Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 16:45:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/04_2023/6kpj_0748_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/04_2023/6kpj_0748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/04_2023/6kpj_0748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/04_2023/6kpj_0748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/04_2023/6kpj_0748_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/04_2023/6kpj_0748_trim_updated.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.332 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 24 5.21 5 S 120 5.16 5 C 20316 2.51 5 N 5160 2.21 5 O 5976 1.98 5 H 31225 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 62845 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "B" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "F" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "K" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 19.41, per 1000 atoms: 0.31 Number of scatterers: 62845 At special positions: 0 Unit cell: (143.64, 143.64, 143.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 24 15.00 Mg 24 11.99 O 5976 8.00 N 5160 7.00 C 20316 6.00 H 31225 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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=0, symmetry=0 Time building additional restraints: 37.52 Conformation dependent library (CDL) restraints added in 3.7 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 24 sheets defined 56.7% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 49 through 56 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 109 through 112 No H-bonds generated for 'chain 'A' and resid 109 through 112' Processing helix chain 'A' and resid 134 through 142 removed outlier: 4.725A pdb=" N GLN A 142 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.880A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 269 through 285 Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 49 through 56 Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 92 through 96 Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.726A pdb=" N GLN B 142 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.880A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 215 Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 269 through 285 Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 64 through 70 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 92 through 96 Processing helix chain 'C' and resid 109 through 112 No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 134 through 142 removed outlier: 4.725A pdb=" N GLN C 142 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 171 Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.879A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 215 Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 269 through 285 Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 49 through 56 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 83 through 90 Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 109 through 112 No H-bonds generated for 'chain 'D' and resid 109 through 112' Processing helix chain 'D' and resid 134 through 142 removed outlier: 4.725A pdb=" N GLN D 142 " --> pdb=" O ASP D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 184 through 196 removed outlier: 3.880A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 215 Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 269 through 285 Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 49 through 56 Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 83 through 90 Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 109 through 112 No H-bonds generated for 'chain 'E' and resid 109 through 112' Processing helix chain 'E' and resid 134 through 142 removed outlier: 4.726A pdb=" N GLN E 142 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 184 through 196 removed outlier: 3.879A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 215 Processing helix chain 'E' and resid 221 through 228 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 269 through 285 Processing helix chain 'E' and resid 287 through 298 Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 49 through 56 Processing helix chain 'F' and resid 64 through 70 Processing helix chain 'F' and resid 83 through 90 Processing helix chain 'F' and resid 92 through 96 Processing helix chain 'F' and resid 109 through 112 No H-bonds generated for 'chain 'F' and resid 109 through 112' Processing helix chain 'F' and resid 134 through 142 removed outlier: 4.726A pdb=" N GLN F 142 " --> pdb=" O ASP F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 184 through 196 removed outlier: 3.879A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 215 Processing helix chain 'F' and resid 221 through 228 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 255 through 267 Processing helix chain 'F' and resid 269 through 285 Processing helix chain 'F' and resid 287 through 298 Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 314 through 325 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 64 through 70 Processing helix chain 'G' and resid 83 through 90 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'G' and resid 109 through 112 No H-bonds generated for 'chain 'G' and resid 109 through 112' Processing helix chain 'G' and resid 134 through 142 removed outlier: 4.726A pdb=" N GLN G 142 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 Processing helix chain 'G' and resid 184 through 196 removed outlier: 3.880A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 215 Processing helix chain 'G' and resid 221 through 228 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 248 through 252 Processing helix chain 'G' and resid 255 through 267 Processing helix chain 'G' and resid 269 through 285 Processing helix chain 'G' and resid 287 through 298 Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 49 through 56 Processing helix chain 'H' and resid 64 through 70 Processing helix chain 'H' and resid 83 through 90 Processing helix chain 'H' and resid 92 through 96 Processing helix chain 'H' and resid 109 through 112 No H-bonds generated for 'chain 'H' and resid 109 through 112' Processing helix chain 'H' and resid 134 through 142 removed outlier: 4.725A pdb=" N GLN H 142 " --> pdb=" O ASP H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 171 Processing helix chain 'H' and resid 184 through 196 removed outlier: 3.879A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 215 Processing helix chain 'H' and resid 221 through 228 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 248 through 252 Processing helix chain 'H' and resid 255 through 267 Processing helix chain 'H' and resid 269 through 285 Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 301 through 311 Processing helix chain 'H' and resid 314 through 325 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 83 through 90 Processing helix chain 'I' and resid 92 through 96 Processing helix chain 'I' and resid 109 through 112 No H-bonds generated for 'chain 'I' and resid 109 through 112' Processing helix chain 'I' and resid 134 through 142 removed outlier: 4.725A pdb=" N GLN I 142 " --> pdb=" O ASP I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 171 Processing helix chain 'I' and resid 184 through 196 removed outlier: 3.880A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 215 Processing helix chain 'I' and resid 221 through 228 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 255 through 267 Processing helix chain 'I' and resid 269 through 285 Processing helix chain 'I' and resid 287 through 298 Processing helix chain 'I' and resid 301 through 311 Processing helix chain 'I' and resid 314 through 325 Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 49 through 56 Processing helix chain 'J' and resid 64 through 70 Processing helix chain 'J' and resid 83 through 90 Processing helix chain 'J' and resid 92 through 96 Processing helix chain 'J' and resid 109 through 112 No H-bonds generated for 'chain 'J' and resid 109 through 112' Processing helix chain 'J' and resid 134 through 142 removed outlier: 4.725A pdb=" N GLN J 142 " --> pdb=" O ASP J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 171 Processing helix chain 'J' and resid 184 through 196 removed outlier: 3.879A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 215 Processing helix chain 'J' and resid 221 through 228 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 248 through 252 Processing helix chain 'J' and resid 255 through 267 Processing helix chain 'J' and resid 269 through 285 Processing helix chain 'J' and resid 287 through 298 Processing helix chain 'J' and resid 301 through 311 Processing helix chain 'J' and resid 314 through 325 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 49 through 54 Processing helix chain 'K' and resid 64 through 70 Processing helix chain 'K' and resid 83 through 90 Processing helix chain 'K' and resid 92 through 96 Processing helix chain 'K' and resid 109 through 112 No H-bonds generated for 'chain 'K' and resid 109 through 112' Processing helix chain 'K' and resid 134 through 142 removed outlier: 4.726A pdb=" N GLN K 142 " --> pdb=" O ASP K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 171 Processing helix chain 'K' and resid 184 through 196 removed outlier: 3.879A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 215 Processing helix chain 'K' and resid 221 through 228 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 248 through 252 Processing helix chain 'K' and resid 255 through 267 Processing helix chain 'K' and resid 269 through 285 Processing helix chain 'K' and resid 287 through 298 Processing helix chain 'K' and resid 301 through 311 Processing helix chain 'K' and resid 314 through 325 Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 49 through 56 Processing helix chain 'L' and resid 64 through 70 Processing helix chain 'L' and resid 83 through 90 Processing helix chain 'L' and resid 92 through 96 Processing helix chain 'L' and resid 109 through 112 No H-bonds generated for 'chain 'L' and resid 109 through 112' Processing helix chain 'L' and resid 134 through 142 removed outlier: 4.725A pdb=" N GLN L 142 " --> pdb=" O ASP L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 184 through 196 removed outlier: 3.879A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 215 Processing helix chain 'L' and resid 221 through 228 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 248 through 252 Processing helix chain 'L' and resid 255 through 267 Processing helix chain 'L' and resid 269 through 285 Processing helix chain 'L' and resid 287 through 298 Processing helix chain 'L' and resid 301 through 311 Processing helix chain 'L' and resid 314 through 325 Processing sheet with id= A, first strand: chain 'A' and resid 19 through 21 Processing sheet with id= B, first strand: chain 'A' and resid 101 through 105 removed outlier: 3.589A pdb=" N GLN A 154 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL A 152 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA A 128 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LEU A 150 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 19 through 21 Processing sheet with id= D, first strand: chain 'B' and resid 101 through 105 removed outlier: 3.588A pdb=" N GLN B 154 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL B 152 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA B 128 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU B 150 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 19 through 21 Processing sheet with id= F, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.588A pdb=" N GLN C 154 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA C 128 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU C 150 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 19 through 21 Processing sheet with id= H, first strand: chain 'D' and resid 101 through 105 removed outlier: 3.588A pdb=" N GLN D 154 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA D 128 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU D 150 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 19 through 21 Processing sheet with id= J, first strand: chain 'E' and resid 101 through 105 removed outlier: 3.589A pdb=" N GLN E 154 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA E 128 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU E 150 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 19 through 21 Processing sheet with id= L, first strand: chain 'F' and resid 101 through 105 removed outlier: 3.589A pdb=" N GLN F 154 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET F 126 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL F 152 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA F 128 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU F 150 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 19 through 21 Processing sheet with id= N, first strand: chain 'G' and resid 101 through 105 removed outlier: 3.588A pdb=" N GLN G 154 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL G 152 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA G 128 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU G 150 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 19 through 21 Processing sheet with id= P, first strand: chain 'H' and resid 101 through 105 removed outlier: 3.589A pdb=" N GLN H 154 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET H 126 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL H 152 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA H 128 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU H 150 " --> pdb=" O ALA H 128 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 19 through 21 Processing sheet with id= R, first strand: chain 'I' and resid 101 through 105 removed outlier: 3.589A pdb=" N GLN I 154 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA I 128 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU I 150 " --> pdb=" O ALA I 128 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 19 through 21 Processing sheet with id= T, first strand: chain 'J' and resid 101 through 105 removed outlier: 3.589A pdb=" N GLN J 154 " --> pdb=" O THR J 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET J 126 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL J 152 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA J 128 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU J 150 " --> pdb=" O ALA J 128 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 19 through 21 Processing sheet with id= V, first strand: chain 'K' and resid 101 through 105 removed outlier: 3.589A pdb=" N GLN K 154 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET K 126 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL K 152 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA K 128 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU K 150 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 19 through 21 Processing sheet with id= X, first strand: chain 'L' and resid 101 through 105 removed outlier: 3.589A pdb=" N GLN L 154 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N MET L 126 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL L 152 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ALA L 128 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU L 150 " --> pdb=" O ALA L 128 " (cutoff:3.500A) 1474 hydrogen bonds defined for protein. 4350 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: 21.12 Time building geometry restraints manager: 39.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 0.99: 31208 0.99 - 1.19: 5 1.19 - 1.39: 13078 1.39 - 1.60: 18914 1.60 - 1.80: 300 Bond restraints: 63505 Sorted by residual: bond pdb=" C1B NAI A 402 " pdb=" C2B NAI A 402 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1B NAI G 402 " pdb=" C2B NAI G 402 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1B NAI D 403 " pdb=" C2B NAI D 403 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1B NAI F 403 " pdb=" C2B NAI F 403 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1B NAI H 403 " pdb=" C2B NAI H 403 " ideal model delta sigma weight residual 1.528 1.284 0.244 2.00e-02 2.50e+03 1.49e+02 ... (remaining 63500 not shown) Histogram of bond angle deviations from ideal: 55.53 - 76.52: 199 76.52 - 97.51: 118 97.51 - 118.50: 87215 118.50 - 139.49: 27497 139.49 - 160.48: 1 Bond angle restraints: 115030 Sorted by residual: angle pdb=" C GLN K 30 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 125.01 65.62 59.39 3.00e+00 1.11e-01 3.92e+02 angle pdb=" C GLN L 30 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 125.01 65.69 59.32 3.00e+00 1.11e-01 3.91e+02 angle pdb=" C LYS K 55 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 124.93 65.73 59.20 3.00e+00 1.11e-01 3.89e+02 angle pdb=" CA LYS K 56 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 114.63 55.53 59.10 3.00e+00 1.11e-01 3.88e+02 angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.71 55.72 58.99 3.00e+00 1.11e-01 3.87e+02 ... (remaining 115025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 23051 17.52 - 35.03: 1627 35.03 - 52.55: 263 52.55 - 70.07: 40 70.07 - 87.59: 24 Dihedral angle restraints: 25005 sinusoidal: 11652 harmonic: 13353 Sorted by residual: dihedral pdb=" CA VAL I 214 " pdb=" C VAL I 214 " pdb=" N LYS I 215 " pdb=" CA LYS I 215 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA VAL D 214 " pdb=" C VAL D 214 " pdb=" N LYS D 215 " pdb=" CA LYS D 215 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 dihedral pdb=" CA VAL E 214 " pdb=" C VAL E 214 " pdb=" N LYS E 215 " pdb=" CA LYS E 215 " ideal model delta harmonic sigma weight residual -180.00 -163.27 -16.73 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 25002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3883 0.071 - 0.141: 736 0.141 - 0.212: 72 0.212 - 0.282: 49 0.282 - 0.353: 24 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CB VAL L 127 " pdb=" CA VAL L 127 " pdb=" CG1 VAL L 127 " pdb=" CG2 VAL L 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CB VAL I 127 " pdb=" CA VAL I 127 " pdb=" CG1 VAL I 127 " pdb=" CG2 VAL I 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CB VAL J 127 " pdb=" CA VAL J 127 " pdb=" CG1 VAL J 127 " pdb=" CG2 VAL J 127 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 4761 not shown) Planarity restraints: 9268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA J 128 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO J 129 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO J 129 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 129 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA E 128 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO E 129 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA I 128 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO I 129 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO I 129 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO I 129 " -0.028 5.00e-02 4.00e+02 ... (remaining 9265 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.89: 553 1.89 - 2.57: 63375 2.57 - 3.25: 190358 3.25 - 3.92: 234635 3.92 - 4.60: 388194 Nonbonded interactions: 877115 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb="MG MG C 404 " model vdw 1.218 1.300 nonbonded pdb="MG MG A 401 " pdb="MG MG A 404 " model vdw 1.222 1.300 nonbonded pdb="MG MG G 401 " pdb="MG MG G 404 " model vdw 1.238 1.300 nonbonded pdb="MG MG I 401 " pdb="MG MG I 404 " model vdw 1.243 1.300 nonbonded pdb="MG MG E 401 " pdb="MG MG E 404 " model vdw 1.257 1.300 ... (remaining 877110 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 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'C' and (resid 2 through 329 or resid 401)) selection = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'H' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'I' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'J' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 329 or res \ id 401)) selection = (chain 'L' and (resid 2 through 329 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.840 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: 0.690 Extract box with map and model: 12.760 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 140.380 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.190 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:10.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 0.244 32280 Z= 0.881 Angle : 0.935 14.258 43704 Z= 0.429 Chirality : 0.060 0.353 4764 Planarity : 0.004 0.051 5484 Dihedral : 12.223 87.586 11904 Min Nonbonded Distance : 1.218 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -4.33 (0.10), residues: 3912 helix: -2.36 (0.08), residues: 2448 sheet: -2.56 (0.18), residues: 504 loop : -3.76 (0.14), residues: 960 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 2 residues processed: 442 average time/residue: 3.3920 time to fit residues: 1709.3303 Evaluate side-chains 342 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 340 time to evaluate : 3.746 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.3488 time to fit residues: 8.2897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 37 ASN A 278 ASN B 30 GLN B 37 ASN C 37 ASN C 278 ASN D 30 GLN D 37 ASN D 278 ASN E 37 ASN E 278 ASN F 30 GLN F 37 ASN F 278 ASN G 30 GLN G 37 ASN H 30 GLN H 37 ASN I 30 GLN I 37 ASN I 278 ASN J 30 GLN J 37 ASN J 278 ASN K 30 GLN K 37 ASN K 278 ASN K 312 GLN L 30 GLN L 37 ASN L 278 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 32280 Z= 0.243 Angle : 0.688 16.860 43704 Z= 0.349 Chirality : 0.131 1.759 4764 Planarity : 0.003 0.076 5484 Dihedral : 7.007 60.617 4452 Min Nonbonded Distance : 1.131 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % 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: -1.80 (0.12), residues: 3912 helix: -0.38 (0.10), residues: 2448 sheet: -1.65 (0.20), residues: 540 loop : -2.75 (0.17), residues: 924 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 365 time to evaluate : 3.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 18 residues processed: 378 average time/residue: 3.1436 time to fit residues: 1369.7175 Evaluate side-chains 346 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 328 time to evaluate : 3.829 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 5 residues processed: 16 average time/residue: 1.4804 time to fit residues: 36.0409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 chunk 237 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN B 249 GLN B 278 ASN D 30 GLN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN G 30 GLN G 249 GLN G 278 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 30 GLN H 278 ASN I 30 GLN J 30 GLN J 249 GLN K 253 HIS L 30 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.041 32280 Z= 0.448 Angle : 0.747 15.972 43704 Z= 0.387 Chirality : 0.131 1.667 4764 Planarity : 0.003 0.031 5484 Dihedral : 7.431 73.315 4452 Min Nonbonded Distance : 1.119 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: -1.14 (0.13), residues: 3912 helix: 0.12 (0.10), residues: 2400 sheet: -1.07 (0.22), residues: 540 loop : -2.54 (0.17), residues: 972 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 324 time to evaluate : 3.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 19 residues processed: 342 average time/residue: 3.1547 time to fit residues: 1249.0528 Evaluate side-chains 322 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 303 time to evaluate : 3.876 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 14 average time/residue: 0.7167 time to fit residues: 21.6128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 96 GLN B 30 GLN B 96 GLN C 96 GLN D 30 GLN E 30 GLN F 30 GLN G 30 GLN H 30 GLN H 96 GLN I 30 GLN J 30 GLN J 297 GLN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 GLN L 96 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 32280 Z= 0.224 Angle : 0.667 17.032 43704 Z= 0.338 Chirality : 0.133 1.696 4764 Planarity : 0.002 0.030 5484 Dihedral : 6.856 67.282 4452 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: -0.16 (0.13), residues: 3912 helix: 0.83 (0.10), residues: 2400 sheet: -0.74 (0.23), residues: 540 loop : -1.95 (0.18), residues: 972 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 368 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 20 residues processed: 381 average time/residue: 3.0241 time to fit residues: 1342.6533 Evaluate side-chains 336 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 316 time to evaluate : 3.787 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 13 residues processed: 12 average time/residue: 1.1997 time to fit residues: 24.8633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN B 297 GLN D 30 GLN D 96 GLN E 30 GLN E 96 GLN F 30 GLN G 30 GLN H 30 GLN I 30 GLN I 96 GLN J 30 GLN K 30 GLN K 96 GLN L 30 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 32280 Z= 0.287 Angle : 0.678 16.933 43704 Z= 0.346 Chirality : 0.134 1.700 4764 Planarity : 0.002 0.030 5484 Dihedral : 6.753 66.817 4452 Min Nonbonded Distance : 1.130 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.26 (0.14), residues: 3912 helix: 1.09 (0.10), residues: 2388 sheet: -0.51 (0.23), residues: 540 loop : -1.58 (0.19), residues: 984 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 320 time to evaluate : 3.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 18 residues processed: 335 average time/residue: 3.2083 time to fit residues: 1258.4898 Evaluate side-chains 316 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 298 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 13 residues processed: 9 average time/residue: 1.7454 time to fit residues: 25.4069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 371 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN D 30 GLN D 96 GLN E 30 GLN E 96 GLN H 30 GLN H 96 GLN I 30 GLN K 96 GLN L 30 GLN L 96 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 32280 Z= 0.188 Angle : 0.655 17.209 43704 Z= 0.329 Chirality : 0.134 1.710 4764 Planarity : 0.002 0.026 5484 Dihedral : 6.240 62.454 4452 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.73 (0.14), residues: 3912 helix: 1.39 (0.11), residues: 2388 sheet: -0.25 (0.23), residues: 540 loop : -1.24 (0.20), residues: 984 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 312 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 9 residues processed: 326 average time/residue: 3.1495 time to fit residues: 1187.1740 Evaluate side-chains 307 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 298 time to evaluate : 3.804 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 2.7866 time to fit residues: 7.9871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 370 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 96 GLN B 30 GLN B 96 GLN C 96 GLN D 30 GLN E 30 GLN E 96 GLN F 30 GLN G 30 GLN H 30 GLN H 96 GLN I 30 GLN J 30 GLN K 96 GLN L 30 GLN L 96 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 32280 Z= 0.307 Angle : 0.686 16.927 43704 Z= 0.349 Chirality : 0.134 1.703 4764 Planarity : 0.002 0.027 5484 Dihedral : 6.439 67.176 4452 Min Nonbonded Distance : 1.115 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.65 (0.14), residues: 3912 helix: 1.31 (0.10), residues: 2388 sheet: -0.24 (0.23), residues: 540 loop : -1.25 (0.20), residues: 984 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 289 time to evaluate : 3.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 301 average time/residue: 3.2610 time to fit residues: 1139.1790 Evaluate side-chains 293 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 283 time to evaluate : 3.928 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 2.5758 time to fit residues: 11.0946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 7.9990 chunk 147 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 290 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 96 GLN B 30 GLN B 96 GLN C 96 GLN D 30 GLN D 96 GLN E 30 GLN E 96 GLN E 154 GLN F 30 GLN G 30 GLN H 30 GLN I 30 GLN J 30 GLN K 96 GLN L 30 GLN L 96 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 32280 Z= 0.289 Angle : 0.684 16.965 43704 Z= 0.347 Chirality : 0.134 1.701 4764 Planarity : 0.002 0.026 5484 Dihedral : 6.405 68.563 4452 Min Nonbonded Distance : 1.118 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.72 (0.14), residues: 3912 helix: 1.35 (0.10), residues: 2388 sheet: -0.19 (0.23), residues: 540 loop : -1.18 (0.20), residues: 984 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 283 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 293 average time/residue: 3.3149 time to fit residues: 1142.0730 Evaluate side-chains 286 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 277 time to evaluate : 3.804 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 4.7933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 3.9990 chunk 354 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 344 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 150 optimal weight: 4.9990 chunk 270 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 311 optimal weight: 0.8980 chunk 326 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 96 GLN B 30 GLN B 96 GLN C 96 GLN D 30 GLN D 96 GLN E 30 GLN E 96 GLN F 30 GLN G 30 GLN H 30 GLN H 96 GLN I 30 GLN J 30 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 32280 Z= 0.185 Angle : 0.665 17.247 43704 Z= 0.332 Chirality : 0.134 1.708 4764 Planarity : 0.002 0.024 5484 Dihedral : 5.941 61.732 4452 Min Nonbonded Distance : 1.149 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.99 (0.14), residues: 3912 helix: 1.55 (0.10), residues: 2412 sheet: -0.05 (0.23), residues: 540 loop : -1.15 (0.21), residues: 960 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 292 time to evaluate : 3.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 301 average time/residue: 3.1517 time to fit residues: 1098.1346 Evaluate side-chains 289 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 279 time to evaluate : 3.806 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 2.0877 time to fit residues: 7.2386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 7.9990 chunk 364 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 253 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 9.9990 chunk 304 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 96 GLN B 30 GLN B 96 GLN C 96 GLN D 30 GLN D 96 GLN E 96 GLN G 30 GLN H 96 GLN I 30 GLN K 96 GLN L 96 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 32280 Z= 0.222 Angle : 0.671 17.140 43704 Z= 0.336 Chirality : 0.134 1.703 4764 Planarity : 0.002 0.023 5484 Dihedral : 5.801 61.455 4452 Min Nonbonded Distance : 1.133 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 1.05 (0.14), residues: 3912 helix: 1.56 (0.10), residues: 2424 sheet: -0.05 (0.23), residues: 540 loop : -1.00 (0.21), residues: 948 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 282 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 291 average time/residue: 3.1339 time to fit residues: 1057.2647 Evaluate side-chains 284 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 275 time to evaluate : 3.761 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 4.7059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 96 GLN B 30 GLN B 96 GLN C 96 GLN D 96 GLN E 96 GLN G 297 GLN I 30 GLN K 96 GLN K 297 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.078880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.059141 restraints weight = 236361.842| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.21 r_work: 0.2711 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 32280 Z= 0.305 Angle : 0.690 16.950 43704 Z= 0.349 Chirality : 0.134 1.699 4764 Planarity : 0.002 0.025 5484 Dihedral : 5.965 66.780 4452 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % 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: 0.92 (0.14), residues: 3912 helix: 1.44 (0.10), residues: 2400 sheet: -0.19 (0.23), residues: 540 loop : -0.91 (0.21), residues: 972 =============================================================================== Job complete usr+sys time: 18010.96 seconds wall clock time: 310 minutes 5.65 seconds (18605.65 seconds total)