26.01 S 84 16.00 O 2223 8.00 N 1872 7.00 C 6672 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=60, symmetry=0 Number of additional bonds: simple=60, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 895.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 204 " pdb="ZN ZN A 204 " - pdb=" NE2 HIS C 77 " pdb=" ZN A 205 " pdb="ZN ZN A 205 " - pdb=" ND1 HIS B 5 " pdb="ZN ZN A 205 " - pdb=" NE2 HIS A 16 " pdb="ZN ZN A 205 " - pdb=" ND1 HIS B 8 " pdb=" ZN A 206 " pdb="ZN ZN A 206 " - pdb=" ND1 HIS A 5 " pdb="ZN ZN A 206 " - pdb=" NE2 HIS B 16 " pdb="ZN ZN A 206 " - pdb=" ND1 HIS A 8 " pdb=" ZN B 206 " pdb="ZN ZN B 206 " - pdb=" NE2 HIS F 77 " pdb=" ZN C 205 " pdb="ZN ZN C 205 " - pdb=" NE2 HIS D 77 " pdb=" ZN C 206 " pdb="ZN ZN C 206 " - pdb=" NE2 HIS L 16 " pdb="ZN ZN C 206 " - pdb=" ND1 HIS C 5 " pdb="ZN ZN C 206 " - pdb=" ND1 HIS C 8 " pdb=" ZN D 205 " pdb="ZN ZN D 205 " - pdb=" NE2 HIS A 77 " pdb=" ZN D 206 " pdb="ZN ZN D 206 " - pdb=" ND1 HIS G 5 " pdb="ZN ZN D 206 " - pdb=" NE2 HIS D 16 " pdb="ZN ZN D 206 " - pdb=" ND1 HIS G 8 " pdb=" ZN D 207 " pdb="ZN ZN D 207 " - pdb=" ND1 HIS D 5 " pdb="ZN ZN D 207 " - pdb=" NE2 HIS G 16 " pdb="ZN ZN D 207 " - pdb=" ND1 HIS D 8 " pdb=" ZN E 204 " pdb="ZN ZN E 204 " - pdb=" NE2 HIS G 77 " pdb=" ZN E 205 " pdb="ZN ZN E 205 " - pdb=" ND1 HIS F 5 " pdb="ZN ZN E 205 " - pdb=" ND1 HIS F 8 " pdb="ZN ZN E 205 " - pdb=" NE2 HIS E 16 " pdb=" ZN E 206 " pdb="ZN ZN E 206 " - pdb=" ND1 HIS E 5 " pdb="ZN ZN E 206 " - pdb=" NE2 HIS F 16 " pdb="ZN ZN E 206 " - pdb=" ND1 HIS E 8 " pdb=" ZN F 204 " pdb="ZN ZN F 204 " - pdb=" NE2 HIS J 77 " pdb=" ZN G 204 " pdb="ZN ZN G 204 " - pdb=" NE2 HIS H 77 " pdb=" ZN H 205 " pdb="ZN ZN H 205 " - pdb=" NE2 HIS E 77 " pdb=" ZN H 206 " pdb="ZN ZN H 206 " - pdb=" NE2 HIS K 16 " pdb="ZN ZN H 206 " - pdb=" ND1 HIS H 8 " pdb="ZN ZN H 206 " - pdb=" ND1 HIS H 5 " pdb=" ZN I 205 " pdb="ZN ZN I 205 " - pdb=" NE2 HIS K 77 " pdb=" ZN I 206 " pdb="ZN ZN I 206 " - pdb=" ND1 HIS I 5 " pdb="ZN ZN I 206 " - pdb=" NE2 HIS J 16 " pdb="ZN ZN I 206 " - pdb=" ND1 HIS I 8 " pdb=" ZN J 201 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 5 " pdb="ZN ZN J 201 " - pdb=" NE2 HIS I 16 " pdb="ZN ZN J 201 " - pdb=" ND1 HIS J 8 " pdb=" ZN J 205 " pdb="ZN ZN J 205 " - pdb=" NE2 HIS B 77 " pdb=" ZN K 201 " pdb="ZN ZN K 201 " - pdb=" NE2 HIS H 16 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 5 " pdb="ZN ZN K 201 " - pdb=" ND1 HIS K 8 " pdb=" ZN K 205 " pdb="ZN ZN K 205 " - pdb=" NE2 HIS L 77 " pdb=" ZN L 201 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 5 " pdb="ZN ZN L 201 " - pdb=" NE2 HIS C 16 " pdb="ZN ZN L 201 " - pdb=" ND1 HIS L 8 " pdb=" ZN L 205 " pdb="ZN ZN L 205 " - pdb=" NE2 HIS I 77 " 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2520 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 2 through 19 removed outlier: 3.597A pdb=" N LYS A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 40 removed outlier: 3.881A pdb=" N VAL A 26 " --> pdb=" O ASN A 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS A 32 " --> pdb=" O ASP A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU A 49 " --> pdb=" O PRO A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.794A pdb=" N ARG A 62 " --> pdb=" O MET A 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE A 65 " --> pdb=" O PHE A 61 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 70 " --> pdb=" O ATRP A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 101' Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.583A pdb=" N ARG A 106 " --> pdb=" O HIS A 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 19 removed outlier: 3.597A pdb=" N LYS B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU B 18 " --> pdb=" O LEU B 14 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 40 removed outlier: 3.881A pdb=" N VAL B 26 " --> pdb=" O ASN B 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR B 31 " --> pdb=" O LYS B 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 32 " --> pdb=" O ASP B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU B 49 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 80 removed outlier: 3.795A pdb=" N ARG B 62 " --> pdb=" O MET B 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY B 70 " --> pdb=" O ATRP B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 96 through 101' Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.583A pdb=" N ARG B 106 " --> pdb=" O HIS B 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 19 removed outlier: 3.596A pdb=" N LYS C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU C 18 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 40 removed outlier: 3.881A pdb=" N VAL C 26 " --> pdb=" O ASN C 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 32 " --> pdb=" O ASP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU C 49 " --> pdb=" O PRO C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 80 removed outlier: 3.794A pdb=" N ARG C 62 " --> pdb=" O MET C 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 65 " --> pdb=" O PHE C 61 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY C 70 " --> pdb=" O ATRP C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.504A pdb=" N ALA C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS C 101 " --> pdb=" O THR C 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 101' Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.584A pdb=" N ARG C 106 " --> pdb=" O HIS C 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 19 removed outlier: 3.596A pdb=" N LYS D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU D 18 " --> pdb=" O LEU D 14 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 40 removed outlier: 3.881A pdb=" N VAL D 26 " --> pdb=" O ASN D 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR D 31 " --> pdb=" O LYS D 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU D 49 " --> pdb=" O PRO D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.794A pdb=" N ARG D 62 " --> pdb=" O MET D 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY D 70 " --> pdb=" O ATRP D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS D 101 " --> pdb=" O THR D 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 96 through 101' Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.583A pdb=" N ARG D 106 " --> pdb=" O HIS D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 19 removed outlier: 3.596A pdb=" N LYS E 15 " --> pdb=" O ASN E 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 40 removed outlier: 3.882A pdb=" N VAL E 26 " --> pdb=" O ASN E 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS E 32 " --> pdb=" O ASP E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU E 49 " --> pdb=" O PRO E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 removed outlier: 3.795A pdb=" N ARG E 62 " --> pdb=" O MET E 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE E 65 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY E 70 " --> pdb=" O ATRP E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS E 101 " --> pdb=" O THR E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 101' Processing helix chain 'E' and resid 101 through 106 removed outlier: 3.583A pdb=" N ARG E 106 " --> pdb=" O HIS E 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 19 removed outlier: 3.596A pdb=" N LYS F 15 " --> pdb=" O ASN F 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 40 removed outlier: 3.881A pdb=" N VAL F 26 " --> pdb=" O ASN F 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 31 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 32 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU F 49 " --> pdb=" O PRO F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 80 removed outlier: 3.795A pdb=" N ARG F 62 " --> pdb=" O MET F 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY F 70 " --> pdb=" O ATRP F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS F 101 " --> pdb=" O THR F 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 96 through 101' Processing helix chain 'F' and resid 101 through 106 removed outlier: 3.583A pdb=" N ARG F 106 " --> pdb=" O HIS F 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 19 removed outlier: 3.596A pdb=" N LYS G 15 " --> pdb=" O ASN G 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 40 removed outlier: 3.882A pdb=" N VAL G 26 " --> pdb=" O ASN G 22 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 31 " --> pdb=" O LYS G 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS G 32 " --> pdb=" O ASP G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU G 49 " --> pdb=" O PRO G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 80 removed outlier: 3.794A pdb=" N ARG G 62 " --> pdb=" O MET G 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE G 65 " --> pdb=" O PHE G 61 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY G 70 " --> pdb=" O ATRP G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS G 101 " --> pdb=" O THR G 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 96 through 101' Processing helix chain 'G' and resid 101 through 106 removed outlier: 3.583A pdb=" N ARG G 106 " --> pdb=" O HIS G 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 19 removed outlier: 3.596A pdb=" N LYS H 15 " --> pdb=" O ASN H 11 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 40 removed outlier: 3.881A pdb=" N VAL H 26 " --> pdb=" O ASN H 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR H 31 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS H 32 " --> pdb=" O ASP H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU H 49 " --> pdb=" O PRO H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 80 removed outlier: 3.795A pdb=" N ARG H 62 " --> pdb=" O MET H 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE H 65 " --> pdb=" O PHE H 61 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY H 70 " --> pdb=" O ATRP H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 93 removed outlier: 3.560A pdb=" N GLN H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS H 101 " --> pdb=" O THR H 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 96 through 101' Processing helix chain 'H' and resid 101 through 106 removed outlier: 3.584A pdb=" N ARG H 106 " --> pdb=" O HIS H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 19 removed outlier: 3.595A pdb=" N LYS I 15 " --> pdb=" O ASN I 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 40 removed outlier: 3.882A pdb=" N VAL I 26 " --> pdb=" O ASN I 22 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR I 31 " --> pdb=" O LYS I 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS I 32 " --> pdb=" O ASP I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU I 49 " --> pdb=" O PRO I 46 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 80 removed outlier: 3.795A pdb=" N ARG I 62 " --> pdb=" O MET I 58 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE I 65 " --> pdb=" O PHE I 61 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY I 70 " --> pdb=" O ATRP I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 93 removed outlier: 3.562A pdb=" N GLN I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA I 100 " --> pdb=" O THR I 96 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS I 101 " --> pdb=" O THR I 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 96 through 101' Processing helix chain 'I' and resid 101 through 106 removed outlier: 3.584A pdb=" N ARG I 106 " --> pdb=" O HIS I 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 19 removed outlier: 3.597A pdb=" N LYS J 15 " --> pdb=" O ASN J 11 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS J 19 " --> pdb=" O LYS J 15 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 40 removed outlier: 3.882A pdb=" N VAL J 26 " --> pdb=" O ASN J 22 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR J 31 " --> pdb=" O LYS J 27 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS J 32 " --> pdb=" O ASP J 28 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU J 49 " --> pdb=" O PRO J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 80 removed outlier: 3.795A pdb=" N ARG J 62 " --> pdb=" O MET J 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE J 65 " --> pdb=" O PHE J 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY J 70 " --> pdb=" O ATRP J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA J 100 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS J 101 " --> pdb=" O THR J 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 96 through 101' Processing helix chain 'J' and resid 101 through 106 removed outlier: 3.584A pdb=" N ARG J 106 " --> pdb=" O HIS J 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 19 removed outlier: 3.596A pdb=" N LYS K 15 " --> pdb=" O ASN K 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS K 19 " --> pdb=" O LYS K 15 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 40 removed outlier: 3.882A pdb=" N VAL K 26 " --> pdb=" O ASN K 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 31 " --> pdb=" O LYS K 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS K 32 " --> pdb=" O ASP K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU K 49 " --> pdb=" O PRO K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 80 removed outlier: 3.794A pdb=" N ARG K 62 " --> pdb=" O MET K 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE K 65 " --> pdb=" O PHE K 61 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY K 70 " --> pdb=" O ATRP K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA K 100 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS K 101 " --> pdb=" O THR K 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 96 through 101' Processing helix chain 'K' and resid 101 through 106 removed outlier: 3.583A pdb=" N ARG K 106 " --> pdb=" O HIS K 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 19 removed outlier: 3.596A pdb=" N LYS L 15 " --> pdb=" O ASN L 11 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU L 18 " --> pdb=" O LEU L 14 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS L 19 " --> pdb=" O LYS L 15 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 40 removed outlier: 3.881A pdb=" N VAL L 26 " --> pdb=" O ASN L 22 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR L 31 " --> pdb=" O LYS L 27 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS L 32 " --> pdb=" O ASP L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 49 removed outlier: 3.719A pdb=" N GLU L 49 " --> pdb=" O PRO L 46 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 80 removed outlier: 3.794A pdb=" N ARG L 62 " --> pdb=" O MET L 58 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE L 65 " --> pdb=" O PHE L 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY L 70 " --> pdb=" O ATRP L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 93 removed outlier: 3.561A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 101 removed outlier: 3.503A pdb=" N ALA L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS L 101 " --> pdb=" O THR L 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 96 through 101' Processing helix chain 'L' and resid 101 through 106 removed outlier: 3.582A pdb=" N ARG L 106 " --> pdb=" O HIS L 102 " (cutoff:3.500A) 612 hydrogen bonds defined for protein. 1812 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: 1.65 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3674 1.36 - 1.54: 6911 1.54 - 1.71: 215 1.71 - 1.89: 120 1.89 - 2.06: 48 Bond restraints: 10968 Sorted by residual: bond pdb=" CAB HEC G 201 " pdb=" CBB HEC G 201 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CAB HEC K 202 " pdb=" CBB HEC K 202 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CAB HEC L 202 " pdb=" CBB HEC L 202 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CAB HEC B 201 " pdb=" CBB HEC B 201 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" CAB HEC F 201 " pdb=" CBB HEC F 201 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 10963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 14808 3.81 - 7.61: 156 7.61 - 11.42: 24 11.42 - 15.23: 0 15.23 - 19.03: 12 Bond angle restraints: 15000 Sorted by residual: angle pdb=" C3C HEC A 201 " pdb=" CAC HEC A 201 " pdb=" CBC HEC A 201 " ideal model delta sigma weight residual 109.00 128.03 -19.03 3.00e+00 1.11e-01 4.02e+01 angle pdb=" C3C HEC B 201 " pdb=" CAC HEC B 201 " pdb=" CBC HEC B 201 " ideal model delta sigma weight residual 109.00 128.00 -19.00 3.00e+00 1.11e-01 4.01e+01 angle pdb=" C3C HEC E 201 " pdb=" CAC HEC E 201 " pdb=" CBC HEC E 201 " ideal model delta sigma weight residual 109.00 127.99 -18.99 3.00e+00 1.11e-01 4.01e+01 angle pdb=" C3C HEC J 202 " pdb=" CAC HEC J 202 " pdb=" CBC HEC J 202 " ideal model delta sigma weight residual 109.00 127.98 -18.98 3.00e+00 1.11e-01 4.00e+01 angle pdb=" C3C HEC H 202 " pdb=" CAC HEC H 202 " pdb=" CBC HEC H 202 " ideal model delta sigma weight residual 109.00 127.98 -18.98 3.00e+00 1.11e-01 4.00e+01 ... (remaining 14995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 5738 17.65 - 35.31: 466 35.31 - 52.96: 132 52.96 - 70.61: 36 70.61 - 88.27: 48 Dihedral angle restraints: 6420 sinusoidal: 2604 harmonic: 3816 Sorted by residual: dihedral pdb=" C2C HEC H 202 " pdb=" C3C HEC H 202 " pdb=" CAC HEC H 202 " pdb=" CBC HEC H 202 " ideal model delta sinusoidal sigma weight residual 60.00 10.23 49.77 2 1.00e+01 1.00e-02 2.80e+01 dihedral pdb=" C2C HEC K 202 " pdb=" C3C HEC K 202 " pdb=" CAC HEC K 202 " pdb=" CBC HEC K 202 " ideal model delta sinusoidal sigma weight residual 60.00 10.29 49.71 2 1.00e+01 1.00e-02 2.79e+01 dihedral pdb=" C2C HEC C 202 " pdb=" C3C HEC C 202 " pdb=" CAC HEC C 202 " pdb=" CBC HEC C 202 " ideal model delta sinusoidal sigma weight residual 60.00 10.29 49.71 2 1.00e+01 1.00e-02 2.79e+01 ... (remaining 6417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 874 0.032 - 0.064: 484 0.064 - 0.096: 106 0.096 - 0.128: 36 0.128 - 0.160: 12 Chirality restraints: 1512 Sorted by residual: chirality pdb=" CA CYS C 98 " pdb=" N CYS C 98 " pdb=" C CYS C 98 " pdb=" CB CYS C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA CYS E 98 " pdb=" N CYS E 98 " pdb=" C CYS E 98 " pdb=" CB CYS E 98 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA CYS H 98 " pdb=" N CYS H 98 " pdb=" C CYS H 98 " pdb=" CB CYS H 98 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.29e-01 ... (remaining 1509 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO H 45 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO H 46 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO H 46 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 46 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 45 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO F 46 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 46 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 46 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO K 45 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO K 46 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO K 46 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO K 46 " 0.024 5.00e-02 4.00e+02 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.94: 32 1.94 - 2.68: 339 2.68 - 3.42: 13480 3.42 - 4.16: 25640 4.16 - 4.90: 46701 Nonbonded interactions: 86192 Sorted by model distance: nonbonded pdb=" O HAE F 202 " pdb=" O2 HAE J 203 " model vdw 1.203 3.040 nonbonded pdb=" O HAE G 202 " pdb=" O2 HAE H 203 " model vdw 1.246 3.040 nonbonded pdb=" O HAE A 202 " pdb=" O2 HAE C 203 " model vdw 1.250 3.040 nonbonded pdb=" O HAE C 203 " pdb=" O2 HAE D 202 " model vdw 1.254 3.040 nonbonded pdb=" O HAE K 203 " pdb=" O2 HAE L 203 " model vdw 1.286 3.040 ... (remaining 86187 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'B' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'C' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'D' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'E' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'F' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'G' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'H' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'I' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'J' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'K' and (resid 1 through 65 or resid 67 through 106 or resid 203)) selection = (chain 'L' and (resid 1 through 65 or resid 67 through 106 or resid 203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=0.96 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: 1.300 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.650 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 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 : 0.027 0.595 11076 Z= 0.877 Angle : 1.096 19.032 15000 Z= 0.443 Chirality : 0.042 0.160 1512 Planarity : 0.006 0.044 1932 Dihedral : 17.483 88.269 3900 Min Nonbonded Distance : 1.203 Molprobity Statistics. All-atom Clashscore : 1.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.55 % Allowed : 1.14 % Favored : 94.32 % 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: -6.34 (0.13), residues: 1284 helix: -4.57 (0.05), residues: 984 sheet: None (None), residues: 0 loop : -1.58 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG G 62 TYR 0.006 0.002 TYR B 105 PHE 0.007 0.002 PHE G 61 TRP 0.007 0.002 TRP F 41 HIS 0.005 0.001 HIS E 5 Details of bonding type rmsd covalent geometry : bond 0.01421 (10968) covalent geometry : angle 1.09636 (15000) hydrogen bonds : bond 0.39748 ( 612) hydrogen bonds : angle 9.10652 ( 1812) metal coordination : bond 0.17188 ( 48) Misc. bond : bond 0.27079 ( 60) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 305 time to evaluate : 0.440 Fit side-chains REVERT: A 18 GLU cc_start: 0.7230 (mt-10) cc_final: 0.6927 (mp0) REVERT: A 19 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8192 (mtpt) REVERT: A 57 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: A 81 GLN cc_start: 0.8409 (mt0) cc_final: 0.8091 (mt0) REVERT: A 82 CYS cc_start: 0.7253 (m) cc_final: 0.6846 (t) REVERT: A 86 GLU cc_start: 0.8518 (mp0) cc_final: 0.8106 (mp0) REVERT: A 93 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7577 (mt0) REVERT: B 47 LYS cc_start: 0.8530 (mttt) cc_final: 0.8231 (mtpt) REVERT: B 85 LYS cc_start: 0.8491 (mmtp) cc_final: 0.8277 (mptp) REVERT: B 86 GLU cc_start: 0.8235 (mp0) cc_final: 0.7806 (mp0) REVERT: B 92 GLU cc_start: 0.8221 (tp30) cc_final: 0.8006 (tp30) REVERT: C 86 GLU cc_start: 0.8249 (mp0) cc_final: 0.7817 (mp0) REVERT: D 86 GLU cc_start: 0.8174 (mp0) cc_final: 0.7954 (mp0) REVERT: E 19 LYS cc_start: 0.8540 (mmtp) cc_final: 0.8051 (mtmt) REVERT: E 47 LYS cc_start: 0.8149 (mttt) cc_final: 0.7869 (mtmt) REVERT: E 85 LYS cc_start: 0.8518 (mmtp) cc_final: 0.8284 (tptt) REVERT: E 86 GLU cc_start: 0.8146 (mp0) cc_final: 0.7460 (mp0) REVERT: F 82 CYS cc_start: 0.7328 (m) cc_final: 0.7056 (t) REVERT: F 86 GLU cc_start: 0.8233 (mp0) cc_final: 0.8033 (mp0) REVERT: F 93 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7684 (mt0) REVERT: G 18 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6872 (mp0) REVERT: G 60 ASP cc_start: 0.8666 (t0) cc_final: 0.8413 (t0) REVERT: G 86 GLU cc_start: 0.8218 (mp0) cc_final: 0.7949 (mp0) REVERT: H 7 MET cc_start: 0.8643 (mmt) cc_final: 0.7844 (mmt) REVERT: H 86 GLU cc_start: 0.8378 (mp0) cc_final: 0.7999 (mp0) REVERT: I 86 GLU cc_start: 0.8508 (mp0) cc_final: 0.7980 (mp0) REVERT: J 86 GLU cc_start: 0.8238 (mp0) cc_final: 0.7827 (mp0) REVERT: K 18 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7172 (mp0) REVERT: K 28 ASP cc_start: 0.7468 (m-30) cc_final: 0.7222 (m-30) REVERT: K 60 ASP cc_start: 0.8539 (t0) cc_final: 0.8156 (t0) REVERT: K 82 CYS cc_start: 0.7241 (m) cc_final: 0.6969 (t) REVERT: L 86 GLU cc_start: 0.8300 (mp0) cc_final: 0.7992 (mp0) outliers start: 48 outliers final: 0 residues processed: 339 average time/residue: 0.7108 time to fit residues: 255.1932 Evaluate side-chains 235 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.0270 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN B 22 ASN B 34 GLN B 99 ASN C 22 ASN C 99 ASN D 22 ASN E 22 ASN E 81 GLN E 99 ASN F 22 ASN F 34 GLN F 81 GLN G 22 ASN H 22 ASN H 81 GLN H 99 ASN I 22 ASN I 34 GLN I 99 ASN J 22 ASN J 34 GLN J 99 ASN K 38 GLN K 103 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.146954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116750 restraints weight = 48346.216| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.51 r_work: 0.3065 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3016 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3016 r_free = 0.3016 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2974 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 11076 Z= 0.131 Angle : 0.730 11.507 15000 Z= 0.280 Chirality : 0.037 0.113 1512 Planarity : 0.005 0.043 1932 Dihedral : 11.604 98.059 1431 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.38 % Allowed : 9.66 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.20), residues: 1284 helix: -1.50 (0.13), residues: 1020 sheet: None (None), residues: 0 loop : -1.35 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 62 TYR 0.005 0.001 TYR K 105 PHE 0.010 0.002 PHE J 65 TRP 0.007 0.002 TRP F 41 HIS 0.002 0.000 HIS G 16 Details of bonding type rmsd covalent geometry : bond 0.00294 (10968) covalent geometry : angle 0.72996 (15000) hydrogen bonds : bond 0.06605 ( 612) hydrogen bonds : angle 3.55770 ( 1812) metal coordination : bond 0.00528 ( 48) Misc. bond : bond 0.04306 ( 60) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 231 time to evaluate : 0.458 Fit side-chains REVERT: A 62 ARG cc_start: 0.7590 (mtt180) cc_final: 0.7350 (mtt180) REVERT: A 81 GLN cc_start: 0.7950 (mt0) cc_final: 0.7677 (mt0) REVERT: A 82 CYS cc_start: 0.7382 (m) cc_final: 0.6807 (t) REVERT: A 93 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7843 (mt0) REVERT: B 18 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7245 (mt-10) REVERT: C 7 MET cc_start: 0.8987 (mmt) cc_final: 0.8382 (mmt) REVERT: C 27 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8253 (ttpt) REVERT: C 86 GLU cc_start: 0.8504 (mp0) cc_final: 0.8014 (mp0) REVERT: D 81 GLN cc_start: 0.7900 (mt0) cc_final: 0.7685 (mt0) REVERT: E 47 LYS cc_start: 0.8222 (mttt) cc_final: 0.7909 (mtmt) REVERT: E 86 GLU cc_start: 0.8483 (mp0) cc_final: 0.7988 (mp0) REVERT: F 82 CYS cc_start: 0.7528 (m) cc_final: 0.6967 (t) REVERT: F 86 GLU cc_start: 0.8472 (mp0) cc_final: 0.8266 (mp0) REVERT: F 93 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7753 (mt0) REVERT: G 28 ASP cc_start: 0.8147 (m-30) cc_final: 0.7794 (m-30) REVERT: G 86 GLU cc_start: 0.8533 (mp0) cc_final: 0.8240 (mp0) REVERT: H 7 MET cc_start: 0.8899 (mmt) cc_final: 0.8342 (mmt) REVERT: H 82 CYS cc_start: 0.7603 (m) cc_final: 0.6964 (t) REVERT: H 86 GLU cc_start: 0.8528 (mp0) cc_final: 0.8043 (mp0) REVERT: I 82 CYS cc_start: 0.7431 (m) cc_final: 0.6829 (t) REVERT: I 86 GLU cc_start: 0.8778 (mp0) cc_final: 0.8369 (mp0) REVERT: L 18 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7426 (mt-10) REVERT: L 28 ASP cc_start: 0.8319 (m-30) cc_final: 0.8056 (m-30) REVERT: L 82 CYS cc_start: 0.7391 (m) cc_final: 0.6799 (t) REVERT: L 86 GLU cc_start: 0.8552 (mp0) cc_final: 0.8211 (mp0) outliers start: 4 outliers final: 0 residues processed: 233 average time/residue: 0.7873 time to fit residues: 193.4512 Evaluate side-chains 211 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 210 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 69 optimal weight: 6.9990 chunk 35 optimal weight: 0.0060 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 34 GLN C 34 GLN C 71 GLN C 99 ASN D 34 GLN E 34 GLN E 81 GLN E 99 ASN F 34 GLN F 81 GLN F 99 ASN G 99 ASN H 34 GLN H 81 GLN H 99 ASN I 34 GLN I 71 GLN I 99 ASN J 81 GLN J 99 ASN K 103 GLN L 22 ASN L 81 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.136124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101167 restraints weight = 44825.176| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.68 r_work: 0.2955 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 11076 Z= 0.113 Angle : 0.705 12.777 15000 Z= 0.250 Chirality : 0.037 0.108 1512 Planarity : 0.004 0.040 1932 Dihedral : 10.872 78.162 1428 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 0.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.95 % Allowed : 10.70 % Favored : 88.35 % 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: -0.02 (0.23), residues: 1284 helix: 0.35 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -1.03 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.005 0.001 TYR A 105 PHE 0.009 0.002 PHE K 65 TRP 0.004 0.001 TRP I 41 HIS 0.002 0.001 HIS G 16 Details of bonding type rmsd covalent geometry : bond 0.00270 (10968) covalent geometry : angle 0.70535 (15000) hydrogen bonds : bond 0.05623 ( 612) hydrogen bonds : angle 3.04073 ( 1812) metal coordination : bond 0.00296 ( 48) Misc. bond : bond 0.02579 ( 60) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 0.338 Fit side-chains REVERT: A 81 GLN cc_start: 0.7998 (mt0) cc_final: 0.7752 (mt0) REVERT: A 82 CYS cc_start: 0.7466 (m) cc_final: 0.6897 (t) REVERT: A 93 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8156 (mt0) REVERT: C 27 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8329 (mtpp) REVERT: C 86 GLU cc_start: 0.8592 (mp0) cc_final: 0.8150 (mp0) REVERT: D 81 GLN cc_start: 0.8027 (mt0) cc_final: 0.7824 (mt0) REVERT: E 18 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7379 (mt-10) REVERT: E 86 GLU cc_start: 0.8638 (mp0) cc_final: 0.8129 (mp0) REVERT: F 82 CYS cc_start: 0.7552 (m) cc_final: 0.6997 (t) REVERT: F 86 GLU cc_start: 0.8559 (mp0) cc_final: 0.8342 (mp0) REVERT: F 93 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8001 (mt0) REVERT: G 86 GLU cc_start: 0.8649 (mp0) cc_final: 0.8342 (mp0) REVERT: G 93 GLN cc_start: 0.8525 (mm110) cc_final: 0.8099 (mt0) REVERT: H 7 MET cc_start: 0.8975 (mmt) cc_final: 0.8394 (mmt) REVERT: H 86 GLU cc_start: 0.8701 (mp0) cc_final: 0.8200 (mp0) REVERT: I 18 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: I 82 CYS cc_start: 0.7482 (m) cc_final: 0.6908 (t) REVERT: I 86 GLU cc_start: 0.8877 (mp0) cc_final: 0.8511 (mp0) REVERT: J 86 GLU cc_start: 0.8507 (mp0) cc_final: 0.8196 (mp0) REVERT: L 18 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7536 (mt-10) REVERT: L 82 CYS cc_start: 0.7511 (m) cc_final: 0.6994 (t) REVERT: L 86 GLU cc_start: 0.8583 (mp0) cc_final: 0.8341 (mp0) outliers start: 10 outliers final: 1 residues processed: 219 average time/residue: 0.7374 time to fit residues: 170.7185 Evaluate side-chains 204 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain I residue 18 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 35 optimal weight: 0.0020 chunk 16 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 20 optimal weight: 7.9990 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN D 99 ASN E 81 GLN E 99 ASN F 34 GLN F 81 GLN F 99 ASN H 81 GLN H 99 ASN I 99 ASN J 99 ASN L 81 GLN L 99 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.096999 restraints weight = 49862.000| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.85 r_work: 0.2885 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11076 Z= 0.143 Angle : 0.743 12.846 15000 Z= 0.277 Chirality : 0.040 0.132 1512 Planarity : 0.004 0.039 1932 Dihedral : 11.129 78.285 1428 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.70 % Allowed : 10.70 % Favored : 87.59 % 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: 0.58 (0.23), residues: 1284 helix: 0.79 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.89 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 62 TYR 0.006 0.002 TYR I 105 PHE 0.008 0.002 PHE K 65 TRP 0.003 0.001 TRP I 41 HIS 0.003 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00335 (10968) covalent geometry : angle 0.74313 (15000) hydrogen bonds : bond 0.06801 ( 612) hydrogen bonds : angle 3.23701 ( 1812) metal coordination : bond 0.00371 ( 48) Misc. bond : bond 0.02228 ( 60) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.345 Fit side-chains REVERT: A 81 GLN cc_start: 0.8184 (mt0) cc_final: 0.7905 (mt0) REVERT: A 82 CYS cc_start: 0.7523 (m) cc_final: 0.7034 (t) REVERT: A 93 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8164 (mt0) REVERT: C 7 MET cc_start: 0.9088 (mmt) cc_final: 0.8459 (mmt) REVERT: C 18 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: C 27 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8363 (mtpp) REVERT: C 86 GLU cc_start: 0.8629 (mp0) cc_final: 0.8199 (mp0) REVERT: D 81 GLN cc_start: 0.8185 (mt0) cc_final: 0.7955 (mt0) REVERT: E 18 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7521 (mt-10) REVERT: E 86 GLU cc_start: 0.8757 (mp0) cc_final: 0.8187 (mp0) REVERT: F 93 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8064 (mt0) REVERT: G 18 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: G 86 GLU cc_start: 0.8580 (mp0) cc_final: 0.8300 (mp0) REVERT: G 93 GLN cc_start: 0.8567 (mm110) cc_final: 0.8192 (mt0) REVERT: H 7 MET cc_start: 0.9037 (mmt) cc_final: 0.8419 (mmt) REVERT: H 86 GLU cc_start: 0.8733 (mp0) cc_final: 0.8269 (mp0) REVERT: I 18 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: I 82 CYS cc_start: 0.7480 (m) cc_final: 0.6944 (t) REVERT: I 86 GLU cc_start: 0.8917 (mp0) cc_final: 0.8540 (mp0) REVERT: J 86 GLU cc_start: 0.8537 (mp0) cc_final: 0.8222 (mp0) REVERT: K 18 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: L 18 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7699 (mt-10) REVERT: L 82 CYS cc_start: 0.7611 (m) cc_final: 0.7115 (t) REVERT: L 86 GLU cc_start: 0.8584 (mp0) cc_final: 0.8334 (mp0) outliers start: 18 outliers final: 3 residues processed: 213 average time/residue: 0.7657 time to fit residues: 172.1055 Evaluate side-chains 211 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain K residue 18 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 99 ASN D 71 GLN D 99 ASN F 34 GLN F 81 GLN F 99 ASN H 81 GLN H 99 ASN I 99 ASN J 81 GLN J 99 ASN K 22 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.128968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.094551 restraints weight = 44254.378| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.34 r_work: 0.2868 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11076 Z= 0.189 Angle : 0.795 13.222 15000 Z= 0.319 Chirality : 0.043 0.160 1512 Planarity : 0.004 0.048 1932 Dihedral : 11.515 78.872 1428 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.89 % Allowed : 10.51 % Favored : 87.59 % 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: 0.66 (0.23), residues: 1284 helix: 0.83 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.81 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 62 TYR 0.007 0.002 TYR H 105 PHE 0.006 0.002 PHE J 65 TRP 0.004 0.002 TRP B 41 HIS 0.003 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00452 (10968) covalent geometry : angle 0.79511 (15000) hydrogen bonds : bond 0.08199 ( 612) hydrogen bonds : angle 3.40428 ( 1812) metal coordination : bond 0.00486 ( 48) Misc. bond : bond 0.02516 ( 60) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 0.406 Fit side-chains REVERT: A 19 LYS cc_start: 0.8598 (mmtp) cc_final: 0.8159 (mtpt) REVERT: A 27 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8544 (ttpp) REVERT: A 81 GLN cc_start: 0.8242 (mt0) cc_final: 0.7970 (mt0) REVERT: A 82 CYS cc_start: 0.7436 (m) cc_final: 0.7031 (t) REVERT: A 93 GLN cc_start: 0.8440 (mm-40) cc_final: 0.8165 (mt0) REVERT: B 2 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: C 27 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8349 (mtpp) REVERT: C 86 GLU cc_start: 0.8619 (mp0) cc_final: 0.8195 (mp0) REVERT: D 81 GLN cc_start: 0.8215 (mt0) cc_final: 0.7992 (mt0) REVERT: E 18 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7344 (mp0) REVERT: E 86 GLU cc_start: 0.8704 (mp0) cc_final: 0.8150 (mp0) REVERT: F 38 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8370 (mt0) REVERT: F 82 CYS cc_start: 0.7694 (m) cc_final: 0.7223 (t) REVERT: F 93 GLN cc_start: 0.8401 (mm-40) cc_final: 0.7969 (mt0) REVERT: G 86 GLU cc_start: 0.8563 (mp0) cc_final: 0.8271 (mp0) REVERT: G 93 GLN cc_start: 0.8588 (mm110) cc_final: 0.8230 (mt0) REVERT: H 7 MET cc_start: 0.9040 (mmt) cc_final: 0.8383 (mmt) REVERT: H 18 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: H 86 GLU cc_start: 0.8736 (mp0) cc_final: 0.8202 (mp0) REVERT: I 18 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: I 82 CYS cc_start: 0.7578 (m) cc_final: 0.7128 (t) REVERT: I 86 GLU cc_start: 0.8894 (mp0) cc_final: 0.8506 (mp0) REVERT: J 86 GLU cc_start: 0.8509 (mp0) cc_final: 0.8182 (mp0) REVERT: K 18 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: L 18 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7705 (mt-10) REVERT: L 27 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8296 (ttpp) REVERT: L 82 CYS cc_start: 0.7560 (m) cc_final: 0.7144 (t) REVERT: L 86 GLU cc_start: 0.8568 (mp0) cc_final: 0.8302 (mp0) outliers start: 20 outliers final: 5 residues processed: 212 average time/residue: 0.7590 time to fit residues: 170.0122 Evaluate side-chains 213 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain L residue 27 LYS Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 66 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN F 34 GLN F 99 ASN H 34 GLN H 81 GLN H 99 ASN I 99 ASN J 99 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.130773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096153 restraints weight = 45741.124| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 3.41 r_work: 0.2883 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11076 Z= 0.153 Angle : 0.743 13.418 15000 Z= 0.286 Chirality : 0.040 0.140 1512 Planarity : 0.004 0.048 1932 Dihedral : 11.324 77.944 1428 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.42 % Allowed : 11.27 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1284 helix: 1.13 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.68 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 62 TYR 0.006 0.002 TYR I 105 PHE 0.005 0.002 PHE E 61 TRP 0.003 0.001 TRP C 41 HIS 0.003 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00361 (10968) covalent geometry : angle 0.74320 (15000) hydrogen bonds : bond 0.06972 ( 612) hydrogen bonds : angle 3.21815 ( 1812) metal coordination : bond 0.00397 ( 48) Misc. bond : bond 0.02348 ( 60) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 205 time to evaluate : 0.423 Fit side-chains REVERT: A 19 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8051 (mmtt) REVERT: A 27 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8576 (ttpp) REVERT: A 81 GLN cc_start: 0.8188 (mt0) cc_final: 0.7937 (mt0) REVERT: A 82 CYS cc_start: 0.7439 (m) cc_final: 0.7048 (t) REVERT: A 93 GLN cc_start: 0.8429 (mm-40) cc_final: 0.8178 (mt0) REVERT: C 7 MET cc_start: 0.9097 (mmt) cc_final: 0.8489 (mmt) REVERT: C 27 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8396 (mtpp) REVERT: C 86 GLU cc_start: 0.8620 (mp0) cc_final: 0.8218 (mp0) REVERT: D 81 GLN cc_start: 0.8157 (mt0) cc_final: 0.7932 (mt0) REVERT: E 18 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7564 (mt-10) REVERT: E 86 GLU cc_start: 0.8711 (mp0) cc_final: 0.8179 (mp0) REVERT: F 38 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8376 (mt0) REVERT: F 82 CYS cc_start: 0.7640 (m) cc_final: 0.7124 (t) REVERT: F 93 GLN cc_start: 0.8431 (mm-40) cc_final: 0.7968 (mt0) REVERT: G 86 GLU cc_start: 0.8571 (mp0) cc_final: 0.8288 (mp0) REVERT: G 93 GLN cc_start: 0.8571 (mm110) cc_final: 0.8248 (mt0) REVERT: H 7 MET cc_start: 0.9019 (mmt) cc_final: 0.8398 (mmt) REVERT: H 18 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: H 86 GLU cc_start: 0.8794 (mp0) cc_final: 0.8321 (mp0) REVERT: I 18 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: I 82 CYS cc_start: 0.7549 (m) cc_final: 0.7075 (t) REVERT: I 86 GLU cc_start: 0.8926 (mp0) cc_final: 0.8558 (mp0) REVERT: J 86 GLU cc_start: 0.8526 (mp0) cc_final: 0.8206 (mp0) REVERT: K 18 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: L 82 CYS cc_start: 0.7580 (m) cc_final: 0.7111 (t) REVERT: L 86 GLU cc_start: 0.8590 (mp0) cc_final: 0.8345 (mp0) outliers start: 15 outliers final: 4 residues processed: 213 average time/residue: 0.7749 time to fit residues: 174.3753 Evaluate side-chains 215 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 38 GLN Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain K residue 18 GLU Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 109 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN F 34 GLN F 99 ASN H 99 ASN I 99 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098634 restraints weight = 51858.411| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.92 r_work: 0.2907 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11076 Z= 0.119 Angle : 0.697 12.128 15000 Z= 0.256 Chirality : 0.038 0.118 1512 Planarity : 0.004 0.046 1932 Dihedral : 11.063 77.527 1428 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.14 % Allowed : 12.22 % Favored : 86.65 % 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: 1.61 (0.23), residues: 1284 helix: 1.52 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.57 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.005 0.001 TYR I 105 PHE 0.005 0.001 PHE E 61 TRP 0.004 0.001 TRP C 41 HIS 0.002 0.001 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00276 (10968) covalent geometry : angle 0.69711 (15000) hydrogen bonds : bond 0.05662 ( 612) hydrogen bonds : angle 3.00770 ( 1812) metal coordination : bond 0.00313 ( 48) Misc. bond : bond 0.02084 ( 60) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.345 Fit side-chains REVERT: A 27 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8497 (ttpp) REVERT: A 81 GLN cc_start: 0.8070 (mt0) cc_final: 0.7825 (mt0) REVERT: A 82 CYS cc_start: 0.7433 (m) cc_final: 0.7027 (t) REVERT: A 93 GLN cc_start: 0.8406 (mm-40) cc_final: 0.8186 (mt0) REVERT: C 7 MET cc_start: 0.9074 (mmt) cc_final: 0.8468 (mmt) REVERT: C 27 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8405 (mtpp) REVERT: C 86 GLU cc_start: 0.8622 (mp0) cc_final: 0.8227 (mp0) REVERT: D 81 GLN cc_start: 0.8074 (mt0) cc_final: 0.7858 (mt0) REVERT: E 86 GLU cc_start: 0.8723 (mp0) cc_final: 0.8202 (mp0) REVERT: F 82 CYS cc_start: 0.7563 (m) cc_final: 0.7021 (t) REVERT: F 93 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7977 (mt0) REVERT: G 86 GLU cc_start: 0.8582 (mp0) cc_final: 0.8304 (mp0) REVERT: G 93 GLN cc_start: 0.8534 (mm110) cc_final: 0.8213 (mt0) REVERT: H 7 MET cc_start: 0.8999 (mmt) cc_final: 0.8412 (mmt) REVERT: H 82 CYS cc_start: 0.7617 (m) cc_final: 0.7086 (t) REVERT: H 86 GLU cc_start: 0.8790 (mp0) cc_final: 0.8333 (mp0) REVERT: I 18 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: I 82 CYS cc_start: 0.7503 (m) cc_final: 0.6993 (t) REVERT: I 86 GLU cc_start: 0.8902 (mp0) cc_final: 0.8539 (mp0) REVERT: J 86 GLU cc_start: 0.8524 (mp0) cc_final: 0.8213 (mp0) REVERT: L 82 CYS cc_start: 0.7521 (m) cc_final: 0.7026 (t) REVERT: L 86 GLU cc_start: 0.8604 (mp0) cc_final: 0.8360 (mp0) outliers start: 12 outliers final: 4 residues processed: 207 average time/residue: 0.7361 time to fit residues: 161.1485 Evaluate side-chains 209 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 77 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 113 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN F 34 GLN F 99 ASN H 81 GLN H 99 ASN I 99 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.102926 restraints weight = 50340.651| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.93 r_work: 0.2957 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11076 Z= 0.098 Angle : 0.661 11.329 15000 Z= 0.228 Chirality : 0.036 0.098 1512 Planarity : 0.004 0.042 1932 Dihedral : 10.800 78.493 1428 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 0.85 % Allowed : 12.41 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.24), residues: 1284 helix: 1.93 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 62 TYR 0.004 0.001 TYR I 105 PHE 0.005 0.001 PHE G 61 TRP 0.004 0.001 TRP J 41 HIS 0.001 0.000 HIS I 5 Details of bonding type rmsd covalent geometry : bond 0.00238 (10968) covalent geometry : angle 0.66117 (15000) hydrogen bonds : bond 0.04279 ( 612) hydrogen bonds : angle 2.71761 ( 1812) metal coordination : bond 0.00251 ( 48) Misc. bond : bond 0.01732 ( 60) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.396 Fit side-chains REVERT: A 27 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8454 (mtpt) REVERT: A 81 GLN cc_start: 0.7915 (mt0) cc_final: 0.7706 (mt0) REVERT: A 82 CYS cc_start: 0.7407 (m) cc_final: 0.6891 (t) REVERT: A 93 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8135 (mt0) REVERT: C 7 MET cc_start: 0.9049 (mmt) cc_final: 0.8503 (mmt) REVERT: C 27 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8367 (mtpp) REVERT: C 86 GLU cc_start: 0.8605 (mp0) cc_final: 0.8206 (mp0) REVERT: E 86 GLU cc_start: 0.8734 (mp0) cc_final: 0.8292 (mp0) REVERT: F 82 CYS cc_start: 0.7551 (m) cc_final: 0.7060 (t) REVERT: F 93 GLN cc_start: 0.8351 (mm-40) cc_final: 0.8069 (mt0) REVERT: G 86 GLU cc_start: 0.8565 (mp0) cc_final: 0.8295 (mp0) REVERT: G 93 GLN cc_start: 0.8460 (mm110) cc_final: 0.8154 (mt0) REVERT: H 7 MET cc_start: 0.8957 (mmt) cc_final: 0.8414 (mmt) REVERT: H 82 CYS cc_start: 0.7629 (m) cc_final: 0.7067 (t) REVERT: H 86 GLU cc_start: 0.8743 (mp0) cc_final: 0.8250 (mp0) REVERT: I 82 CYS cc_start: 0.7423 (m) cc_final: 0.6922 (t) REVERT: I 86 GLU cc_start: 0.8869 (mp0) cc_final: 0.8505 (mp0) REVERT: J 86 GLU cc_start: 0.8470 (mp0) cc_final: 0.8151 (mp0) REVERT: L 82 CYS cc_start: 0.7382 (m) cc_final: 0.6847 (t) REVERT: L 86 GLU cc_start: 0.8602 (mp0) cc_final: 0.8359 (mp0) outliers start: 9 outliers final: 3 residues processed: 215 average time/residue: 0.7325 time to fit residues: 166.9067 Evaluate side-chains 211 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 206 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 71 GLN B 99 ASN C 34 GLN C 99 ASN E 99 ASN F 34 GLN F 99 ASN H 99 ASN I 99 ASN J 81 GLN J 99 ASN L 71 GLN L 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.104553 restraints weight = 43109.855| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.72 r_work: 0.2992 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11076 Z= 0.094 Angle : 0.662 11.804 15000 Z= 0.221 Chirality : 0.035 0.096 1512 Planarity : 0.004 0.039 1932 Dihedral : 10.668 80.872 1428 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Rotamer: Outliers : 0.57 % Allowed : 13.16 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.24), residues: 1284 helix: 2.28 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 62 TYR 0.003 0.001 TYR C 105 PHE 0.005 0.001 PHE C 61 TRP 0.004 0.001 TRP I 41 HIS 0.001 0.000 HIS D 5 Details of bonding type rmsd covalent geometry : bond 0.00236 (10968) covalent geometry : angle 0.66161 (15000) hydrogen bonds : bond 0.03933 ( 612) hydrogen bonds : angle 2.59493 ( 1812) metal coordination : bond 0.00261 ( 48) Misc. bond : bond 0.01668 ( 60) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 0.254 Fit side-chains REVERT: A 81 GLN cc_start: 0.7866 (mt0) cc_final: 0.7659 (mt0) REVERT: A 82 CYS cc_start: 0.7380 (m) cc_final: 0.6885 (t) REVERT: A 93 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8147 (mt0) REVERT: C 7 MET cc_start: 0.9043 (mmt) cc_final: 0.8503 (mmt) REVERT: C 27 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8334 (mtpp) REVERT: C 82 CYS cc_start: 0.7289 (m) cc_final: 0.6695 (t) REVERT: C 86 GLU cc_start: 0.8557 (mp0) cc_final: 0.8126 (mp0) REVERT: E 86 GLU cc_start: 0.8720 (mp0) cc_final: 0.8273 (mp0) REVERT: F 82 CYS cc_start: 0.7465 (m) cc_final: 0.6909 (t) REVERT: F 93 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8085 (mt0) REVERT: G 86 GLU cc_start: 0.8565 (mp0) cc_final: 0.8293 (mp0) REVERT: G 93 GLN cc_start: 0.8419 (mm110) cc_final: 0.8127 (mt0) REVERT: H 7 MET cc_start: 0.8944 (mmt) cc_final: 0.8357 (mmt) REVERT: H 82 CYS cc_start: 0.7590 (m) cc_final: 0.7060 (t) REVERT: H 86 GLU cc_start: 0.8709 (mp0) cc_final: 0.8237 (mp0) REVERT: I 82 CYS cc_start: 0.7454 (m) cc_final: 0.6996 (t) REVERT: I 86 GLU cc_start: 0.8821 (mp0) cc_final: 0.8452 (mp0) REVERT: J 86 GLU cc_start: 0.8450 (mp0) cc_final: 0.8149 (mp0) REVERT: L 82 CYS cc_start: 0.7500 (m) cc_final: 0.6850 (t) REVERT: L 86 GLU cc_start: 0.8569 (mp0) cc_final: 0.8329 (mp0) outliers start: 6 outliers final: 3 residues processed: 213 average time/residue: 0.7084 time to fit residues: 160.0930 Evaluate side-chains 207 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 203 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 55 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 71 GLN C 99 ASN F 34 GLN F 99 ASN H 99 ASN I 99 ASN J 81 GLN J 99 ASN L 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.100931 restraints weight = 48315.811| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.70 r_work: 0.2946 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11076 Z= 0.113 Angle : 0.716 14.525 15000 Z= 0.245 Chirality : 0.037 0.112 1512 Planarity : 0.004 0.038 1932 Dihedral : 10.859 82.266 1428 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.57 % Allowed : 13.16 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.23), residues: 1284 helix: 2.20 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.004 0.001 TYR I 105 PHE 0.005 0.001 PHE A 65 TRP 0.003 0.001 TRP I 41 HIS 0.003 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00270 (10968) covalent geometry : angle 0.71631 (15000) hydrogen bonds : bond 0.05056 ( 612) hydrogen bonds : angle 2.77699 ( 1812) metal coordination : bond 0.00297 ( 48) Misc. bond : bond 0.02175 ( 60) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2568 Ramachandran restraints generated. 1284 Oldfield, 0 Emsley, 1284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 208 time to evaluate : 0.434 Fit side-chains REVERT: A 27 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8405 (ttpt) REVERT: A 81 GLN cc_start: 0.7996 (mt0) cc_final: 0.7747 (mt0) REVERT: A 82 CYS cc_start: 0.7443 (m) cc_final: 0.6938 (t) REVERT: A 93 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8163 (mt0) REVERT: C 7 MET cc_start: 0.9054 (mmt) cc_final: 0.8440 (mmt) REVERT: C 27 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8372 (mtpp) REVERT: C 82 CYS cc_start: 0.7362 (m) cc_final: 0.6784 (t) REVERT: C 86 GLU cc_start: 0.8614 (mp0) cc_final: 0.8204 (mp0) REVERT: D 81 GLN cc_start: 0.7974 (mt0) cc_final: 0.7762 (mt0) REVERT: E 86 GLU cc_start: 0.8732 (mp0) cc_final: 0.8225 (mp0) REVERT: F 82 CYS cc_start: 0.7546 (m) cc_final: 0.7022 (t) REVERT: F 93 GLN cc_start: 0.8371 (mm-40) cc_final: 0.8120 (mt0) REVERT: G 86 GLU cc_start: 0.8571 (mp0) cc_final: 0.8296 (mp0) REVERT: G 93 GLN cc_start: 0.8463 (mm110) cc_final: 0.8172 (mt0) REVERT: H 7 MET cc_start: 0.8984 (mmt) cc_final: 0.8347 (mmt) REVERT: H 82 CYS cc_start: 0.7598 (m) cc_final: 0.7087 (t) REVERT: H 86 GLU cc_start: 0.8738 (mp0) cc_final: 0.8257 (mp0) REVERT: I 82 CYS cc_start: 0.7508 (m) cc_final: 0.7017 (t) REVERT: I 86 GLU cc_start: 0.8851 (mp0) cc_final: 0.8475 (mp0) REVERT: J 86 GLU cc_start: 0.8512 (mp0) cc_final: 0.8194 (mp0) REVERT: L 82 CYS cc_start: 0.7586 (m) cc_final: 0.6948 (t) REVERT: L 86 GLU cc_start: 0.8573 (mp0) cc_final: 0.8330 (mp0) outliers start: 6 outliers final: 4 residues processed: 212 average time/residue: 0.7225 time to fit residues: 162.2011 Evaluate side-chains 212 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 206 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 18 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 88 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN C 99 ASN D 99 ASN F 34 GLN F 99 ASN H 99 ASN I 99 ASN J 81 GLN J 99 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.101259 restraints weight = 42812.003| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.48 r_work: 0.2961 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 11076 Z= 0.111 Angle : 0.710 14.137 15000 Z= 0.243 Chirality : 0.037 0.110 1512 Planarity : 0.003 0.039 1932 Dihedral : 10.847 81.444 1428 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 0.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.66 % Allowed : 13.07 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.23), residues: 1284 helix: 2.23 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.25 (0.41), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 62 TYR 0.004 0.001 TYR I 105 PHE 0.004 0.001 PHE G 61 TRP 0.003 0.001 TRP I 41 HIS 0.002 0.001 HIS G 5 Details of bonding type rmsd covalent geometry : bond 0.00265 (10968) covalent geometry : angle 0.70953 (15000) hydrogen bonds : bond 0.04952 ( 612) hydrogen bonds : angle 2.78430 ( 1812) metal coordination : bond 0.00288 ( 48) Misc. bond : bond 0.02136 ( 60) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4451.72 seconds wall clock time: 76 minutes 13.60 seconds (4573.60 seconds total)