Starting phenix.real_space_refine on Fri Mar 15 06:41:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ovh_20212/03_2024/6ovh_20212_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ovh_20212/03_2024/6ovh_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ovh_20212/03_2024/6ovh_20212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ovh_20212/03_2024/6ovh_20212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ovh_20212/03_2024/6ovh_20212_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ovh_20212/03_2024/6ovh_20212_neut_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 106": "NH1" <-> "NH2" Residue "B ARG 106": "NH1" <-> "NH2" Residue "C ARG 106": "NH1" <-> "NH2" Residue "D ARG 106": "NH1" <-> "NH2" Residue "E ARG 106": "NH1" <-> "NH2" Residue "F ARG 106": "NH1" <-> "NH2" Residue "G ARG 106": "NH1" <-> "NH2" Residue "H ARG 106": "NH1" <-> "NH2" Residue "I ARG 106": "NH1" <-> "NH2" Residue "J ARG 106": "NH1" <-> "NH2" Residue "K ARG 106": "NH1" <-> "NH2" Residue "L ARG 106": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 10.74, per 1000 atoms: 0.99 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 - 3.50 Amino acid : False - 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: 4.71 Conformation dependent library (CDL) restraints added in 3.7 seconds 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... running ksdssp... Secondary structure from input PDB file: 72 helices and 0 sheets defined 77.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 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) Processing helix chain 'A' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 100 " --> pdb=" O THR A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 105 No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'B' and resid 3 through 18 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) Processing helix chain 'B' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 105 No H-bonds generated for 'chain 'B' and resid 102 through 105' Processing helix chain 'C' and resid 3 through 18 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) Processing helix chain 'C' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS C 95 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR C 97 " --> pdb=" O GLN C 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA C 100 " --> pdb=" O THR C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 105 No H-bonds generated for 'chain 'C' and resid 102 through 105' Processing helix chain 'D' and resid 3 through 18 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) Processing helix chain 'D' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 105 No H-bonds generated for 'chain 'D' and resid 102 through 105' Processing helix chain 'E' and resid 3 through 18 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) Processing helix chain 'E' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN E 93 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 100 " --> pdb=" O THR E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 105 No H-bonds generated for 'chain 'E' and resid 102 through 105' Processing helix chain 'F' and resid 3 through 18 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) Processing helix chain 'F' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR F 97 " --> pdb=" O GLN F 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 105 No H-bonds generated for 'chain 'F' and resid 102 through 105' Processing helix chain 'G' and resid 3 through 18 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) Processing helix chain 'G' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS G 95 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR G 97 " --> pdb=" O GLN G 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 105 No H-bonds generated for 'chain 'G' and resid 102 through 105' Processing helix chain 'H' and resid 3 through 18 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) Processing helix chain 'H' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 56 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 84 through 100 removed outlier: 3.560A pdb=" N GLN H 93 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS H 95 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N THR H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR H 97 " --> pdb=" O GLN H 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 105 No H-bonds generated for 'chain 'H' and resid 102 through 105' Processing helix chain 'I' and resid 3 through 18 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) Processing helix chain 'I' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 56 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 84 through 100 removed outlier: 3.562A pdb=" N GLN I 93 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LYS I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR I 97 " --> pdb=" O GLN I 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 100 " --> pdb=" O THR I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 105 No H-bonds generated for 'chain 'I' and resid 102 through 105' Processing helix chain 'J' and resid 3 through 18 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) Processing helix chain 'J' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN J 93 " --> pdb=" O ALA J 89 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU J 94 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS J 95 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR J 97 " --> pdb=" O GLN J 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA J 100 " --> pdb=" O THR J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 102 through 105 No H-bonds generated for 'chain 'J' and resid 102 through 105' Processing helix chain 'K' and resid 3 through 18 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) Processing helix chain 'K' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'K' and resid 46 through 48' Processing helix chain 'K' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU K 94 " --> pdb=" O ALA K 90 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS K 95 " --> pdb=" O ALA K 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR K 97 " --> pdb=" O GLN K 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA K 100 " --> pdb=" O THR K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 105 No H-bonds generated for 'chain 'K' and resid 102 through 105' Processing helix chain 'L' and resid 3 through 18 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) Processing helix chain 'L' and resid 23 through 39 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 46 through 48 No H-bonds generated for 'chain 'L' and resid 46 through 48' Processing helix chain 'L' and resid 56 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 84 through 100 removed outlier: 3.561A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU L 94 " --> pdb=" O ALA L 90 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS L 95 " --> pdb=" O ALA L 91 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N THR L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR L 97 " --> pdb=" O GLN L 93 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA L 100 " --> pdb=" O THR L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 105 No H-bonds generated for 'chain 'L' and resid 102 through 105' 564 hydrogen bonds defined for protein. 1704 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: 2.71 Time building geometry restraints manager: 5.10 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: 87.45 - 104.91: 228 104.91 - 122.37: 12892 122.37 - 139.83: 1856 139.83 - 157.28: 0 157.28 - 174.74: 24 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: 13528 3.42 - 4.16: 25724 4.16 - 4.90: 46761 Nonbonded interactions: 86384 Sorted by model distance: nonbonded pdb=" O HAE F 202 " pdb=" O2 HAE J 203 " model vdw 1.203 2.440 nonbonded pdb=" O HAE G 202 " pdb=" O2 HAE H 203 " model vdw 1.246 2.440 nonbonded pdb=" O HAE A 202 " pdb=" O2 HAE C 203 " model vdw 1.250 2.440 nonbonded pdb=" O HAE C 203 " pdb=" O2 HAE D 202 " model vdw 1.254 2.440 nonbonded pdb=" O HAE K 203 " pdb=" O2 HAE L 203 " model vdw 1.286 2.440 ... (remaining 86379 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.920 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: 0.000 Extract box with map and model: 4.010 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 40.840 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.820 ------------------------------------------------------------------------------- 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 : 0.014 0.207 10968 Z= 0.875 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.002 TRP F 41 HIS 0.005 0.001 HIS E 5 PHE 0.007 0.002 PHE G 61 TYR 0.006 0.002 TYR B 105 ARG 0.006 0.002 ARG G 62 *********************** 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 fitting. rotamer outliers: 48 poor density : 305 time to evaluate : 1.136 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: 1.4303 time to fit residues: 514.9552 Evaluate side-chains 235 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 101 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 34 GLN A 73 ASN A 99 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 F 99 ASN 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 L 22 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10968 Z= 0.177 Angle : 0.705 11.232 15000 Z= 0.278 Chirality : 0.037 0.123 1512 Planarity : 0.005 0.040 1932 Dihedral : 11.497 98.775 1431 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.76 % Allowed : 9.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.19), residues: 1284 helix: -1.37 (0.14), residues: 984 sheet: None (None), residues: 0 loop : -1.29 (0.29), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 41 HIS 0.002 0.001 HIS E 8 PHE 0.009 0.002 PHE B 65 TYR 0.005 0.001 TYR K 105 ARG 0.001 0.000 ARG A 62 *********************** 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 241 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 233 time to evaluate : 1.270 Fit side-chains REVERT: A 62 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7232 (mtt180) REVERT: A 81 GLN cc_start: 0.8000 (mt0) cc_final: 0.7771 (mt0) REVERT: A 82 CYS cc_start: 0.7145 (m) cc_final: 0.6865 (t) REVERT: B 18 GLU cc_start: 0.7230 (mt-10) cc_final: 0.7025 (mt-10) REVERT: B 86 GLU cc_start: 0.8190 (mp0) cc_final: 0.7739 (mp0) REVERT: C 7 MET cc_start: 0.8791 (mmt) cc_final: 0.8097 (mmt) REVERT: C 27 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8027 (ttpp) REVERT: C 86 GLU cc_start: 0.8188 (mp0) cc_final: 0.7755 (mp0) REVERT: E 47 LYS cc_start: 0.8164 (mttt) cc_final: 0.7894 (mtmt) REVERT: E 86 GLU cc_start: 0.8164 (mp0) cc_final: 0.7470 (mp0) REVERT: F 82 CYS cc_start: 0.7091 (m) cc_final: 0.6790 (t) REVERT: F 86 GLU cc_start: 0.8231 (mp0) cc_final: 0.7991 (mp0) REVERT: G 28 ASP cc_start: 0.7366 (m-30) cc_final: 0.7060 (m-30) REVERT: G 86 GLU cc_start: 0.8176 (mp0) cc_final: 0.7881 (mp0) REVERT: G 93 GLN cc_start: 0.8145 (mm110) cc_final: 0.7859 (mt0) REVERT: H 7 MET cc_start: 0.8750 (mmt) cc_final: 0.8176 (mmt) REVERT: H 86 GLU cc_start: 0.8278 (mp0) cc_final: 0.7771 (mp0) REVERT: I 82 CYS cc_start: 0.6955 (m) cc_final: 0.6596 (t) REVERT: I 86 GLU cc_start: 0.8422 (mp0) cc_final: 0.7926 (mp0) REVERT: J 86 GLU cc_start: 0.8145 (mp0) cc_final: 0.7771 (mp0) REVERT: L 18 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6837 (mt-10) REVERT: L 86 GLU cc_start: 0.8211 (mp0) cc_final: 0.7964 (mp0) outliers start: 8 outliers final: 2 residues processed: 236 average time/residue: 1.5104 time to fit residues: 378.7308 Evaluate side-chains 215 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain J residue 103 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 99 ASN C 34 GLN C 81 GLN C 99 ASN D 34 GLN E 34 GLN F 34 GLN F 81 GLN F 99 ASN G 34 GLN H 34 GLN H 81 GLN H 99 ASN I 34 GLN I 99 ASN J 99 ASN K 34 GLN K 103 GLN L 99 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10968 Z= 0.157 Angle : 0.658 11.731 15000 Z= 0.235 Chirality : 0.035 0.110 1512 Planarity : 0.004 0.036 1932 Dihedral : 10.765 77.596 1428 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 1.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.23 % Allowed : 11.74 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.23), residues: 1284 helix: 0.46 (0.16), residues: 984 sheet: None (None), residues: 0 loop : -0.88 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 41 HIS 0.002 0.001 HIS G 16 PHE 0.008 0.002 PHE K 65 TYR 0.004 0.001 TYR J 105 ARG 0.002 0.000 ARG H 62 *********************** 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 241 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 1.237 Fit side-chains REVERT: A 81 GLN cc_start: 0.7878 (mt0) cc_final: 0.7610 (mt0) REVERT: A 82 CYS cc_start: 0.7012 (m) cc_final: 0.6726 (t) REVERT: A 93 GLN cc_start: 0.7812 (mm110) cc_final: 0.7307 (mt0) REVERT: B 86 GLU cc_start: 0.8244 (mp0) cc_final: 0.7907 (mp0) REVERT: C 7 MET cc_start: 0.8815 (mmt) cc_final: 0.8187 (mmt) REVERT: C 27 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8034 (mtpp) REVERT: C 86 GLU cc_start: 0.8162 (mp0) cc_final: 0.7710 (mp0) REVERT: D 81 GLN cc_start: 0.7875 (mt0) cc_final: 0.7665 (mt0) REVERT: E 18 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6738 (mt-10) REVERT: E 86 GLU cc_start: 0.8310 (mp0) cc_final: 0.7589 (mp0) REVERT: F 86 GLU cc_start: 0.8180 (mp0) cc_final: 0.7946 (mp0) REVERT: F 93 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7518 (mt0) REVERT: G 86 GLU cc_start: 0.8182 (mp0) cc_final: 0.7869 (mp0) REVERT: G 93 GLN cc_start: 0.8091 (mm110) cc_final: 0.7803 (mt0) REVERT: H 7 MET cc_start: 0.8760 (mmt) cc_final: 0.8146 (mmt) REVERT: H 19 LYS cc_start: 0.8304 (mmtp) cc_final: 0.7843 (mtpt) REVERT: H 86 GLU cc_start: 0.8331 (mp0) cc_final: 0.7743 (mp0) REVERT: I 18 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: I 86 GLU cc_start: 0.8461 (mp0) cc_final: 0.7992 (mp0) REVERT: J 86 GLU cc_start: 0.8102 (mp0) cc_final: 0.7735 (mp0) REVERT: L 86 GLU cc_start: 0.8185 (mp0) cc_final: 0.7961 (mp0) outliers start: 13 outliers final: 2 residues processed: 238 average time/residue: 1.4284 time to fit residues: 361.7756 Evaluate side-chains 217 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain G residue 2 ASP 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 107 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 103 optimal weight: 0.3980 chunk 31 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 34 GLN C 99 ASN D 34 GLN D 99 ASN E 81 GLN F 34 GLN F 81 GLN F 99 ASN G 99 ASN H 99 ASN K 34 GLN L 99 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10968 Z= 0.204 Angle : 0.712 12.211 15000 Z= 0.271 Chirality : 0.039 0.143 1512 Planarity : 0.004 0.032 1932 Dihedral : 11.034 78.537 1428 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.80 % Allowed : 11.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1284 helix: 0.67 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -1.46 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 41 HIS 0.002 0.001 HIS D 5 PHE 0.009 0.002 PHE K 65 TYR 0.006 0.002 TYR H 105 ARG 0.003 0.000 ARG H 62 *********************** 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 239 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 220 time to evaluate : 1.220 Fit side-chains REVERT: A 27 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8140 (ttpp) REVERT: A 81 GLN cc_start: 0.8074 (mt0) cc_final: 0.7840 (mt0) REVERT: A 82 CYS cc_start: 0.7095 (m) cc_final: 0.6836 (t) REVERT: A 93 GLN cc_start: 0.7802 (mm110) cc_final: 0.7366 (mt0) REVERT: C 7 MET cc_start: 0.8875 (mmt) cc_final: 0.8147 (mmt) REVERT: C 18 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: C 27 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8062 (mtpp) REVERT: C 86 GLU cc_start: 0.8176 (mp0) cc_final: 0.7720 (mp0) REVERT: D 81 GLN cc_start: 0.8108 (mt0) cc_final: 0.7857 (mt0) REVERT: E 18 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6908 (mt-10) REVERT: E 86 GLU cc_start: 0.8385 (mp0) cc_final: 0.7694 (mp0) REVERT: F 86 GLU cc_start: 0.8171 (mp0) cc_final: 0.7951 (mp0) REVERT: F 93 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7616 (mt0) REVERT: G 18 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6933 (mt-10) REVERT: G 86 GLU cc_start: 0.8187 (mp0) cc_final: 0.7877 (mp0) REVERT: G 93 GLN cc_start: 0.8091 (mm110) cc_final: 0.7735 (mt0) REVERT: H 7 MET cc_start: 0.8827 (mmt) cc_final: 0.8146 (mmt) REVERT: H 18 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6797 (mt-10) REVERT: H 86 GLU cc_start: 0.8347 (mp0) cc_final: 0.7740 (mp0) REVERT: I 18 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: I 86 GLU cc_start: 0.8500 (mp0) cc_final: 0.8018 (mp0) REVERT: I 92 GLU cc_start: 0.8213 (tp30) cc_final: 0.7999 (tp30) REVERT: J 86 GLU cc_start: 0.8124 (mp0) cc_final: 0.7752 (mp0) REVERT: L 86 GLU cc_start: 0.8226 (mp0) cc_final: 0.7971 (mp0) outliers start: 19 outliers final: 5 residues processed: 230 average time/residue: 1.5172 time to fit residues: 371.1617 Evaluate side-chains 228 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 GLU 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 G residue 2 ASP Chi-restraints excluded: chain G residue 18 GLU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 104 optimal weight: 0.2980 chunk 29 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 34 GLN C 99 ASN D 99 ASN F 34 GLN F 99 ASN G 99 ASN H 81 GLN H 99 ASN K 34 GLN L 99 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10968 Z= 0.155 Angle : 0.639 11.146 15000 Z= 0.232 Chirality : 0.036 0.118 1512 Planarity : 0.003 0.036 1932 Dihedral : 10.798 78.174 1428 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.95 % Allowed : 13.16 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1284 helix: 1.50 (0.17), residues: 984 sheet: None (None), residues: 0 loop : -0.45 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 41 HIS 0.002 0.000 HIS D 5 PHE 0.006 0.002 PHE K 65 TYR 0.004 0.001 TYR I 105 ARG 0.002 0.000 ARG H 62 *********************** 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 230 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 220 time to evaluate : 1.150 Fit side-chains REVERT: A 27 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8013 (ttpp) REVERT: A 81 GLN cc_start: 0.7959 (mt0) cc_final: 0.7722 (mt0) REVERT: A 82 CYS cc_start: 0.7021 (m) cc_final: 0.6759 (t) REVERT: A 93 GLN cc_start: 0.7751 (mm110) cc_final: 0.7368 (mt0) REVERT: C 7 MET cc_start: 0.8841 (mmt) cc_final: 0.8214 (mmt) REVERT: C 27 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7971 (mtpp) REVERT: C 86 GLU cc_start: 0.8169 (mp0) cc_final: 0.7720 (mp0) REVERT: D 81 GLN cc_start: 0.7985 (mt0) cc_final: 0.7754 (mt0) REVERT: E 86 GLU cc_start: 0.8379 (mp0) cc_final: 0.7698 (mp0) REVERT: F 86 GLU cc_start: 0.8159 (mp0) cc_final: 0.7908 (mp0) REVERT: F 93 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7631 (mt0) REVERT: G 86 GLU cc_start: 0.8192 (mp0) cc_final: 0.7872 (mp0) REVERT: G 93 GLN cc_start: 0.8010 (mm110) cc_final: 0.7681 (mt0) REVERT: H 7 MET cc_start: 0.8784 (mmt) cc_final: 0.8137 (mmt) REVERT: H 86 GLU cc_start: 0.8333 (mp0) cc_final: 0.7726 (mp0) REVERT: I 18 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: I 86 GLU cc_start: 0.8470 (mp0) cc_final: 0.7983 (mp0) REVERT: J 86 GLU cc_start: 0.8112 (mp0) cc_final: 0.7734 (mp0) REVERT: L 86 GLU cc_start: 0.8216 (mp0) cc_final: 0.7967 (mp0) outliers start: 10 outliers final: 2 residues processed: 226 average time/residue: 1.4679 time to fit residues: 352.8015 Evaluate side-chains 222 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 217 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain B residue 96 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 99 ASN C 99 ASN D 99 ASN E 99 ASN F 34 GLN F 99 ASN G 34 GLN G 99 ASN H 99 ASN K 34 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10968 Z= 0.155 Angle : 0.640 11.399 15000 Z= 0.229 Chirality : 0.036 0.119 1512 Planarity : 0.003 0.034 1932 Dihedral : 10.736 79.144 1428 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.95 % Allowed : 13.54 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.23), residues: 1284 helix: 1.86 (0.16), residues: 984 sheet: None (None), residues: 0 loop : -0.33 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 41 HIS 0.002 0.000 HIS D 5 PHE 0.005 0.002 PHE A 65 TYR 0.004 0.001 TYR I 105 ARG 0.002 0.000 ARG H 62 *********************** 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 230 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 220 time to evaluate : 1.233 Fit side-chains REVERT: A 27 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8018 (ttpp) REVERT: A 81 GLN cc_start: 0.7930 (mt0) cc_final: 0.7680 (mt0) REVERT: A 82 CYS cc_start: 0.7004 (m) cc_final: 0.6662 (t) REVERT: A 93 GLN cc_start: 0.7756 (mm110) cc_final: 0.7387 (mt0) REVERT: C 7 MET cc_start: 0.8836 (mmt) cc_final: 0.8219 (mmt) REVERT: C 18 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: C 27 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8061 (mtpp) REVERT: C 86 GLU cc_start: 0.8184 (mp0) cc_final: 0.7725 (mp0) REVERT: D 81 GLN cc_start: 0.7951 (mt0) cc_final: 0.7719 (mt0) REVERT: E 86 GLU cc_start: 0.8383 (mp0) cc_final: 0.7700 (mp0) REVERT: F 86 GLU cc_start: 0.8150 (mp0) cc_final: 0.7932 (mp0) REVERT: F 93 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7585 (mt0) REVERT: G 86 GLU cc_start: 0.8190 (mp0) cc_final: 0.7869 (mp0) REVERT: G 93 GLN cc_start: 0.7995 (mm110) cc_final: 0.7687 (mt0) REVERT: H 7 MET cc_start: 0.8793 (mmt) cc_final: 0.8163 (mmt) REVERT: H 18 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6734 (mt-10) REVERT: H 86 GLU cc_start: 0.8334 (mp0) cc_final: 0.7669 (mp0) REVERT: I 18 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6735 (mp0) REVERT: I 86 GLU cc_start: 0.8478 (mp0) cc_final: 0.7993 (mp0) REVERT: J 86 GLU cc_start: 0.8128 (mp0) cc_final: 0.7749 (mp0) REVERT: L 86 GLU cc_start: 0.8218 (mp0) cc_final: 0.7965 (mp0) outliers start: 10 outliers final: 5 residues processed: 223 average time/residue: 1.4122 time to fit residues: 335.1590 Evaluate side-chains 228 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 218 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 18 GLU 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 H residue 18 GLU Chi-restraints excluded: chain H residue 21 ASP Chi-restraints excluded: chain I 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 111 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN B 71 GLN C 99 ASN D 99 ASN E 99 ASN F 34 GLN G 99 ASN H 81 GLN H 99 ASN K 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10968 Z= 0.149 Angle : 0.625 11.235 15000 Z= 0.222 Chirality : 0.036 0.117 1512 Planarity : 0.003 0.035 1932 Dihedral : 10.688 79.639 1428 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.95 % Allowed : 14.02 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.23), residues: 1284 helix: 2.21 (0.16), residues: 984 sheet: None (None), residues: 0 loop : -0.20 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 41 HIS 0.002 0.000 HIS G 5 PHE 0.005 0.001 PHE E 61 TYR 0.004 0.001 TYR J 105 ARG 0.002 0.000 ARG H 62 *********************** 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 233 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 223 time to evaluate : 1.188 Fit side-chains REVERT: A 27 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8019 (ttpp) REVERT: A 81 GLN cc_start: 0.7873 (mt0) cc_final: 0.7633 (mt0) REVERT: A 82 CYS cc_start: 0.6975 (m) cc_final: 0.6620 (t) REVERT: A 93 GLN cc_start: 0.7745 (mm110) cc_final: 0.7385 (mt0) REVERT: C 7 MET cc_start: 0.8822 (mmt) cc_final: 0.8205 (mmt) REVERT: C 18 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6917 (mt-10) REVERT: C 27 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8045 (mtpp) REVERT: C 86 GLU cc_start: 0.8182 (mp0) cc_final: 0.7718 (mp0) REVERT: D 81 GLN cc_start: 0.7872 (mt0) cc_final: 0.7663 (mt0) REVERT: E 86 GLU cc_start: 0.8396 (mp0) cc_final: 0.7714 (mp0) REVERT: F 86 GLU cc_start: 0.8148 (mp0) cc_final: 0.7927 (mp0) REVERT: F 93 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7625 (mt0) REVERT: G 86 GLU cc_start: 0.8185 (mp0) cc_final: 0.7863 (mp0) REVERT: G 93 GLN cc_start: 0.7963 (mm110) cc_final: 0.7672 (mt0) REVERT: H 7 MET cc_start: 0.8786 (mmt) cc_final: 0.8209 (mmt) REVERT: H 18 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: H 86 GLU cc_start: 0.8335 (mp0) cc_final: 0.7674 (mp0) REVERT: I 18 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: I 86 GLU cc_start: 0.8466 (mp0) cc_final: 0.7982 (mp0) REVERT: J 86 GLU cc_start: 0.8129 (mp0) cc_final: 0.7751 (mp0) REVERT: L 86 GLU cc_start: 0.8215 (mp0) cc_final: 0.7960 (mp0) outliers start: 10 outliers final: 2 residues processed: 226 average time/residue: 1.4082 time to fit residues: 339.2992 Evaluate side-chains 229 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 222 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain B residue 96 THR 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 H residue 18 GLU Chi-restraints excluded: chain I residue 18 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 0.0050 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN D 71 GLN D 99 ASN E 99 ASN F 34 GLN G 99 ASN H 99 ASN J 81 GLN K 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10968 Z= 0.210 Angle : 0.705 13.474 15000 Z= 0.269 Chirality : 0.040 0.152 1512 Planarity : 0.003 0.032 1932 Dihedral : 11.038 80.876 1428 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.33 % Allowed : 14.02 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.23), residues: 1284 helix: 1.97 (0.16), residues: 984 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 41 HIS 0.003 0.001 HIS D 5 PHE 0.005 0.002 PHE A 65 TYR 0.005 0.002 TYR I 105 ARG 0.003 0.001 ARG H 62 *********************** 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 241 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 227 time to evaluate : 1.288 Fit side-chains REVERT: A 27 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8035 (ttpp) REVERT: A 81 GLN cc_start: 0.8084 (mt0) cc_final: 0.7836 (mt0) REVERT: A 93 GLN cc_start: 0.7832 (mm110) cc_final: 0.7490 (mt0) REVERT: C 7 MET cc_start: 0.8870 (mmt) cc_final: 0.8187 (mmt) REVERT: C 27 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: C 86 GLU cc_start: 0.8185 (mp0) cc_final: 0.7722 (mp0) REVERT: D 81 GLN cc_start: 0.8061 (mt0) cc_final: 0.7822 (mt0) REVERT: E 86 GLU cc_start: 0.8402 (mp0) cc_final: 0.7744 (mp0) REVERT: F 86 GLU cc_start: 0.8085 (mp0) cc_final: 0.7883 (mp0) REVERT: F 93 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7667 (mt0) REVERT: G 86 GLU cc_start: 0.8194 (mp0) cc_final: 0.7870 (mp0) REVERT: G 93 GLN cc_start: 0.8022 (mm110) cc_final: 0.7742 (mt0) REVERT: H 7 MET cc_start: 0.8843 (mmt) cc_final: 0.8221 (mmt) REVERT: H 18 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6792 (mt-10) REVERT: H 86 GLU cc_start: 0.8348 (mp0) cc_final: 0.7730 (mp0) REVERT: I 18 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6746 (mp0) REVERT: I 86 GLU cc_start: 0.8495 (mp0) cc_final: 0.8006 (mp0) REVERT: J 86 GLU cc_start: 0.8140 (mp0) cc_final: 0.7760 (mp0) REVERT: K 18 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: L 86 GLU cc_start: 0.8228 (mp0) cc_final: 0.7957 (mp0) outliers start: 14 outliers final: 4 residues processed: 230 average time/residue: 1.3685 time to fit residues: 335.8595 Evaluate side-chains 232 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain B residue 96 THR 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 H residue 18 GLU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain K residue 18 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN D 71 GLN D 99 ASN E 99 ASN F 34 GLN G 99 ASN H 81 GLN H 99 ASN K 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10968 Z= 0.174 Angle : 0.666 12.589 15000 Z= 0.248 Chirality : 0.038 0.136 1512 Planarity : 0.003 0.034 1932 Dihedral : 10.917 79.399 1428 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.23 % Allowed : 14.11 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.23), residues: 1284 helix: 2.14 (0.16), residues: 984 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 41 HIS 0.003 0.001 HIS D 5 PHE 0.005 0.002 PHE A 65 TYR 0.005 0.001 TYR I 105 ARG 0.002 0.000 ARG H 62 *********************** 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 236 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 223 time to evaluate : 1.184 Fit side-chains REVERT: A 27 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8014 (ttpp) REVERT: A 81 GLN cc_start: 0.7934 (mt0) cc_final: 0.7696 (mt0) REVERT: A 93 GLN cc_start: 0.7793 (mm110) cc_final: 0.7466 (mt0) REVERT: C 7 MET cc_start: 0.8864 (mmt) cc_final: 0.8270 (mmt) REVERT: C 27 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: C 86 GLU cc_start: 0.8177 (mp0) cc_final: 0.7723 (mp0) REVERT: D 81 GLN cc_start: 0.7990 (mt0) cc_final: 0.7758 (mt0) REVERT: E 86 GLU cc_start: 0.8393 (mp0) cc_final: 0.7713 (mp0) REVERT: F 86 GLU cc_start: 0.8156 (mp0) cc_final: 0.7898 (mp0) REVERT: F 93 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7629 (mt0) REVERT: G 86 GLU cc_start: 0.8203 (mp0) cc_final: 0.7874 (mp0) REVERT: G 93 GLN cc_start: 0.7983 (mm110) cc_final: 0.7707 (mt0) REVERT: H 7 MET cc_start: 0.8812 (mmt) cc_final: 0.8177 (mmt) REVERT: H 18 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6768 (mt-10) REVERT: H 86 GLU cc_start: 0.8351 (mp0) cc_final: 0.7658 (mp0) REVERT: I 18 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: I 86 GLU cc_start: 0.8488 (mp0) cc_final: 0.8000 (mp0) REVERT: J 86 GLU cc_start: 0.8134 (mp0) cc_final: 0.7753 (mp0) REVERT: L 86 GLU cc_start: 0.8221 (mp0) cc_final: 0.7957 (mp0) outliers start: 13 outliers final: 5 residues processed: 227 average time/residue: 1.4161 time to fit residues: 342.2800 Evaluate side-chains 232 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain B residue 96 THR 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 H residue 18 GLU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 9 optimal weight: 0.0980 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN F 34 GLN G 99 ASN H 99 ASN K 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10968 Z= 0.204 Angle : 0.707 13.713 15000 Z= 0.268 Chirality : 0.039 0.150 1512 Planarity : 0.003 0.032 1932 Dihedral : 11.065 80.427 1428 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.85 % Allowed : 14.58 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.23), residues: 1284 helix: 2.00 (0.16), residues: 984 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 41 HIS 0.003 0.001 HIS G 5 PHE 0.006 0.002 PHE A 65 TYR 0.006 0.002 TYR H 105 ARG 0.003 0.000 ARG H 62 ********************** 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 234 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 225 time to evaluate : 1.286 Fit side-chains REVERT: A 27 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8036 (ttpp) REVERT: A 81 GLN cc_start: 0.8072 (mt0) cc_final: 0.7800 (mt0) REVERT: A 93 GLN cc_start: 0.7831 (mm110) cc_final: 0.7478 (mt0) REVERT: C 7 MET cc_start: 0.8870 (mmt) cc_final: 0.8176 (mmt) REVERT: C 27 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8049 (mtpp) REVERT: C 86 GLU cc_start: 0.8188 (mp0) cc_final: 0.7728 (mp0) REVERT: D 81 GLN cc_start: 0.8031 (mt0) cc_final: 0.7802 (mt0) REVERT: E 86 GLU cc_start: 0.8396 (mp0) cc_final: 0.7743 (mp0) REVERT: F 86 GLU cc_start: 0.8083 (mp0) cc_final: 0.7855 (mp0) REVERT: F 93 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7633 (mt0) REVERT: G 86 GLU cc_start: 0.8184 (mp0) cc_final: 0.7857 (mp0) REVERT: G 93 GLN cc_start: 0.8014 (mm110) cc_final: 0.7743 (mt0) REVERT: H 7 MET cc_start: 0.8838 (mmt) cc_final: 0.8210 (mmt) REVERT: H 18 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: H 86 GLU cc_start: 0.8354 (mp0) cc_final: 0.7713 (mp0) REVERT: I 18 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6725 (mp0) REVERT: I 86 GLU cc_start: 0.8497 (mp0) cc_final: 0.8010 (mp0) REVERT: J 86 GLU cc_start: 0.8144 (mp0) cc_final: 0.7763 (mp0) REVERT: L 86 GLU cc_start: 0.8231 (mp0) cc_final: 0.7960 (mp0) outliers start: 9 outliers final: 5 residues processed: 228 average time/residue: 1.4088 time to fit residues: 342.2709 Evaluate side-chains 233 residues out of total 1032 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 224 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain B residue 96 THR 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 H residue 18 GLU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain I residue 18 GLU Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN C 99 ASN D 99 ASN F 34 GLN G 99 ASN H 99 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098287 restraints weight = 48270.232| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.90 r_work: 0.2924 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2881 r_free = 0.2881 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2881 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10968 Z= 0.221 Angle : 0.720 14.040 15000 Z= 0.279 Chirality : 0.040 0.157 1512 Planarity : 0.003 0.032 1932 Dihedral : 11.164 79.862 1428 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.85 % Allowed : 14.58 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.23), residues: 1284 helix: 1.57 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -0.69 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 41 HIS 0.003 0.001 HIS G 5 PHE 0.006 0.002 PHE A 65 TYR 0.006 0.002 TYR H 105 ARG 0.003 0.001 ARG H 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5439.86 seconds wall clock time: 95 minutes 47.08 seconds (5747.08 seconds total)