Starting phenix.real_space_refine on Thu Feb 15 00:57:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/02_2024/6kpj_0748_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/02_2024/6kpj_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_0748/02_2024/6kpj_0748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/02_2024/6kpj_0748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/02_2024/6kpj_0748_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kpj_0748/02_2024/6kpj_0748_trim_updated.pdb" } resolution = 2.56 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= -0.001 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 20.00, per 1000 atoms: 0.32 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: 38.66 Conformation dependent library (CDL) restraints added in 4.7 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: 6.97 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: 40.88 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: 27031 17.52 - 35.03: 2150 35.03 - 52.55: 623 52.55 - 70.07: 159 70.07 - 87.59: 26 Dihedral angle restraints: 29989 sinusoidal: 16636 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 29986 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: 2.320 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: 0.860 Extract box with map and model: 11.220 Check model and map are aligned: 0.680 Set scattering table: 0.430 Process input model: 151.870 Find NCS groups from input model: 2.790 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:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.230 ------------------------------------------------------------------------------- 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 : 13.400 87.586 12504 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 % Allowed : 2.93 % Favored : 97.07 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 198 HIS 0.003 0.001 HIS E 140 PHE 0.012 0.002 PHE J 288 TYR 0.008 0.001 TYR L 87 ARG 0.001 0.000 ARG F 28 *********************** 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 : 3.723 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 REVERT: C 26 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8106 (mp10) REVERT: C 30 GLN cc_start: 0.8591 (mt0) cc_final: 0.8287 (mm110) REVERT: D 308 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8261 (mm-30) REVERT: E 187 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7753 (tm-30) REVERT: F 187 GLU cc_start: 0.8365 (tm-30) cc_final: 0.8135 (tm-30) REVERT: G 3 LYS cc_start: 0.9117 (mttt) cc_final: 0.8781 (mmpt) REVERT: H 187 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7866 (tm-30) REVERT: J 187 GLU cc_start: 0.8254 (tm-30) cc_final: 0.8031 (tm-30) REVERT: K 308 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8207 (mm-30) REVERT: L 187 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7895 (tm-30) outliers start: 0 outliers final: 2 residues processed: 442 average time/residue: 3.4669 time to fit residues: 1744.9429 Evaluate side-chains 341 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 339 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain G residue 104 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32280 Z= 0.235 Angle : 0.686 17.001 43704 Z= 0.348 Chirality : 0.134 1.807 4764 Planarity : 0.003 0.077 5484 Dihedral : 8.329 88.171 5057 Min Nonbonded Distance : 1.140 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.44 % Allowed : 8.90 % Favored : 89.67 % 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: -1.79 (0.12), residues: 3912 helix: -0.38 (0.10), residues: 2448 sheet: -1.65 (0.20), residues: 540 loop : -2.72 (0.17), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 198 HIS 0.003 0.001 HIS I 140 PHE 0.007 0.001 PHE K 288 TYR 0.009 0.001 TYR L 217 ARG 0.007 0.000 ARG F 274 *********************** 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 414 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 368 time to evaluate : 3.736 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: A 96 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: B 99 LYS cc_start: 0.8566 (pmtt) cc_final: 0.7677 (pmtt) REVERT: B 215 LYS cc_start: 0.9210 (mppt) cc_final: 0.8927 (mttp) REVERT: C 26 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8395 (mm110) REVERT: C 96 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8466 (mp10) REVERT: C 99 LYS cc_start: 0.8562 (pmtt) cc_final: 0.7748 (pmtt) REVERT: C 215 LYS cc_start: 0.9177 (mppt) cc_final: 0.8875 (mttp) REVERT: E 187 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8071 (tm-30) REVERT: F 26 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8379 (mp10) REVERT: G 3 LYS cc_start: 0.9191 (mttt) cc_final: 0.8814 (mmpt) REVERT: H 96 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8299 (mp10) REVERT: H 131 MET cc_start: 0.6414 (mtm) cc_final: 0.5052 (mtm) REVERT: J 3 LYS cc_start: 0.9202 (mttt) cc_final: 0.8821 (mmpt) REVERT: K 187 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8176 (tm-30) REVERT: L 96 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: L 131 MET cc_start: 0.6581 (mtm) cc_final: 0.5271 (mtm) REVERT: L 187 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8209 (tm-30) outliers start: 46 outliers final: 15 residues processed: 381 average time/residue: 3.1616 time to fit residues: 1385.5830 Evaluate side-chains 358 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 339 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain J residue 96 GLN Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain L residue 96 GLN 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: 4.9990 chunk 290 optimal weight: 8.9990 chunk 237 optimal weight: 0.0980 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 311 optimal weight: 10.0000 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 280 optimal weight: 7.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 278 ASN B 30 GLN B 249 GLN 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: 0.8662 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 32280 Z= 0.328 Angle : 0.696 16.109 43704 Z= 0.359 Chirality : 0.130 1.674 4764 Planarity : 0.003 0.034 5484 Dihedral : 7.304 75.987 5052 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.00 % Allowed : 9.83 % Favored : 88.17 % 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: -0.76 (0.13), residues: 3912 helix: 0.37 (0.10), residues: 2400 sheet: -0.93 (0.22), residues: 540 loop : -2.25 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 198 HIS 0.007 0.002 HIS C 196 PHE 0.011 0.001 PHE L 288 TYR 0.012 0.001 TYR E 217 ARG 0.002 0.000 ARG B 274 *********************** 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 407 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 343 time to evaluate : 3.765 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: A 96 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8323 (mp10) REVERT: B 96 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8351 (mp10) REVERT: B 249 GLN cc_start: 0.9553 (OUTLIER) cc_final: 0.9283 (pp30) REVERT: C 96 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8332 (mp10) REVERT: D 96 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8610 (mp10) REVERT: E 96 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8341 (mp10) REVERT: F 26 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8524 (mp10) REVERT: F 96 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8562 (mp10) REVERT: G 3 LYS cc_start: 0.9257 (mttt) cc_final: 0.8837 (mmpt) REVERT: G 96 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8352 (mp10) REVERT: G 249 GLN cc_start: 0.9506 (OUTLIER) cc_final: 0.9283 (pp30) REVERT: H 96 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8333 (mp10) REVERT: H 131 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.5402 (mtm) REVERT: J 3 LYS cc_start: 0.9237 (mttt) cc_final: 0.8881 (mmpt) REVERT: J 215 LYS cc_start: 0.9140 (mttt) cc_final: 0.8937 (mttp) REVERT: J 249 GLN cc_start: 0.9540 (OUTLIER) cc_final: 0.9287 (pp30) REVERT: K 96 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8344 (mp10) REVERT: K 131 MET cc_start: 0.7352 (mpt) cc_final: 0.7053 (mmm) REVERT: L 96 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: L 131 MET cc_start: 0.6686 (OUTLIER) cc_final: 0.5403 (mtm) outliers start: 64 outliers final: 18 residues processed: 364 average time/residue: 3.2087 time to fit residues: 1356.1860 Evaluate side-chains 332 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 299 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 96 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 249 GLN Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 96 GLN Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain F residue 96 GLN Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain G residue 249 GLN Chi-restraints excluded: chain H residue 96 GLN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 104 ASP Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 96 GLN Chi-restraints excluded: chain L residue 96 GLN Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 201 ILE 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: 2.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 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: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 278 ASN D 30 GLN E 30 GLN F 30 GLN F 297 GLN G 30 GLN H 30 GLN I 30 GLN J 30 GLN J 297 GLN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32280 Z= 0.271 Angle : 0.670 17.001 43704 Z= 0.344 Chirality : 0.134 1.705 4764 Planarity : 0.002 0.034 5484 Dihedral : 6.802 73.718 5052 Min Nonbonded Distance : 1.138 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.62 % Allowed : 11.39 % Favored : 86.99 % 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: -0.14 (0.13), residues: 3912 helix: 0.82 (0.10), residues: 2400 sheet: -0.67 (0.23), residues: 540 loop : -1.91 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 198 HIS 0.004 0.001 HIS C 196 PHE 0.009 0.001 PHE G 288 TYR 0.008 0.001 TYR L 300 ARG 0.001 0.000 ARG G 35 *********************** 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 395 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 343 time to evaluate : 3.719 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: A 131 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6283 (mmm) REVERT: B 96 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8353 (mp10) REVERT: C 96 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8340 (mp10) REVERT: F 26 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8550 (mp10) REVERT: G 3 LYS cc_start: 0.9265 (mttt) cc_final: 0.8876 (mmpt) REVERT: G 96 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8494 (mp10) REVERT: H 131 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.5388 (mtm) REVERT: I 96 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8287 (mp10) REVERT: J 3 LYS cc_start: 0.9247 (mttt) cc_final: 0.8884 (mmpt) REVERT: L 131 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.5372 (mtm) outliers start: 52 outliers final: 13 residues processed: 354 average time/residue: 3.0410 time to fit residues: 1244.9057 Evaluate side-chains 333 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 313 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 96 GLN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain C residue 96 GLN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain G residue 96 GLN Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 249 GLN Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 4 THR Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 201 ILE Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 250 MET Chi-restraints excluded: chain L residue 321 GLU 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: 4.9990 chunk 5 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 333 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 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 B 30 GLN D 30 GLN E 30 GLN G 30 GLN H 30 GLN I 30 GLN L 30 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3681 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= 0.215 Angle : 0.649 17.080 43704 Z= 0.330 Chirality : 0.134 1.703 4764 Planarity : 0.002 0.032 5484 Dihedral : 6.495 74.491 5052 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.15 % Allowed : 12.27 % Favored : 86.58 % 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: 0.46 (0.14), residues: 3912 helix: 1.21 (0.10), residues: 2388 sheet: -0.38 (0.24), residues: 540 loop : -1.41 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 198 HIS 0.003 0.001 HIS I 196 PHE 0.008 0.001 PHE I 288 TYR 0.007 0.001 TYR L 300 ARG 0.001 0.000 ARG F 130 *********************** 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 375 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 338 time to evaluate : 3.726 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: A 131 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.6293 (mmm) REVERT: F 26 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8495 (mp10) REVERT: G 3 LYS cc_start: 0.9265 (mttt) cc_final: 0.8877 (mmpt) REVERT: H 131 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5278 (mtm) REVERT: I 96 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: J 3 LYS cc_start: 0.9233 (mttt) cc_final: 0.8885 (mmpt) REVERT: L 131 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.5195 (mtm) outliers start: 37 outliers final: 14 residues processed: 343 average time/residue: 3.1769 time to fit residues: 1265.2487 Evaluate side-chains 327 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 309 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain I residue 96 GLN Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 321 GLU 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: 2.9990 chunk 73 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.6980 chunk 308 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 195 optimal weight: 6.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 E 30 GLN E 96 GLN F 30 GLN G 30 GLN H 30 GLN I 30 GLN J 30 GLN K 96 GLN L 30 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3879 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= 0.213 Angle : 0.651 17.114 43704 Z= 0.330 Chirality : 0.134 1.698 4764 Planarity : 0.002 0.030 5484 Dihedral : 6.404 76.272 5052 Min Nonbonded Distance : 1.137 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.97 % Allowed : 12.73 % Favored : 86.30 % 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: 1.36 (0.10), residues: 2412 sheet: -0.11 (0.24), residues: 540 loop : -1.32 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 198 HIS 0.003 0.001 HIS E 196 PHE 0.008 0.001 PHE D 288 TYR 0.006 0.001 TYR C 304 ARG 0.001 0.000 ARG E 130 *********************** 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 355 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 324 time to evaluate : 3.695 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: A 131 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6333 (mmm) REVERT: B 215 LYS cc_start: 0.9275 (OUTLIER) cc_final: 0.9008 (mttp) REVERT: C 215 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8993 (mttp) REVERT: F 26 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8500 (mp10) REVERT: F 215 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.9035 (mttp) REVERT: G 3 LYS cc_start: 0.9260 (mttt) cc_final: 0.8874 (mmpt) REVERT: H 131 MET cc_start: 0.6413 (OUTLIER) cc_final: 0.5183 (mtm) REVERT: J 3 LYS cc_start: 0.9231 (mttt) cc_final: 0.8890 (mmpt) REVERT: K 131 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6152 (mmm) outliers start: 31 outliers final: 10 residues processed: 329 average time/residue: 3.0949 time to fit residues: 1181.8799 Evaluate side-chains 316 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 300 time to evaluate : 3.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 215 LYS Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 215 LYS Chi-restraints excluded: chain E residue 215 LYS Chi-restraints excluded: chain F residue 215 LYS Chi-restraints excluded: chain F residue 321 GLU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain I residue 201 ILE Chi-restraints excluded: chain J residue 321 GLU Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain L residue 321 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.0980 chunk 41 optimal weight: 4.9990 chunk 211 optimal weight: 0.6980 chunk 271 optimal weight: 9.9990 chunk 210 optimal weight: 0.7980 chunk 312 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: