Starting phenix.real_space_refine on Thu Feb 15 05:09:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqj_0752/02_2024/6kqj_0752_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqj_0752/02_2024/6kqj_0752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqj_0752/02_2024/6kqj_0752.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqj_0752/02_2024/6kqj_0752.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqj_0752/02_2024/6kqj_0752_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqj_0752/02_2024/6kqj_0752_trim_updated.pdb" } resolution = 2.54 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= -0.005 sd= 0.370 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 48 5.49 5 Mg 24 5.21 5 S 120 5.16 5 C 20568 2.51 5 N 5244 2.21 5 O 6144 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 ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 63373 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: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "B" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "C" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "D" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "E" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "F" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "G" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "H" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "I" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "J" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "K" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "L" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1BANAI A 402 " occ=0.62 ... (86 atoms not shown) pdb=" PN BNAI A 402 " occ=0.38 residue: pdb=" C1BANAI B 403 " occ=0.63 ... (86 atoms not shown) pdb=" PN BNAI B 403 " occ=0.37 residue: pdb=" C1BANAI C 402 " occ=0.63 ... (86 atoms not shown) pdb=" PN BNAI C 402 " occ=0.37 residue: pdb=" C1BANAI D 403 " occ=0.63 ... (86 atoms not shown) pdb=" PN BNAI D 403 " occ=0.37 residue: pdb=" C1BANAI E 402 " occ=0.63 ... (86 atoms not shown) pdb=" PN BNAI E 402 " occ=0.37 residue: pdb=" C1BANAI F 403 " occ=0.63 ... (86 atoms not shown) pdb=" PN BNAI F 403 " occ=0.37 residue: pdb=" C1BANAI G 402 " occ=0.65 ... (86 atoms not shown) pdb=" PN BNAI G 402 " occ=0.35 residue: pdb=" C1BANAI H 403 " occ=0.64 ... (86 atoms not shown) pdb=" PN BNAI H 403 " occ=0.36 residue: pdb=" C1BANAI I 402 " occ=0.63 ... (86 atoms not shown) pdb=" PN BNAI I 402 " occ=0.37 residue: pdb=" C1BANAI J 403 " occ=0.64 ... (86 atoms not shown) pdb=" PN BNAI J 403 " occ=0.36 residue: pdb=" C1BANAI K 402 " occ=0.64 ... (86 atoms not shown) pdb=" PN BNAI K 402 " occ=0.36 residue: pdb=" C1BANAI L 403 " occ=0.63 ... (86 atoms not shown) pdb=" PN BNAI L 403 " occ=0.37 Time building chain proxies: 20.18, per 1000 atoms: 0.32 Number of scatterers: 63373 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 48 15.00 Mg 24 11.99 O 6144 8.00 N 5244 7.00 C 20568 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: 38.73 Conformation dependent library (CDL) restraints added in 4.6 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 12 sheets defined 56.6% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.82 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 97 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 140 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 216 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 284 Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.574A pdb=" N THR A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 217 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 284 Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.575A pdb=" N THR B 311 " --> pdb=" O TRP B 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'C' and resid 160 through 171 Processing helix chain 'C' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 217 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 284 Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'C' and resid 301 through 311 removed outlier: 3.575A pdb=" N THR C 311 " --> pdb=" O TRP C 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 217 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 284 Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'D' and resid 301 through 311 removed outlier: 3.575A pdb=" N THR D 311 " --> pdb=" O TRP D 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 217 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 284 Processing helix chain 'E' and resid 287 through 298 Processing helix chain 'E' and resid 301 through 311 removed outlier: 3.575A pdb=" N THR E 311 " --> pdb=" O TRP E 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 217 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 284 Processing helix chain 'F' and resid 287 through 298 Processing helix chain 'F' and resid 301 through 311 removed outlier: 3.574A pdb=" N THR F 311 " --> pdb=" O TRP F 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'G' and resid 160 through 171 Processing helix chain 'G' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 198 through 216 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 284 Processing helix chain 'G' and resid 287 through 298 Processing helix chain 'G' and resid 301 through 311 removed outlier: 3.574A pdb=" N THR G 311 " --> pdb=" O TRP G 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'H' and resid 160 through 171 Processing helix chain 'H' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 217 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 284 Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 301 through 311 removed outlier: 3.575A pdb=" N THR H 311 " --> pdb=" O TRP H 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'I' and resid 160 through 171 Processing helix chain 'I' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 217 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 284 Processing helix chain 'I' and resid 287 through 298 Processing helix chain 'I' and resid 301 through 311 removed outlier: 3.574A pdb=" N THR I 311 " --> pdb=" O TRP I 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'J' and resid 160 through 171 Processing helix chain 'J' and resid 184 through 196 removed outlier: 3.807A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 217 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 284 Processing helix chain 'J' and resid 287 through 298 Processing helix chain 'J' and resid 301 through 311 removed outlier: 3.574A pdb=" N THR J 311 " --> pdb=" O TRP J 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'K' and resid 160 through 171 Processing helix chain 'K' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 198 through 217 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 284 Processing helix chain 'K' and resid 287 through 298 Processing helix chain 'K' and resid 301 through 311 removed outlier: 3.575A pdb=" N THR K 311 " --> pdb=" O TRP K 307 " (cutoff:3.500A) 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 97 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 140 Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 184 through 196 removed outlier: 3.808A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 217 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 284 Processing helix chain 'L' and resid 287 through 298 Processing helix chain 'L' and resid 301 through 311 removed outlier: 3.575A pdb=" N THR L 311 " --> pdb=" O TRP L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 325 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 73 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 21 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 75 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 102 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP A 104 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL A 152 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA A 128 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU A 150 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL B 73 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE B 21 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 75 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 102 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP B 104 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL B 152 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B 128 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU B 150 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.555A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL C 73 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE C 21 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU C 75 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C 102 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP C 104 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE C 105 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA C 128 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU C 150 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 73 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE D 21 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU D 75 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL D 102 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU D 76 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP D 104 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE D 105 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA D 128 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU D 150 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 73 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE E 21 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU E 75 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL E 102 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU E 76 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP E 104 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE E 105 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA E 128 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU E 150 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL F 73 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE F 21 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU F 75 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL F 102 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU F 76 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP F 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE F 105 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET F 126 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL F 152 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA F 128 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU F 150 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL G 73 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE G 21 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU G 75 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL G 102 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU G 76 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP G 104 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE G 105 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL G 152 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA G 128 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU G 150 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL H 73 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE H 21 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU H 75 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU H 76 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP H 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET H 126 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL H 152 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA H 128 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU H 150 " --> pdb=" O ALA H 128 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.555A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL I 73 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE I 21 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU I 75 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL I 102 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU I 76 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP I 104 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA I 128 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU I 150 " --> pdb=" O ALA I 128 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL J 73 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE J 21 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU J 75 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL J 102 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU J 76 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP J 104 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE J 105 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET J 126 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL J 152 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA J 128 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LEU J 150 " --> pdb=" O ALA J 128 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL K 73 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE K 21 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU K 75 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL K 102 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N LEU K 76 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ASP K 104 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE K 105 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N MET K 126 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL K 152 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA K 128 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N LEU K 150 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.556A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL L 73 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE L 21 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU L 75 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL L 102 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU L 76 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP L 104 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE L 105 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET L 126 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL L 152 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA L 128 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N LEU L 150 " --> pdb=" O ALA L 128 " (cutoff:3.500A) 1448 hydrogen bonds defined for protein. 4272 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: 21.25 Time building geometry restraints manager: 40.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 31213 1.03 - 1.22: 36 1.22 - 1.42: 13567 1.42 - 1.61: 18893 1.61 - 1.80: 372 Bond restraints: 64081 Sorted by residual: bond pdb=" C SER A 220 " pdb=" N PRO A 221 " ideal model delta sigma weight residual 1.334 1.548 -0.213 1.51e-02 4.39e+03 2.00e+02 bond pdb=" C SER G 220 " pdb=" N PRO G 221 " ideal model delta sigma weight residual 1.334 1.547 -0.213 1.51e-02 4.39e+03 1.99e+02 bond pdb=" C1BANAI I 402 " pdb=" C2BANAI I 402 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.47e+02 bond pdb=" C1BBNAI I 402 " pdb=" C2BBNAI I 402 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1BANAI K 402 " pdb=" C2BANAI K 402 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 ... (remaining 64076 not shown) Histogram of bond angle deviations from ideal: 55.86 - 71.74: 83 71.74 - 87.63: 237 87.63 - 103.51: 371 103.51 - 119.40: 89455 119.40 - 135.28: 25760 Bond angle restraints: 115906 Sorted by residual: angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.63 55.87 58.76 3.00e+00 1.11e-01 3.84e+02 angle pdb=" CA ALA K 31 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 114.63 55.89 58.74 3.00e+00 1.11e-01 3.83e+02 angle pdb=" CA LYS J 49 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 114.58 55.86 58.72 3.00e+00 1.11e-01 3.83e+02 angle pdb=" C GLN L 30 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 124.93 66.22 58.71 3.00e+00 1.11e-01 3.83e+02 angle pdb=" C GLN K 30 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 124.93 66.22 58.71 3.00e+00 1.11e-01 3.83e+02 ... (remaining 115901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 26681 17.87 - 35.74: 2822 35.74 - 53.60: 941 53.60 - 71.47: 233 71.47 - 89.34: 44 Dihedral angle restraints: 30721 sinusoidal: 17368 harmonic: 13353 Sorted by residual: dihedral pdb=" CA LYS C 89 " pdb=" C LYS C 89 " pdb=" N LYS C 90 " pdb=" CA LYS C 90 " ideal model delta harmonic sigma weight residual -180.00 -160.28 -19.72 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS D 89 " pdb=" C LYS D 89 " pdb=" N LYS D 90 " pdb=" CA LYS D 90 " ideal model delta harmonic sigma weight residual 180.00 -160.29 -19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS K 89 " pdb=" C LYS K 89 " pdb=" N LYS K 90 " pdb=" CA LYS K 90 " ideal model delta harmonic sigma weight residual -180.00 -160.30 -19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 30718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3776 0.066 - 0.132: 886 0.132 - 0.198: 116 0.198 - 0.264: 58 0.264 - 0.330: 24 Chirality restraints: 4860 Sorted by residual: chirality pdb=" CG LEU A 95 " pdb=" CB LEU A 95 " pdb=" CD1 LEU A 95 " pdb=" CD2 LEU A 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CG LEU E 95 " pdb=" CB LEU E 95 " pdb=" CD1 LEU E 95 " pdb=" CD2 LEU E 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CG LEU F 95 " pdb=" CB LEU F 95 " pdb=" CD1 LEU F 95 " pdb=" CD2 LEU F 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.69e+00 ... (remaining 4857 not shown) Planarity restraints: 9304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 216 " -0.023 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" N TYR C 217 " 0.071 2.00e-02 2.50e+03 pdb=" CA TYR C 217 " -0.018 2.00e-02 2.50e+03 pdb=" H TYR C 217 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU K 216 " 0.023 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" N TYR K 217 " -0.071 2.00e-02 2.50e+03 pdb=" CA TYR K 217 " 0.018 2.00e-02 2.50e+03 pdb=" H TYR K 217 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU I 216 " -0.023 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" N TYR I 217 " 0.071 2.00e-02 2.50e+03 pdb=" CA TYR I 217 " -0.017 2.00e-02 2.50e+03 pdb=" H TYR I 217 " -0.030 2.00e-02 2.50e+03 ... (remaining 9301 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 1062 2.01 - 2.66: 90203 2.66 - 3.30: 181306 3.30 - 3.95: 232120 3.95 - 4.60: 380685 Nonbonded interactions: 885376 Sorted by model distance: nonbonded pdb=" H PHE K 59 " pdb=" HA PHE K 59 " model vdw 1.360 1.816 nonbonded pdb=" H GLY G 232 " pdb=" HA2 GLY G 232 " model vdw 1.437 1.816 nonbonded pdb=" O LEU F 150 " pdb=" H SER F 182 " model vdw 1.489 1.850 nonbonded pdb=" O LEU K 150 " pdb=" H SER K 182 " model vdw 1.489 1.850 nonbonded pdb=" O LEU B 150 " pdb=" H SER B 182 " model vdw 1.489 1.850 ... (remaining 885371 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=0.35 max=1.00 mean=0.99 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: 1.910 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: 0.680 Extract box with map and model: 11.010 Check model and map are aligned: 0.710 Set scattering table: 0.450 Process input model: 151.200 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.170 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:9.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 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 : 0.018 0.242 32856 Z= 1.222 Angle : 1.167 14.165 44580 Z= 0.511 Chirality : 0.063 0.330 4860 Planarity : 0.004 0.039 5520 Dihedral : 16.988 89.338 13236 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -4.78 (0.10), residues: 3912 helix: -2.68 (0.08), residues: 2448 sheet: -2.36 (0.21), residues: 504 loop : -4.28 (0.12), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 198 HIS 0.003 0.001 HIS C 196 PHE 0.011 0.002 PHE L 303 TYR 0.010 0.001 TYR I 304 ARG 0.002 0.000 ARG J 130 *********************** 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 513 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 4.808 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 revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9508 (mp) cc_final: 0.8919 (mp) REVERT: B 75 LEU cc_start: 0.9451 (mp) cc_final: 0.8968 (mp) REVERT: E 53 LEU cc_start: 0.8953 (tp) cc_final: 0.8749 (tm) REVERT: G 75 LEU cc_start: 0.9465 (mp) cc_final: 0.8919 (mp) REVERT: I 75 LEU cc_start: 0.9314 (mp) cc_final: 0.8854 (mp) REVERT: K 53 LEU cc_start: 0.9048 (tp) cc_final: 0.8829 (tm) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 3.1615 time to fit residues: 1865.5432 Evaluate side-chains 274 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 3.671 ------------------------------------------------------------------------------- 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: 3.9990 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 0.3980 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 249 GLN A 278 ASN B 278 ASN C 25 ASN C 96 GLN C 278 ASN D 96 GLN D 249 GLN D 278 ASN E 25 ASN E 278 ASN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN F 278 ASN G 25 ASN ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 278 ASN H 25 ASN H 249 GLN H 278 ASN I 96 GLN I 249 GLN I 278 ASN J 25 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 ASN K 249 GLN K 278 ASN K 296 GLN L 25 ASN L 278 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32856 Z= 0.272 Angle : 0.743 20.222 44580 Z= 0.371 Chirality : 0.122 1.715 4860 Planarity : 0.005 0.065 5520 Dihedral : 9.246 87.855 5784 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.97 % Allowed : 8.33 % Favored : 90.70 % 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: -2.04 (0.12), residues: 3912 helix: -0.38 (0.10), residues: 2400 sheet: -1.81 (0.20), residues: 540 loop : -3.28 (0.15), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 198 HIS 0.005 0.001 HIS K 196 PHE 0.010 0.001 PHE D 184 TYR 0.017 0.001 TYR J 217 ARG 0.010 0.001 ARG G 28 *********************** 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 305 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 274 time to evaluate : 4.092 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: A 216 GLU cc_start: 0.8339 (mp0) cc_final: 0.7874 (mp0) REVERT: B 215 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8859 (mttm) REVERT: E 131 MET cc_start: 0.4530 (OUTLIER) cc_final: 0.4111 (mtt) REVERT: E 216 GLU cc_start: 0.8292 (mp0) cc_final: 0.7782 (mp0) REVERT: F 216 GLU cc_start: 0.8295 (mp0) cc_final: 0.7814 (mp0) REVERT: H 215 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8889 (mttm) REVERT: I 216 GLU cc_start: 0.8264 (mp0) cc_final: 0.7774 (mp0) REVERT: J 96 GLN cc_start: 0.8985 (mm-40) cc_final: 0.8775 (tp-100) outliers start: 31 outliers final: 3 residues processed: 294 average time/residue: 2.8103 time to fit residues: 969.3938 Evaluate side-chains 203 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 199 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 53 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 290 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 8.9990 chunk 346 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 96 GLN ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 GLN D 26 GLN ** E 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 GLN G 249 GLN H 96 GLN I 26 GLN I 96 GLN J 26 GLN J 249 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 32856 Z= 0.408 Angle : 0.740 18.511 44580 Z= 0.378 Chirality : 0.121 1.760 4860 Planarity : 0.004 0.043 5520 Dihedral : 10.036 87.923 5784 Min Nonbonded Distance : 1.719 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.19 % Allowed : 8.68 % Favored : 90.14 % 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: -1.18 (0.13), residues: 3912 helix: 0.25 (0.10), residues: 2412 sheet: -1.30 (0.21), residues: 540 loop : -2.97 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 198 HIS 0.010 0.002 HIS C 196 PHE 0.012 0.002 PHE F 288 TYR 0.011 0.001 TYR C 300 ARG 0.003 0.000 ARG A 28 *********************** 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 271 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 233 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8757 (tp-100) REVERT: B 131 MET cc_start: 0.3702 (OUTLIER) cc_final: 0.3344 (mtt) REVERT: C 131 MET cc_start: 0.3989 (OUTLIER) cc_final: 0.3774 (mtt) REVERT: D 131 MET cc_start: 0.3898 (OUTLIER) cc_final: 0.3544 (mtt) REVERT: E 96 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8751 (tp-100) REVERT: E 131 MET cc_start: 0.4824 (OUTLIER) cc_final: 0.4428 (mtt) REVERT: H 131 MET cc_start: 0.3974 (OUTLIER) cc_final: 0.3574 (mtt) REVERT: I 131 MET cc_start: 0.3844 (OUTLIER) cc_final: 0.3481 (mtt) REVERT: K 131 MET cc_start: 0.3831 (OUTLIER) cc_final: 0.3468 (mtt) REVERT: L 96 GLN cc_start: 0.8990 (tp-100) cc_final: 0.8776 (tp-100) outliers start: 38 outliers final: 10 residues processed: 247 average time/residue: 2.7361 time to fit residues: 823.6386 Evaluate side-chains 216 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 199 time to evaluate : 3.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 285 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.8980 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 GLN C 96 GLN D 96 GLN F 96 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 96 GLN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 GLN L 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 32856 Z= 0.297 Angle : 0.682 20.089 44580 Z= 0.348 Chirality : 0.124 1.721 4860 Planarity : 0.004 0.040 5520 Dihedral : 9.778 88.163 5784 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.81 % Allowed : 9.30 % Favored : 89.89 % 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: -0.54 (0.13), residues: 3912 helix: 0.73 (0.11), residues: 2400 sheet: -1.00 (0.21), residues: 540 loop : -2.65 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 198 HIS 0.006 0.001 HIS B 196 PHE 0.010 0.002 PHE C 228 TYR 0.009 0.001 TYR K 304 ARG 0.002 0.000 ARG A 28 *********************** 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 256 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 230 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 96 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8772 (tp-100) REVERT: D 26 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7881 (mp10) REVERT: D 131 MET cc_start: 0.3911 (OUTLIER) cc_final: 0.3563 (mtt) REVERT: E 131 MET cc_start: 0.5079 (OUTLIER) cc_final: 0.4860 (mtt) REVERT: I 131 MET cc_start: 0.3958 (OUTLIER) cc_final: 0.3612 (mtt) REVERT: K 131 MET cc_start: 0.3975 (OUTLIER) cc_final: 0.3606 (mtt) outliers start: 26 outliers final: 5 residues processed: 235 average time/residue: 2.4145 time to fit residues: 684.1200 Evaluate side-chains 219 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 209 time to evaluate : 3.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.9990 chunk 333 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 96 GLN D 96 GLN E 96 GLN E 249 GLN F 96 GLN G 26 GLN ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 GLN ** H 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN ** J 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 32856 Z= 0.311 Angle : 0.678 19.822 44580 Z= 0.347 Chirality : 0.124 1.724 4860 Planarity : 0.004 0.038 5520 Dihedral : 10.278 89.606 5784 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.28 % Allowed : 9.77 % Favored : 88.95 % 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: -0.24 (0.13), residues: 3912 helix: 0.99 (0.11), residues: 2376 sheet: -0.78 (0.21), residues: 540 loop : -2.57 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 198 HIS 0.007 0.001 HIS G 196 PHE 0.011 0.002 PHE F 288 TYR 0.010 0.001 TYR K 304 ARG 0.002 0.000 ARG A 28 *********************** 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 267 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 226 time to evaluate : 4.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: B 26 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: C 26 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7935 (mp10) REVERT: D 26 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7675 (mp10) REVERT: D 53 LEU cc_start: 0.8867 (tp) cc_final: 0.8656 (tm) REVERT: D 131 MET cc_start: 0.3813 (OUTLIER) cc_final: 0.3510 (mtt) REVERT: E 131 MET cc_start: 0.5129 (OUTLIER) cc_final: 0.4814 (mtt) REVERT: F 26 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: I 26 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: I 131 MET cc_start: 0.3925 (OUTLIER) cc_final: 0.3604 (mtt) REVERT: K 26 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: K 131 MET cc_start: 0.3969 (OUTLIER) cc_final: 0.3621 (mtt) REVERT: L 26 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7978 (mp10) REVERT: L 131 MET cc_start: 0.5380 (OUTLIER) cc_final: 0.5174 (mtt) outliers start: 41 outliers final: 9 residues processed: 240 average time/residue: 2.5293 time to fit residues: 730.2326 Evaluate side-chains 234 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 26 GLN Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain I residue 26 GLN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 131 MET 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: 5.9990 chunk 73 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 195 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 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 32856 Z= 0.305 Angle : 0.677 19.982 44580 Z= 0.346 Chirality : 0.124 1.724 4860 Planarity : 0.003 0.038 5520 Dihedral : 10.267 89.421 5784 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.94 % Allowed : 11.05 % Favored : 88.01 % 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: -0.05 (0.13), residues: 3912 helix: 1.04 (0.11), residues: 2412 sheet: -0.74 (0.21), residues: 540 loop : -2.28 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 198 HIS 0.005 0.001 HIS L 196 PHE 0.011 0.002 PHE L 288 TYR 0.009 0.001 TYR K 304 ARG 0.001 0.000 ARG J 28 *********************** 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 245 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 3.734 Fit side-chains revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: A 131 MET cc_start: 0.4880 (OUTLIER) cc_final: 0.4676 (mtt) REVERT: B 26 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: C 26 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: D 131 MET cc_start: 0.3949 (OUTLIER) cc_final: 0.3614 (mtt) REVERT: E 131 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4858 (mtt) REVERT: F 26 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7783 (mp10) REVERT: I 131 MET cc_start: 0.4057 (OUTLIER) cc_final: 0.3698 (mtt) REVERT: K 26 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8127 (mp10) REVERT: L 26 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7843 (mp10) outliers start: 30 outliers final: 7 residues processed: 220 average time/residue: 2.5892 time to fit residues: 688.3794 Evaluate side-chains 222 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 205 time to evaluate : 3.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain L residue 26 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.4740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 32856 Z= 0.371 Angle : 0.698 19.841 44580 Z= 0.358 Chirality : 0.124 1.723 4860 Planarity : 0.004 0.039 5520 Dihedral : 10.919 83.597 5784 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.97 % Allowed : 11.58 % Favored : 87.45 % 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: 0.00 (0.13), residues: 3912 helix: 1.10 (0.11), residues: 2388 sheet: -0.75 (0.21), residues: 540 loop : -2.23 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 198 HIS 0.006 0.001 HIS G 196 PHE 0.011 0.002 PHE A 288 TYR 0.011 0.001 TYR K 304 ARG 0.001 0.000 ARG A 305 *********************** 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 234 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7877 (mp10) REVERT: B 26 GLN cc_start: 0.8320 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: C 26 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: D 131 MET cc_start: 0.4122 (OUTLIER) cc_final: 0.3779 (mtt) REVERT: E 131 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4978 (mtt) REVERT: F 26 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7741 (mp10) REVERT: I 26 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7673 (mp10) REVERT: K 26 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: L 26 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7830 (mp10) outliers start: 31 outliers final: 12 residues processed: 218 average time/residue: 2.5233 time to fit residues: 658.8188 Evaluate side-chains 218 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 197 time to evaluate : 3.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 26 GLN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 250 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 26 GLN H 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32856 Z= 0.179 Angle : 0.638 20.317 44580 Z= 0.323 Chirality : 0.124 1.724 4860 Planarity : 0.003 0.034 5520 Dihedral : 9.250 85.142 5784 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.56 % Allowed : 12.02 % Favored : 87.42 % 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: 0.49 (0.14), residues: 3912 helix: 1.47 (0.11), residues: 2388 sheet: -0.62 (0.21), residues: 540 loop : -1.93 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 198 HIS 0.002 0.000 HIS B 196 PHE 0.011 0.001 PHE J 184 TYR 0.007 0.001 TYR J 304 ARG 0.001 0.000 ARG A 130 *********************** 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 249 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 231 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7759 (mp10) REVERT: B 26 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7668 (mp10) REVERT: C 131 MET cc_start: 0.4217 (mtt) cc_final: 0.3941 (ptp) REVERT: D 131 MET cc_start: 0.3843 (OUTLIER) cc_final: 0.3630 (mtt) REVERT: F 131 MET cc_start: 0.4210 (mtt) cc_final: 0.3794 (ptp) REVERT: G 131 MET cc_start: 0.3933 (mtt) cc_final: 0.3630 (ptp) REVERT: H 131 MET cc_start: 0.4106 (mtt) cc_final: 0.3836 (ptp) REVERT: K 26 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8013 (mp10) REVERT: L 26 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7795 (mp10) outliers start: 18 outliers final: 2 residues processed: 238 average time/residue: 2.5983 time to fit residues: 739.8804 Evaluate side-chains 205 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 198 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain L residue 26 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 6.9990 chunk 354 optimal weight: 7.9990 chunk 323 optimal weight: 8.9990 chunk 344 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 270 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 32856 Z= 0.393 Angle : 0.715 19.961 44580 Z= 0.363 Chirality : 0.124 1.719 4860 Planarity : 0.004 0.036 5520 Dihedral : 10.375 82.016 5784 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.69 % Allowed : 12.80 % Favored : 86.52 % 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: 0.31 (0.13), residues: 3912 helix: 1.30 (0.11), residues: 2388 sheet: -0.68 (0.21), residues: 540 loop : -1.95 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 198 HIS 0.006 0.001 HIS B 196 PHE 0.012 0.002 PHE C 288 TYR 0.022 0.001 TYR D 23 ARG 0.001 0.000 ARG K 305 *********************** 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 228 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 206 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7799 (mp10) REVERT: B 26 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7670 (mp10) REVERT: C 26 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: C 131 MET cc_start: 0.4443 (mtt) cc_final: 0.4129 (ptp) REVERT: E 131 MET cc_start: 0.4880 (mtt) cc_final: 0.4634 (mtt) REVERT: F 26 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7620 (mp10) REVERT: G 131 MET cc_start: 0.4217 (mtt) cc_final: 0.3886 (ptp) REVERT: H 131 MET cc_start: 0.4323 (mtt) cc_final: 0.4007 (ptp) REVERT: I 26 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: K 26 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: L 26 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7802 (mp10) outliers start: 22 outliers final: 9 residues processed: 218 average time/residue: 2.6290 time to fit residues: 696.7579 Evaluate side-chains 215 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain I residue 26 GLN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain L residue 26 GLN 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: 0.9980 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 0.8980 chunk 352 optimal weight: 10.0000 chunk 304 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32856 Z= 0.174 Angle : 0.659 20.442 44580 Z= 0.329 Chirality : 0.125 1.723 4860 Planarity : 0.003 0.033 5520 Dihedral : 8.796 84.603 5784 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.16 % Allowed : 13.33 % Favored : 86.52 % 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: 0.87 (0.14), residues: 3912 helix: 1.77 (0.11), residues: 2316 sheet: -0.54 (0.22), residues: 540 loop : -1.48 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 198 HIS 0.001 0.000 HIS B 196 PHE 0.011 0.001 PHE J 184 TYR 0.020 0.001 TYR D 23 ARG 0.001 0.000 ARG D 274 ********************** 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 219 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 214 time to evaluate : 3.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7744 (mp10) REVERT: B 26 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7634 (mp10) REVERT: C 131 MET cc_start: 0.4185 (mtt) cc_final: 0.3963 (ptp) REVERT: E 131 MET cc_start: 0.4736 (mtt) cc_final: 0.4488 (mtt) REVERT: G 131 MET cc_start: 0.4012 (mtt) cc_final: 0.3740 (ptp) REVERT: H 131 MET cc_start: 0.4164 (mtt) cc_final: 0.3887 (ptp) REVERT: K 26 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7962 (mp10) REVERT: L 26 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7753 (mp10) outliers start: 5 outliers final: 1 residues processed: 215 average time/residue: 2.6454 time to fit residues: 675.7022 Evaluate side-chains 202 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 3.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain L residue 26 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 4.9990 chunk 324 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.066261 restraints weight = 213350.697| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.99 r_work: 0.2712 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 32856 Z= 0.387 Angle : 0.721 19.842 44580 Z= 0.366 Chirality : 0.125 1.737 4860 Planarity : 0.003 0.035 5520 Dihedral : 10.127 80.861 5784 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.41 % Allowed : 13.08 % Favored : 86.52 % 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: 0.43 (0.14), residues: 3912 helix: 1.34 (0.11), residues: 2388 sheet: -0.60 (0.22), residues: 540 loop : -1.77 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 198 HIS 0.006 0.001 HIS G 196 PHE 0.013 0.002 PHE C 288 TYR 0.020 0.001 TYR D 23 ARG 0.002 0.000 ARG D 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15820.06 seconds wall clock time: 273 minutes 5.66 seconds (16385.66 seconds total)