Starting phenix.real_space_refine on Tue Mar 12 16:44:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/03_2024/6kqk_0753_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/03_2024/6kqk_0753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/03_2024/6kqk_0753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/03_2024/6kqk_0753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/03_2024/6kqk_0753_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/03_2024/6kqk_0753_trim_updated.pdb" } resolution = 2.17 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 ------------------------------------------------------------------------------- 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= -0.014 sd= 0.407 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-5265/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: 98 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Conformer: "B" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} bond proxies already assigned to first conformer: 9 Chain: "L" Number of atoms: 100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Conformer: "B" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} bond proxies already assigned to first conformer: 9 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1BANAI A 402 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI A 402 " occ=0.54 residue: pdb=" C1BANAI B 403 " occ=0.47 ... (86 atoms not shown) pdb=" PN BNAI B 403 " occ=0.53 residue: pdb=" C1BANAI C 402 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI C 402 " occ=0.54 residue: pdb=" C1BANAI D 403 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI D 403 " occ=0.54 residue: pdb=" C1BANAI E 402 " occ=0.47 ... (86 atoms not shown) pdb=" PN BNAI E 402 " occ=0.53 residue: pdb=" C1BANAI F 403 " occ=0.45 ... (86 atoms not shown) pdb=" PN BNAI F 403 " occ=0.55 residue: pdb=" C1BANAI G 402 " occ=0.47 ... (86 atoms not shown) pdb=" PN BNAI G 402 " occ=0.53 residue: pdb=" C1BANAI H 403 " occ=0.47 ... (86 atoms not shown) pdb=" PN BNAI H 403 " occ=0.53 residue: pdb=" C1BANAI I 402 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI I 402 " occ=0.54 residue: pdb=" C1BANAI J 403 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI J 403 " occ=0.54 residue: pdb=" C1BANAI K 402 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI K 402 " occ=0.54 residue: pdb=" C1BANAI L 404 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI L 404 " occ=0.54 Time building chain proxies: 20.32, per 1000 atoms: 0.32 Number of scatterers: 63373 At special positions: 0 Unit cell: (141.96, 141.96, 141.96, 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: 39.88 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: 204 helices and 12 sheets defined 57.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.71 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 217 removed outlier: 3.600A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.571A pdb=" N TYR A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.601A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.571A pdb=" N TYR B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.601A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix removed outlier: 3.572A pdb=" N TYR C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.601A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix removed outlier: 3.572A pdb=" N TYR D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.600A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Proline residue: E 200 - end of helix removed outlier: 3.572A pdb=" N TYR E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.601A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Proline residue: F 200 - end of helix removed outlier: 3.571A pdb=" N TYR F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.600A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL G 199 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Proline residue: G 200 - end of helix removed outlier: 3.571A pdb=" N TYR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.600A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Proline residue: H 200 - end of helix removed outlier: 3.571A pdb=" N TYR H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.601A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 200 - end of helix removed outlier: 3.571A pdb=" N TYR I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.600A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Proline residue: J 200 - end of helix removed outlier: 3.572A pdb=" N TYR J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.601A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Proline residue: K 200 - end of helix removed outlier: 3.572A pdb=" N TYR K 217 " --> pdb=" O ALA K 213 " (cutoff:3.500A) 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 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 217 removed outlier: 3.601A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP L 198 " --> pdb=" O SER L 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix removed outlier: 3.571A pdb=" N TYR L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) 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 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: 6.521A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 73 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 7.681A 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: 6.029A pdb=" N VAL A 102 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP A 104 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL A 152 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 128 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.521A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 73 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 7.680A 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: 6.028A pdb=" N VAL B 102 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP B 104 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL B 152 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA B 128 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.522A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 73 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 7.681A 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: 6.030A pdb=" N VAL C 102 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP C 104 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 105 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA C 128 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.062A 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: 6.521A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D 73 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE D 21 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU D 75 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL D 102 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU D 76 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP D 104 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 105 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA D 128 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.521A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL E 73 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.680A 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: 6.029A pdb=" N VAL E 102 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU E 76 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP E 104 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE E 105 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA E 128 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.521A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL F 73 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 7.681A 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: 6.029A pdb=" N VAL F 102 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU F 76 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP F 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 105 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET F 126 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL F 152 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA F 128 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.521A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 73 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE G 21 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU G 75 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL G 102 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU G 76 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP G 104 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE G 105 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL G 152 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA G 128 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.521A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 73 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.680A 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: 6.029A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU H 76 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP H 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET H 126 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL H 152 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA H 128 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.520A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL I 73 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.680A 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: 6.030A pdb=" N VAL I 102 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU I 76 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP I 104 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA I 128 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.521A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL J 73 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.680A 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: 6.029A pdb=" N VAL J 102 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU J 76 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP J 104 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE J 105 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET J 126 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL J 152 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA J 128 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.521A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL K 73 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE K 21 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU K 75 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL K 102 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU K 76 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP K 104 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE K 105 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET K 126 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL K 152 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA K 128 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 6.061A 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: 6.521A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL L 73 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 7.680A 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: 6.029A pdb=" N VAL L 102 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU L 76 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP L 104 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE L 105 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET L 126 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL L 152 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA L 128 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU L 150 " --> pdb=" O ALA L 128 " (cutoff:3.500A) 1426 hydrogen bonds defined for protein. 4206 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: 19.71 Time building geometry restraints manager: 42.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 31211 1.02 - 1.22: 38 1.22 - 1.41: 13392 1.41 - 1.61: 19068 1.61 - 1.81: 372 Bond restraints: 64081 Sorted by residual: bond pdb=" C1BANAI F 403 " pdb=" C2BANAI F 403 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1BANAI D 403 " pdb=" C2BANAI D 403 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1BANAI G 402 " pdb=" C2BANAI G 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 J 403 " pdb=" C2BANAI J 403 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1BANAI A 402 " pdb=" C2BANAI A 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: 55.67 - 77.84: 208 77.84 - 100.01: 247 100.01 - 122.19: 105494 122.19 - 144.36: 9953 144.36 - 166.53: 4 Bond angle restraints: 115906 Sorted by residual: angle pdb=" C ASP J 48 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 124.96 65.90 59.06 3.00e+00 1.11e-01 3.88e+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 55.67 58.96 3.00e+00 1.11e-01 3.86e+02 angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.63 55.78 58.85 3.00e+00 1.11e-01 3.85e+02 angle pdb=" CA LYS J 49 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 114.66 55.88 58.78 3.00e+00 1.11e-01 3.84e+02 angle pdb=" C LYS K 55 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 124.83 66.05 58.77 3.00e+00 1.11e-01 3.84e+02 ... (remaining 115901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 26811 17.96 - 35.93: 2798 35.93 - 53.89: 842 53.89 - 71.85: 242 71.85 - 89.82: 28 Dihedral angle restraints: 30721 sinusoidal: 17368 harmonic: 13353 Sorted by residual: dihedral pdb=" CA MET C 126 " pdb=" C MET C 126 " pdb=" N VAL C 127 " pdb=" CA VAL C 127 " ideal model delta harmonic sigma weight residual 180.00 143.97 36.03 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA MET E 126 " pdb=" C MET E 126 " pdb=" N VAL E 127 " pdb=" CA VAL E 127 " ideal model delta harmonic sigma weight residual 180.00 143.99 36.01 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA MET F 126 " pdb=" C MET F 126 " pdb=" N VAL F 127 " pdb=" CA VAL F 127 " ideal model delta harmonic sigma weight residual 180.00 144.00 36.00 0 5.00e+00 4.00e-02 5.18e+01 ... (remaining 30718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3863 0.067 - 0.133: 809 0.133 - 0.200: 116 0.200 - 0.267: 36 0.267 - 0.334: 36 Chirality restraints: 4860 Sorted by residual: 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 2.78e+00 chirality pdb=" CG LEU C 95 " pdb=" CB LEU C 95 " pdb=" CD1 LEU C 95 " pdb=" CD2 LEU C 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU L 95 " pdb=" CB LEU L 95 " pdb=" CD1 LEU L 95 " pdb=" CD2 LEU L 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 4857 not shown) Planarity restraints: 9304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 9 " 0.006 2.00e-02 2.50e+03 2.72e-02 1.11e+01 pdb=" CG ASN F 9 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN F 9 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN F 9 " 0.020 2.00e-02 2.50e+03 pdb="HD21 ASN F 9 " 0.020 2.00e-02 2.50e+03 pdb="HD22 ASN F 9 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 9 " 0.007 2.00e-02 2.50e+03 2.71e-02 1.10e+01 pdb=" CG ASN J 9 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN J 9 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN J 9 " 0.024 2.00e-02 2.50e+03 pdb="HD21 ASN J 9 " 0.017 2.00e-02 2.50e+03 pdb="HD22 ASN J 9 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 9 " -0.014 2.00e-02 2.50e+03 2.63e-02 1.04e+01 pdb=" CG ASN I 9 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN I 9 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN I 9 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN I 9 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN I 9 " -0.012 2.00e-02 2.50e+03 ... (remaining 9301 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 1056 2.01 - 2.66: 90409 2.66 - 3.30: 184532 3.30 - 3.95: 238501 3.95 - 4.60: 386472 Nonbonded interactions: 900970 Sorted by model distance: nonbonded pdb=" H PHE K 59 " pdb=" HA PHE K 59 " model vdw 1.358 1.816 nonbonded pdb=" H GLY G 232 " pdb=" HA2 GLY G 232 " model vdw 1.406 1.816 nonbonded pdb=" O LEU I 150 " pdb=" H SER I 182 " model vdw 1.415 1.850 nonbonded pdb=" H LEU I 150 " pdb=" O VAL I 180 " model vdw 1.415 1.850 nonbonded pdb=" O LEU A 150 " pdb=" H SER A 182 " model vdw 1.418 1.850 ... (remaining 900965 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=0.45 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: 2.490 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: 0.720 Extract box with map and model: 11.160 Check model and map are aligned: 0.690 Set scattering table: 0.440 Process input model: 149.980 Find NCS groups from input model: 2.700 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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= 1.143 Angle : 1.172 14.690 44580 Z= 0.511 Chirality : 0.063 0.334 4860 Planarity : 0.005 0.045 5520 Dihedral : 16.504 89.817 13236 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -4.38 (0.10), residues: 3912 helix: -2.32 (0.08), residues: 2448 sheet: -2.62 (0.20), residues: 480 loop : -4.01 (0.13), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 198 HIS 0.002 0.001 HIS E 196 PHE 0.013 0.002 PHE I 184 TYR 0.009 0.001 TYR F 304 ARG 0.002 0.000 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 719 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8220 (mp) cc_final: 0.7150 (mp) REVERT: B 75 LEU cc_start: 0.8290 (mp) cc_final: 0.7172 (mp) REVERT: C 75 LEU cc_start: 0.8359 (mp) cc_final: 0.7336 (mp) REVERT: D 75 LEU cc_start: 0.8165 (mp) cc_final: 0.6472 (mp) REVERT: E 75 LEU cc_start: 0.8289 (mp) cc_final: 0.7286 (mp) REVERT: F 75 LEU cc_start: 0.7968 (mp) cc_final: 0.6379 (mp) REVERT: G 75 LEU cc_start: 0.8056 (mp) cc_final: 0.6508 (mp) REVERT: H 75 LEU cc_start: 0.8251 (mp) cc_final: 0.7249 (mp) REVERT: I 75 LEU cc_start: 0.8060 (mp) cc_final: 0.7022 (mp) REVERT: J 75 LEU cc_start: 0.8035 (mp) cc_final: 0.6518 (mp) REVERT: K 75 LEU cc_start: 0.8060 (mp) cc_final: 0.6979 (mp) REVERT: L 75 LEU cc_start: 0.8351 (mp) cc_final: 0.7207 (mp) outliers start: 0 outliers final: 0 residues processed: 719 average time/residue: 2.8697 time to fit residues: 2408.2690 Evaluate side-chains 457 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 3.683 ------------------------------------------------------------------------------- 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: 9.9990 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 312 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 278 ASN B 296 GLN B 312 GLN C 278 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 40 ASN D 278 ASN D 312 GLN E 25 ASN E 249 GLN E 278 ASN E 296 GLN E 312 GLN F 37 ASN F 40 ASN F 278 ASN F 296 GLN G 26 GLN G 278 ASN G 296 GLN G 312 GLN H 37 ASN H 278 ASN I 37 ASN I 40 ASN I 278 ASN I 296 GLN J 37 ASN J 40 ASN J 278 ASN J 312 GLN K 37 ASN K 40 ASN K 278 ASN K 296 GLN K 312 GLN L 26 GLN L 278 ASN ** L 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32856 Z= 0.316 Angle : 0.730 19.548 44580 Z= 0.372 Chirality : 0.120 1.644 4860 Planarity : 0.005 0.050 5520 Dihedral : 9.158 79.755 5784 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.40 % Allowed : 10.80 % Favored : 87.80 % 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: -2.09 (0.12), residues: 3912 helix: -0.37 (0.10), residues: 2436 sheet: -2.15 (0.20), residues: 504 loop : -3.29 (0.16), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 198 HIS 0.009 0.002 HIS L 196 PHE 0.016 0.002 PHE F 105 TYR 0.012 0.002 TYR L 51 ARG 0.011 0.001 ARG L 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 511 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 215 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8190 (mppt) REVERT: F 26 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7397 (mp10) REVERT: H 131 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.4813 (mtt) REVERT: I 26 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7531 (mp10) outliers start: 45 outliers final: 10 residues processed: 537 average time/residue: 2.6262 time to fit residues: 1667.3011 Evaluate side-chains 455 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 442 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 124 THR Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain I residue 26 GLN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 162 ASP 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: 3.9990 chunk 290 optimal weight: 10.0000 chunk 237 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 312 GLN B 40 ASN B 312 GLN C 40 ASN D 40 ASN D 296 GLN D 312 GLN E 40 ASN E 296 GLN F 40 ASN F 296 GLN G 296 GLN G 312 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 ASN K 40 ASN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 32856 Z= 0.358 Angle : 0.714 18.805 44580 Z= 0.370 Chirality : 0.123 1.882 4860 Planarity : 0.005 0.050 5520 Dihedral : 8.972 87.663 5784 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.12 % Allowed : 13.33 % Favored : 84.55 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3912 helix: 0.25 (0.10), residues: 2424 sheet: -1.91 (0.20), residues: 504 loop : -3.01 (0.16), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 198 HIS 0.011 0.002 HIS L 196 PHE 0.016 0.002 PHE J 288 TYR 0.014 0.002 TYR F 51 ARG 0.006 0.000 ARG H 70 *********************** 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 582 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 514 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 26 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7299 (mp10) REVERT: C 26 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: C 131 MET cc_start: 0.4461 (mtt) cc_final: 0.4123 (mtt) REVERT: D 26 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: E 26 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7347 (mp10) REVERT: F 26 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7270 (mp10) REVERT: H 26 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: H 131 MET cc_start: 0.5093 (OUTLIER) cc_final: 0.4746 (mtt) REVERT: I 26 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7248 (mp10) REVERT: J 26 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7201 (mp10) REVERT: K 26 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7434 (mp10) REVERT: L 26 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7473 (mp10) REVERT: L 131 MET cc_start: 0.4371 (mtt) cc_final: 0.4113 (mtt) outliers start: 68 outliers final: 21 residues processed: 537 average time/residue: 2.7943 time to fit residues: 1757.0365 Evaluate side-chains 501 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 469 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain D residue 26 GLN Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 26 GLN Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain I residue 26 GLN Chi-restraints excluded: chain I residue 65 ASP Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 162 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: 0.8980 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 312 GLN B 296 GLN D 296 GLN D 312 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 GLN K 296 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 32856 Z= 0.245 Angle : 0.667 19.816 44580 Z= 0.341 Chirality : 0.124 1.787 4860 Planarity : 0.004 0.046 5520 Dihedral : 8.429 81.946 5784 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.03 % Allowed : 15.48 % Favored : 83.49 % 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: -0.65 (0.13), residues: 3912 helix: 0.77 (0.10), residues: 2400 sheet: -1.56 (0.21), residues: 504 loop : -2.68 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 198 HIS 0.005 0.001 HIS J 196 PHE 0.012 0.002 PHE L 288 TYR 0.012 0.001 TYR H 51 ARG 0.003 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 534 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 501 time to evaluate : 3.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 LEU cc_start: 0.8725 (tt) cc_final: 0.8465 (tm) REVERT: C 26 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: C 95 LEU cc_start: 0.8689 (tt) cc_final: 0.8480 (tm) REVERT: C 131 MET cc_start: 0.4406 (mtt) cc_final: 0.4100 (mtt) REVERT: H 137 MET cc_start: 0.7347 (tpp) cc_final: 0.6673 (tpp) REVERT: K 26 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7398 (mp10) REVERT: K 137 MET cc_start: 0.7242 (tpp) cc_final: 0.6625 (tpp) REVERT: L 26 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7328 (mp10) REVERT: L 70 ARG cc_start: 0.8919 (mtt-85) cc_final: 0.8705 (mtt-85) REVERT: L 131 MET cc_start: 0.4400 (mtt) cc_final: 0.3985 (mtt) outliers start: 33 outliers final: 9 residues processed: 508 average time/residue: 2.8817 time to fit residues: 1718.7121 Evaluate side-chains 461 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 449 time to evaluate : 4.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain F residue 30 GLN Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 162 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN D 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 32856 Z= 0.273 Angle : 0.680 19.738 44580 Z= 0.349 Chirality : 0.124 1.793 4860 Planarity : 0.004 0.046 5520 Dihedral : 8.568 81.843 5784 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.50 % Allowed : 16.07 % Favored : 82.43 % 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: -0.47 (0.13), residues: 3912 helix: 0.86 (0.10), residues: 2400 sheet: -1.43 (0.21), residues: 504 loop : -2.49 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 198 HIS 0.006 0.001 HIS G 196 PHE 0.014 0.002 PHE J 288 TYR 0.011 0.001 TYR K 23 ARG 0.002 0.000 ARG C 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 532 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 484 time to evaluate : 3.631 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 70 ARG cc_start: 0.8885 (mtt-85) cc_final: 0.8654 (mtt-85) REVERT: B 95 LEU cc_start: 0.8751 (tt) cc_final: 0.8517 (tm) REVERT: B 131 MET cc_start: 0.4625 (mtt) cc_final: 0.4373 (mtt) REVERT: C 26 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7311 (mp10) REVERT: C 131 MET cc_start: 0.4393 (mtt) cc_final: 0.3982 (mtt) REVERT: D 95 LEU cc_start: 0.8616 (tt) cc_final: 0.8393 (tm) REVERT: E 95 LEU cc_start: 0.8714 (tt) cc_final: 0.8503 (tm) REVERT: F 95 LEU cc_start: 0.8658 (tt) cc_final: 0.8445 (tm) REVERT: G 95 LEU cc_start: 0.8612 (tt) cc_final: 0.8397 (tm) REVERT: H 26 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7357 (mp10) REVERT: I 26 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: I 95 LEU cc_start: 0.8719 (tt) cc_final: 0.8487 (tm) REVERT: J 95 LEU cc_start: 0.8650 (tt) cc_final: 0.8418 (tm) REVERT: J 127 VAL cc_start: 0.8174 (p) cc_final: 0.7974 (m) REVERT: K 26 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7320 (mp10) REVERT: L 26 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7301 (mp10) REVERT: L 70 ARG cc_start: 0.8899 (mtt-85) cc_final: 0.8669 (mtt-85) REVERT: L 131 MET cc_start: 0.4527 (mtt) cc_final: 0.4096 (mtt) outliers start: 48 outliers final: 28 residues processed: 499 average time/residue: 2.9247 time to fit residues: 1711.5044 Evaluate side-chains 481 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 448 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain H residue 26 GLN Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 26 GLN Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 162 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 2.9990 chunk 334 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 2.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 32856 Z= 0.252 Angle : 0.674 19.818 44580 Z= 0.344 Chirality : 0.124 1.816 4860 Planarity : 0.004 0.045 5520 Dihedral : 8.582 86.210 5784 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.22 % Allowed : 16.89 % Favored : 81.90 % 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: -0.27 (0.13), residues: 3912 helix: 0.93 (0.10), residues: 2424 sheet: -1.31 (0.21), residues: 504 loop : -2.24 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 198 HIS 0.005 0.001 HIS G 196 PHE 0.012 0.002 PHE H 288 TYR 0.009 0.001 TYR I 300 ARG 0.002 0.000 ARG E 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 519 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 480 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ARG cc_start: 0.8872 (mtt-85) cc_final: 0.8632 (mtt-85) REVERT: B 95 LEU cc_start: 0.8707 (tt) cc_final: 0.8499 (tm) REVERT: C 131 MET cc_start: 0.4405 (mtt) cc_final: 0.3991 (mtt) REVERT: I 95 LEU cc_start: 0.8706 (tt) cc_final: 0.8492 (tm) REVERT: K 26 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7267 (mp10) REVERT: L 70 ARG cc_start: 0.8906 (mtt-85) cc_final: 0.8654 (mtt-85) REVERT: L 131 MET cc_start: 0.4352 (mtt) cc_final: 0.3959 (mtt) outliers start: 39 outliers final: 10 residues processed: 492 average time/residue: 2.8905 time to fit residues: 1658.3411 Evaluate side-chains 458 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 447 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 65 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 271 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN F 296 GLN G 296 GLN I 296 GLN K 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 32856 Z= 0.375 Angle : 0.719 19.260 44580 Z= 0.371 Chirality : 0.125 1.785 4860 Planarity : 0.004 0.050 5520 Dihedral : 9.424 88.107 5784 Min Nonbonded Distance : 1.676 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.47 % Allowed : 17.20 % Favored : 81.34 % 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: -0.48 (0.13), residues: 3912 helix: 0.78 (0.10), residues: 2400 sheet: -1.31 (0.21), residues: 504 loop : -2.35 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 284 HIS 0.006 0.001 HIS B 196 PHE 0.017 0.002 PHE H 288 TYR 0.015 0.002 TYR K 23 ARG 0.002 0.000 ARG K 69 *********************** 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 522 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 475 time to evaluate : 3.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.6811 (mm-40) cc_final: 0.6049 (mm-40) REVERT: B 95 LEU cc_start: 0.8757 (tt) cc_final: 0.8543 (tm) REVERT: B 131 MET cc_start: 0.4127 (mtt) cc_final: 0.3925 (mtt) REVERT: C 131 MET cc_start: 0.4287 (mtt) cc_final: 0.3762 (mtt) REVERT: H 131 MET cc_start: 0.3992 (mtt) cc_final: 0.3765 (mtt) REVERT: I 95 LEU cc_start: 0.8741 (tt) cc_final: 0.8529 (tm) REVERT: K 26 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7282 (mp10) REVERT: L 26 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7269 (mp10) REVERT: L 131 MET cc_start: 0.4632 (mtt) cc_final: 0.4132 (mtt) REVERT: L 137 MET cc_start: 0.7174 (tpp) cc_final: 0.6963 (tpp) outliers start: 47 outliers final: 29 residues processed: 490 average time/residue: 2.9708 time to fit residues: 1703.0424 Evaluate side-chains 476 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 445 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 85 GLU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 85 GLU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 85 GLU Chi-restraints excluded: chain F residue 26 GLN Chi-restraints excluded: chain G residue 65 ASP Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain H residue 65 ASP Chi-restraints excluded: chain H residue 85 GLU Chi-restraints excluded: chain H residue 124 THR Chi-restraints excluded: chain I residue 124 THR Chi-restraints excluded: chain J residue 65 ASP Chi-restraints excluded: chain J residue 85 GLU Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain K residue 85 GLU Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 85 GLU Chi-restraints excluded: chain L residue 162 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 8.9990 chunk 147 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 235 optimal weight: 0.0270 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 290 optimal weight: 9.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN B 312 GLN H 296 GLN J 296 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32856 Z= 0.176 Angle : 0.659 20.262 44580 Z= 0.334 Chirality : 0.124 1.778 4860 Planarity : 0.003 0.039 5520 Dihedral : 8.266 88.854 5784 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.47 % Allowed : 18.76 % Favored : 80.77 % 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: 0.03 (0.13), residues: 3912 helix: 1.12 (0.10), residues: 2424 sheet: -1.14 (0.23), residues: 444 loop : -2.01 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 198 HIS 0.002 0.000 HIS F 196 PHE 0.010 0.001 PHE A 184 TYR 0.007 0.001 TYR F 304 ARG 0.004 0.000 ARG A 70 *********************** 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 493 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 478 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 MET cc_start: 0.4258 (mtt) cc_final: 0.3874 (mtt) REVERT: K 26 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: L 26 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: L 70 ARG cc_start: 0.8919 (mtt-85) cc_final: 0.8643 (mtt-85) outliers start: 15 outliers final: 8 residues processed: 484 average time/residue: 3.0180 time to fit residues: 1726.9190 Evaluate side-chains 459 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 449 time to evaluate : 3.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 162 ASP 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: 10.0000 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 311 optimal weight: 6.9990 chunk 326 optimal weight: 6.9990 chunk 343 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 32856 Z= 0.384 Angle : 0.726 19.334 44580 Z= 0.374 Chirality : 0.125 1.790 4860 Planarity : 0.004 0.048 5520 Dihedral : 9.154 89.458 5784 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.75 % Allowed : 18.73 % Favored : 80.52 % Cbeta Deviations : 0.11 % 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: -0.34 (0.13), residues: 3912 helix: 0.88 (0.10), residues: 2400 sheet: -1.25 (0.21), residues: 504 loop : -2.27 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 284 HIS 0.007 0.001 HIS K 196 PHE 0.017 0.002 PHE D 288 TYR 0.015 0.002 TYR K 23 ARG 0.003 0.000 ARG A 70 *********************** 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 471 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 447 time to evaluate : 3.664 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: A 26 GLN cc_start: 0.6706 (mm-40) cc_final: 0.5952 (mm-40) REVERT: K 26 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7253 (mp10) REVERT: L 26 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7301 (mp10) outliers start: 24 outliers final: 12 residues processed: 456 average time/residue: 2.9018 time to fit residues: 1541.0716 Evaluate side-chains 451 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 437 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 85 GLU Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain E residue 18 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain K residue 26 GLN Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 162 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 10.0000 chunk 364 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 253 optimal weight: 1.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 0.5980 chunk 304 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN F 25 ASN F 296 GLN G 296 GLN I 296 GLN K 296 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32856 Z= 0.189 Angle : 0.678 20.192 44580 Z= 0.341 Chirality : 0.124 1.781 4860 Planarity : 0.003 0.041 5520 Dihedral : 8.133 87.951 5784 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.41 % Allowed : 19.38 % Favored : 80.21 % Cbeta Deviations : 0.08 % 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: 0.04 (0.13), residues: 3912 helix: 1.18 (0.10), residues: 2400 sheet: -1.13 (0.23), residues: 444 loop : -2.08 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 198 HIS 0.002 0.000 HIS B 196 PHE 0.010 0.001 PHE A 184 TYR 0.007 0.001 TYR H 304 ARG 0.003 0.000 ARG A 70 ********************** 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 471 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 458 time to evaluate : 3.668 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: L 26 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7156 (mp10) outliers start: 13 outliers final: 10 residues processed: 464 average time/residue: 2.9750 time to fit residues: 1614.7306 Evaluate side-chains 459 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 448 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain C residue 18 ILE Chi-restraints excluded: chain E residue 62 TYR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain I residue 125 ILE Chi-restraints excluded: chain K residue 65 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 162 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 4.9990 chunk 127 optimal weight: 0.3980 chunk 313 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN F 296 GLN H 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.125691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.081827 restraints weight = 169247.318| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.81 r_work: 0.2840 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 32856 Z= 0.281 Angle : 0.705 19.788 44580 Z= 0.358 Chirality : 0.125 1.787 4860 Planarity : 0.004 0.049 5520 Dihedral : 8.468 85.410 5784 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.50 % Allowed : 19.60 % Favored : 79.90 % Cbeta Deviations : 0.11 % 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: -0.08 (0.13), residues: 3912 helix: 1.08 (0.10), residues: 2400 sheet: -1.19 (0.23), residues: 444 loop : -2.10 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 284 HIS 0.005 0.001 HIS J 196 PHE 0.015 0.002 PHE E 288 TYR 0.011 0.001 TYR K 23 ARG 0.005 0.000 ARG C 70 =============================================================================== Job complete usr+sys time: 25906.74 seconds wall clock time: 443 minutes 33.24 seconds (26613.24 seconds total)