Starting phenix.real_space_refine on Sun Apr 7 18:08:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqo_0754/04_2024/6kqo_0754_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqo_0754/04_2024/6kqo_0754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqo_0754/04_2024/6kqo_0754.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqo_0754/04_2024/6kqo_0754.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqo_0754/04_2024/6kqo_0754_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqo_0754/04_2024/6kqo_0754_trim_updated.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.356 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 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 Chain: "B" 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: "C" 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 Chain: "D" 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: "E" 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 Chain: "F" 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: "G" 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 Chain: "H" 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: "I" 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 Chain: "J" 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: "K" 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 Chain: "L" 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 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1BANAI A 403 " occ=0.51 ... (86 atoms not shown) pdb=" PN BNAI A 403 " occ=0.49 residue: pdb=" C1BANAI B 402 " occ=0.50 ... (86 atoms not shown) pdb=" PN BNAI B 402 " occ=0.50 residue: pdb=" C1BANAI C 403 " occ=0.50 ... (86 atoms not shown) pdb=" PN BNAI C 403 " occ=0.50 residue: pdb=" C1BANAI D 402 " occ=0.50 ... (86 atoms not shown) pdb=" PN BNAI D 402 " occ=0.50 residue: pdb=" C1BANAI E 403 " occ=0.50 ... (86 atoms not shown) pdb=" PN BNAI E 403 " occ=0.50 residue: pdb=" C1BANAI F 402 " occ=0.51 ... (86 atoms not shown) pdb=" PN BNAI F 402 " occ=0.49 residue: pdb=" C1BANAI G 403 " occ=0.50 ... (86 atoms not shown) pdb=" PN BNAI G 403 " occ=0.50 residue: pdb=" C1BANAI H 402 " occ=0.50 ... (86 atoms not shown) pdb=" PN BNAI H 402 " occ=0.50 residue: pdb=" C1BANAI I 403 " occ=0.50 ... (86 atoms not shown) pdb=" PN BNAI I 403 " occ=0.50 residue: pdb=" C1BANAI J 402 " occ=0.49 ... (86 atoms not shown) pdb=" PN BNAI J 402 " occ=0.51 residue: pdb=" C1BANAI K 403 " occ=0.50 ... (86 atoms not shown) pdb=" PN BNAI K 403 " occ=0.50 residue: pdb=" C1BANAI L 402 " occ=0.49 ... (86 atoms not shown) pdb=" PN BNAI L 402 " occ=0.51 Time building chain proxies: 22.13, per 1000 atoms: 0.35 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: 42.56 Conformation dependent library (CDL) restraints added in 4.8 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 56.4% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.01 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 170 Processing helix chain 'A' and resid 184 through 216 removed outlier: 3.904A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 301 through 311 removed outlier: 3.596A pdb=" N THR A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 49 through 56 Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 160 through 170 Processing helix chain 'B' and resid 184 through 216 removed outlier: 3.904A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.597A pdb=" N THR B 311 " --> pdb=" O TRP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 64 through 70 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 109 through 112 No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 160 through 170 Processing helix chain 'C' and resid 184 through 216 removed outlier: 3.904A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'C' and resid 301 through 311 removed outlier: 3.598A pdb=" N THR C 311 " --> pdb=" O TRP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 49 through 56 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 83 through 90 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 109 through 112 No H-bonds generated for 'chain 'D' and resid 109 through 112' Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 160 through 170 Processing helix chain 'D' and resid 184 through 216 removed outlier: 3.903A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'D' and resid 301 through 311 removed outlier: 3.596A pdb=" N THR D 311 " --> pdb=" O TRP D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 49 through 56 Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 83 through 90 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 109 through 112 No H-bonds generated for 'chain 'E' and resid 109 through 112' Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 160 through 170 Processing helix chain 'E' and resid 184 through 216 removed outlier: 3.904A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Proline residue: E 200 - end of helix Processing helix chain 'E' and resid 221 through 228 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 287 through 298 Processing helix chain 'E' and resid 301 through 311 removed outlier: 3.597A pdb=" N THR E 311 " --> pdb=" O TRP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 49 through 56 Processing helix chain 'F' and resid 64 through 70 Processing helix chain 'F' and resid 83 through 90 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 109 through 112 No H-bonds generated for 'chain 'F' and resid 109 through 112' Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 160 through 170 Processing helix chain 'F' and resid 184 through 217 removed outlier: 3.904A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Proline residue: F 200 - end of helix Processing helix chain 'F' and resid 221 through 228 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 255 through 267 Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 287 through 298 Processing helix chain 'F' and resid 301 through 311 removed outlier: 3.597A pdb=" N THR F 311 " --> pdb=" O TRP F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 325 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 64 through 70 Processing helix chain 'G' and resid 83 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 109 through 112 No H-bonds generated for 'chain 'G' and resid 109 through 112' Processing helix chain 'G' and resid 134 through 140 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 184 through 216 removed outlier: 3.903A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL G 199 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Proline residue: G 200 - end of helix Processing helix chain 'G' and resid 221 through 228 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 248 through 252 Processing helix chain 'G' and resid 255 through 267 Processing helix chain 'G' and resid 269 through 284 Processing helix chain 'G' and resid 287 through 298 Processing helix chain 'G' and resid 301 through 311 removed outlier: 3.597A pdb=" N THR G 311 " --> pdb=" O TRP G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 49 through 56 Processing helix chain 'H' and resid 64 through 70 Processing helix chain 'H' and resid 83 through 90 Processing helix chain 'H' and resid 92 through 97 Processing helix chain 'H' and resid 109 through 112 No H-bonds generated for 'chain 'H' and resid 109 through 112' Processing helix chain 'H' and resid 134 through 140 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 184 through 216 removed outlier: 3.905A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Proline residue: H 200 - end of helix Processing helix chain 'H' and resid 221 through 228 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 248 through 252 Processing helix chain 'H' and resid 255 through 267 Processing helix chain 'H' and resid 269 through 284 Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 301 through 311 removed outlier: 3.597A pdb=" N THR H 311 " --> pdb=" O TRP H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 325 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 83 through 90 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'I' and resid 109 through 112 No H-bonds generated for 'chain 'I' and resid 109 through 112' Processing helix chain 'I' and resid 134 through 140 Processing helix chain 'I' and resid 160 through 170 Processing helix chain 'I' and resid 184 through 216 removed outlier: 3.904A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 200 - end of helix Processing helix chain 'I' and resid 221 through 228 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 255 through 267 Processing helix chain 'I' and resid 269 through 284 Processing helix chain 'I' and resid 287 through 298 Processing helix chain 'I' and resid 301 through 311 removed outlier: 3.597A pdb=" N THR I 311 " --> pdb=" O TRP I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 325 Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 49 through 56 Processing helix chain 'J' and resid 64 through 70 Processing helix chain 'J' and resid 83 through 90 Processing helix chain 'J' and resid 92 through 97 Processing helix chain 'J' and resid 109 through 112 No H-bonds generated for 'chain 'J' and resid 109 through 112' Processing helix chain 'J' and resid 134 through 140 Processing helix chain 'J' and resid 160 through 170 Processing helix chain 'J' and resid 184 through 216 removed outlier: 3.904A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Proline residue: J 200 - end of helix Processing helix chain 'J' and resid 221 through 228 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 248 through 252 Processing helix chain 'J' and resid 255 through 267 Processing helix chain 'J' and resid 269 through 284 Processing helix chain 'J' and resid 287 through 298 Processing helix chain 'J' and resid 301 through 311 removed outlier: 3.596A pdb=" N THR J 311 " --> pdb=" O TRP J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 325 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 49 through 54 Processing helix chain 'K' and resid 64 through 70 Processing helix chain 'K' and resid 83 through 90 Processing helix chain 'K' and resid 92 through 97 Processing helix chain 'K' and resid 109 through 112 No H-bonds generated for 'chain 'K' and resid 109 through 112' Processing helix chain 'K' and resid 134 through 140 Processing helix chain 'K' and resid 160 through 170 Processing helix chain 'K' and resid 184 through 216 removed outlier: 3.903A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N VAL K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Proline residue: K 200 - end of helix Processing helix chain 'K' and resid 221 through 228 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 248 through 252 Processing helix chain 'K' and resid 255 through 267 Processing helix chain 'K' and resid 269 through 284 Processing helix chain 'K' and resid 287 through 298 Processing helix chain 'K' and resid 301 through 311 removed outlier: 3.597A pdb=" N THR K 311 " --> pdb=" O TRP K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 325 Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 49 through 56 Processing helix chain 'L' and resid 64 through 70 Processing helix chain 'L' and resid 83 through 90 Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 109 through 112 No H-bonds generated for 'chain 'L' and resid 109 through 112' Processing helix chain 'L' and resid 134 through 140 Processing helix chain 'L' and resid 160 through 170 Processing helix chain 'L' and resid 184 through 216 removed outlier: 3.904A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP L 198 " --> pdb=" O SER L 194 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 221 through 228 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 248 through 252 Processing helix chain 'L' and resid 255 through 267 Processing helix chain 'L' and resid 269 through 284 Processing helix chain 'L' and resid 287 through 298 Processing helix chain 'L' and resid 301 through 311 removed outlier: 3.596A pdb=" N THR L 311 " --> pdb=" O TRP L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 314 through 325 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.479A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.670A 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: 6.653A pdb=" N LEU A 75 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL A 102 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP A 104 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL A 152 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA A 128 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.429A 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: 6.480A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 73 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE B 21 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU B 75 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 102 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP B 104 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL B 152 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA B 128 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 5.430A 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: 6.479A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.670A 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: 6.653A pdb=" N LEU C 75 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL C 102 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP C 104 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE C 105 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA C 128 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 5.429A 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: 6.479A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.670A 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: 6.653A pdb=" N LEU D 75 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 102 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU D 76 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP D 104 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE D 105 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA D 128 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 5.430A 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: 6.479A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL E 73 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE E 21 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU E 75 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL E 102 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU E 76 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP E 104 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE E 105 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA E 128 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 5.430A 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: 6.479A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.670A 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: 6.653A pdb=" N LEU F 75 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL F 102 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU F 76 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP F 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE F 105 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET F 126 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL F 152 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA F 128 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 5.430A 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: 6.479A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL G 73 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE G 21 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU G 75 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL G 102 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU G 76 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.261A 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: 6.734A pdb=" N MET G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL G 152 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA G 128 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 5.430A 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: 6.479A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL H 73 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE H 21 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU H 75 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU H 76 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.261A 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: 6.735A pdb=" N MET H 126 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL H 152 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ALA H 128 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 5.430A 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: 6.478A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL I 73 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE I 21 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU I 75 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL I 102 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU I 76 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP I 104 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA I 128 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 5.429A 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: 6.478A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL J 73 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE J 21 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU J 75 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL J 102 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU J 76 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.261A 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: 6.734A pdb=" N MET J 126 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL J 152 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA J 128 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 5.429A 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: 6.479A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.670A 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: 6.653A pdb=" N LEU K 75 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL K 102 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU K 76 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASP K 104 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE K 105 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET K 126 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N VAL K 152 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA K 128 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 5.430A 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: 6.479A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL L 73 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE L 21 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU L 75 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL L 102 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU L 76 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ASP L 104 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE L 105 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET L 126 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL L 152 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ALA L 128 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU L 150 " --> pdb=" O ALA L 128 " (cutoff:3.500A) 1427 hydrogen bonds defined for protein. 4209 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: 22.89 Time building geometry restraints manager: 45.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 31210 1.01 - 1.21: 39 1.21 - 1.41: 13392 1.41 - 1.61: 19068 1.61 - 1.81: 372 Bond restraints: 64081 Sorted by residual: bond pdb=" C1BANAI E 403 " pdb=" C2BANAI E 403 " ideal model delta sigma weight residual 1.528 1.280 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C1BANAI A 403 " pdb=" C2BANAI A 403 " ideal model delta sigma weight residual 1.528 1.280 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C1BANAI D 402 " pdb=" C2BANAI D 402 " ideal model delta sigma weight residual 1.528 1.280 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C1BANAI K 403 " pdb=" C2BANAI K 403 " ideal model delta sigma weight residual 1.528 1.280 0.248 2.00e-02 2.50e+03 1.53e+02 bond pdb=" C1BANAI F 402 " pdb=" C2BANAI F 402 " ideal model delta sigma weight residual 1.528 1.281 0.247 2.00e-02 2.50e+03 1.53e+02 ... (remaining 64076 not shown) Histogram of bond angle deviations from ideal: 55.74 - 71.71: 81 71.71 - 87.68: 240 87.68 - 103.65: 436 103.65 - 119.62: 90667 119.62 - 135.59: 24482 Bond angle restraints: 115906 Sorted by residual: angle pdb=" CA LYS J 49 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 114.58 55.74 58.84 3.00e+00 1.11e-01 3.85e+02 angle pdb=" C GLN L 30 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 124.93 66.17 58.76 3.00e+00 1.11e-01 3.84e+02 angle pdb=" CA ALA K 31 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 114.63 55.87 58.76 3.00e+00 1.11e-01 3.84e+02 angle pdb=" C GLN K 30 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 124.93 66.19 58.74 3.00e+00 1.11e-01 3.83e+02 angle pdb=" C ASP J 48 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 124.88 66.20 58.68 3.00e+00 1.11e-01 3.83e+02 ... (remaining 115901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 26590 17.39 - 34.77: 3017 34.77 - 52.16: 817 52.16 - 69.54: 258 69.54 - 86.93: 39 Dihedral angle restraints: 30721 sinusoidal: 17368 harmonic: 13353 Sorted by residual: dihedral pdb=" CA LYS F 89 " pdb=" C LYS F 89 " pdb=" N LYS F 90 " pdb=" CA LYS F 90 " ideal model delta harmonic sigma weight residual 180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA LYS L 89 " pdb=" C LYS L 89 " pdb=" N LYS L 90 " pdb=" CA LYS L 90 " ideal model delta harmonic sigma weight residual -180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA LYS H 89 " pdb=" C LYS H 89 " pdb=" N LYS H 90 " pdb=" CA LYS H 90 " ideal model delta harmonic sigma weight residual -180.00 -160.74 -19.26 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 30718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3661 0.068 - 0.135: 991 0.135 - 0.203: 127 0.203 - 0.270: 57 0.270 - 0.338: 24 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 -2.25 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" CG LEU F 95 " pdb=" CB LEU F 95 " pdb=" CD1 LEU F 95 " pdb=" CD2 LEU F 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.82e+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 -2.25 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 4857 not shown) Planarity restraints: 9304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU K 216 " 0.023 2.00e-02 2.50e+03 4.14e-02 1.72e+01 pdb=" N TYR K 217 " -0.071 2.00e-02 2.50e+03 pdb=" CA TYR K 217 " 0.018 2.00e-02 2.50e+03 pdb=" H TYR K 217 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU G 216 " 0.023 2.00e-02 2.50e+03 4.13e-02 1.70e+01 pdb=" N TYR G 217 " -0.071 2.00e-02 2.50e+03 pdb=" CA TYR G 217 " 0.018 2.00e-02 2.50e+03 pdb=" H TYR G 217 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU J 216 " 0.023 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" N TYR J 217 " -0.071 2.00e-02 2.50e+03 pdb=" CA TYR J 217 " 0.018 2.00e-02 2.50e+03 pdb=" H TYR J 217 " 0.031 2.00e-02 2.50e+03 ... (remaining 9301 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 1090 2.01 - 2.65: 92148 2.65 - 3.30: 182878 3.30 - 3.95: 232519 3.95 - 4.60: 382247 Nonbonded interactions: 890882 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 1.438 1.816 nonbonded pdb=" H ALA L 31 " pdb=" HA ALA L 31 " model vdw 1.494 1.816 nonbonded pdb=" H ALA K 31 " pdb=" HA ALA K 31 " model vdw 1.494 1.816 nonbonded pdb=" O LEU L 150 " pdb=" H SER L 182 " model vdw 1.511 1.850 ... (remaining 890877 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=0.49 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: 2.140 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: 0.710 Extract box with map and model: 11.360 Check model and map are aligned: 0.710 Set scattering table: 0.460 Process input model: 163.830 Find NCS groups from input model: 3.390 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 195.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.019 0.248 32856 Z= 1.251 Angle : 1.163 14.294 44580 Z= 0.512 Chirality : 0.067 0.338 4860 Planarity : 0.004 0.044 5520 Dihedral : 16.217 86.926 13236 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.03 % Allowed : 0.84 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.10), residues: 3912 helix: -2.87 (0.08), residues: 2448 sheet: -2.86 (0.19), residues: 540 loop : -4.27 (0.13), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 198 HIS 0.004 0.001 HIS F 196 PHE 0.010 0.001 PHE C 303 TYR 0.010 0.001 TYR G 23 ARG 0.002 0.000 ARG F 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 549 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.8797 (mt) cc_final: 0.8543 (mm) REVERT: A 75 LEU cc_start: 0.9083 (mp) cc_final: 0.8602 (mp) REVERT: G 18 ILE cc_start: 0.8780 (mt) cc_final: 0.8531 (mm) REVERT: I 18 ILE cc_start: 0.8695 (mt) cc_final: 0.8472 (mm) REVERT: I 75 LEU cc_start: 0.9119 (mp) cc_final: 0.8646 (mp) REVERT: L 89 LYS cc_start: 0.8814 (mttt) cc_final: 0.8561 (mttm) outliers start: 1 outliers final: 0 residues processed: 550 average time/residue: 2.8751 time to fit residues: 1840.9689 Evaluate side-chains 305 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 3.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 161 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 348 optimal weight: 0.6980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN A 249 GLN A 278 ASN B 37 ASN B 278 ASN C 37 ASN C 278 ASN D 37 ASN D 249 GLN D 278 ASN E 37 ASN E 278 ASN F 37 ASN F 278 ASN G 37 ASN G 278 ASN H 37 ASN H 278 ASN I 37 ASN I 249 GLN I 278 ASN J 37 ASN J 249 GLN J 278 ASN K 37 ASN K 249 GLN K 278 ASN L 37 ASN L 249 GLN L 278 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32856 Z= 0.210 Angle : 0.705 20.140 44580 Z= 0.352 Chirality : 0.121 1.735 4860 Planarity : 0.004 0.052 5520 Dihedral : 9.031 79.237 5784 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.84 % Allowed : 9.80 % Favored : 88.36 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.12), residues: 3912 helix: -0.49 (0.10), residues: 2388 sheet: -1.92 (0.19), residues: 552 loop : -3.26 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 198 HIS 0.002 0.001 HIS B 196 PHE 0.009 0.001 PHE J 184 TYR 0.014 0.001 TYR F 217 ARG 0.005 0.000 ARG G 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 349 time to evaluate : 3.947 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: A 18 ILE cc_start: 0.8726 (mt) cc_final: 0.8493 (mm) REVERT: A 131 MET cc_start: 0.3963 (OUTLIER) cc_final: 0.3635 (mtm) REVERT: A 216 GLU cc_start: 0.8108 (mp0) cc_final: 0.7759 (mp0) REVERT: B 76 LEU cc_start: 0.8732 (tt) cc_final: 0.8291 (tt) REVERT: B 131 MET cc_start: 0.3455 (OUTLIER) cc_final: 0.3035 (mtm) REVERT: C 76 LEU cc_start: 0.8746 (tt) cc_final: 0.8455 (tt) REVERT: C 131 MET cc_start: 0.3649 (OUTLIER) cc_final: 0.3277 (mtm) REVERT: D 131 MET cc_start: 0.3452 (OUTLIER) cc_final: 0.3105 (mtm) REVERT: E 76 LEU cc_start: 0.8699 (tt) cc_final: 0.8264 (tt) REVERT: E 131 MET cc_start: 0.3753 (OUTLIER) cc_final: 0.3464 (mtm) REVERT: E 216 GLU cc_start: 0.8039 (mp0) cc_final: 0.7697 (mp0) REVERT: F 76 LEU cc_start: 0.8639 (tt) cc_final: 0.8410 (tt) REVERT: F 131 MET cc_start: 0.3704 (OUTLIER) cc_final: 0.3393 (mtm) REVERT: G 131 MET cc_start: 0.3716 (OUTLIER) cc_final: 0.3442 (mtm) REVERT: G 215 LYS cc_start: 0.9042 (mmtp) cc_final: 0.8735 (mttm) REVERT: H 76 LEU cc_start: 0.8673 (tt) cc_final: 0.8248 (tt) REVERT: H 131 MET cc_start: 0.3741 (OUTLIER) cc_final: 0.3130 (mtm) REVERT: H 215 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8760 (mttm) REVERT: I 131 MET cc_start: 0.3644 (OUTLIER) cc_final: 0.3286 (mtm) REVERT: I 216 GLU cc_start: 0.8073 (mp0) cc_final: 0.7733 (mp0) REVERT: J 26 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.7350 (mp10) REVERT: J 131 MET cc_start: 0.3782 (OUTLIER) cc_final: 0.3427 (mtm) REVERT: J 216 GLU cc_start: 0.8029 (mp0) cc_final: 0.7707 (mp0) REVERT: K 131 MET cc_start: 0.3474 (OUTLIER) cc_final: 0.3117 (mtm) REVERT: L 26 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7251 (mp10) REVERT: L 76 LEU cc_start: 0.8551 (tt) cc_final: 0.8099 (tt) REVERT: L 131 MET cc_start: 0.3789 (OUTLIER) cc_final: 0.3457 (mtm) outliers start: 59 outliers final: 22 residues processed: 369 average time/residue: 2.6132 time to fit residues: 1142.0380 Evaluate side-chains 320 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 284 time to evaluate : 3.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LYS Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 154 GLN Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 154 GLN Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 154 GLN Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain J residue 26 GLN Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 250 MET Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 131 MET 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: 10.0000 chunk 290 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 0.0980 chunk 377 optimal weight: 5.9990 chunk 311 optimal weight: 8.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 280 optimal weight: 5.9990 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 249 GLN E 249 GLN F 249 GLN G 249 GLN H 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 32856 Z= 0.452 Angle : 0.781 19.143 44580 Z= 0.402 Chirality : 0.123 1.867 4860 Planarity : 0.005 0.062 5520 Dihedral : 9.172 88.406 5784 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.15 % Allowed : 10.49 % Favored : 87.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3912 helix: 0.01 (0.10), residues: 2424 sheet: -1.68 (0.21), residues: 504 loop : -3.12 (0.17), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 198 HIS 0.009 0.002 HIS L 196 PHE 0.014 0.002 PHE D 288 TYR 0.022 0.002 TYR K 23 ARG 0.004 0.000 ARG H 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 286 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 MET cc_start: 0.4269 (OUTLIER) cc_final: 0.3819 (mtm) REVERT: B 76 LEU cc_start: 0.8832 (tt) cc_final: 0.8550 (tt) REVERT: C 76 LEU cc_start: 0.8899 (tt) cc_final: 0.8688 (tt) REVERT: C 131 MET cc_start: 0.3982 (OUTLIER) cc_final: 0.3510 (mtm) REVERT: E 131 MET cc_start: 0.4187 (OUTLIER) cc_final: 0.3743 (mtm) REVERT: F 131 MET cc_start: 0.4084 (OUTLIER) cc_final: 0.3635 (mtm) REVERT: G 131 MET cc_start: 0.3894 (OUTLIER) cc_final: 0.3481 (mtm) REVERT: H 76 LEU cc_start: 0.8901 (tt) cc_final: 0.8657 (tt) REVERT: H 131 MET cc_start: 0.3823 (OUTLIER) cc_final: 0.3408 (mtm) REVERT: I 76 LEU cc_start: 0.8886 (tt) cc_final: 0.8624 (tt) REVERT: I 131 MET cc_start: 0.4148 (OUTLIER) cc_final: 0.3692 (mtm) REVERT: J 131 MET cc_start: 0.4055 (OUTLIER) cc_final: 0.3623 (mtm) REVERT: L 26 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7087 (mp10) REVERT: L 131 MET cc_start: 0.4242 (OUTLIER) cc_final: 0.3765 (mtm) outliers start: 69 outliers final: 24 residues processed: 329 average time/residue: 2.5239 time to fit residues: 989.6790 Evaluate side-chains 289 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 255 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 131 MET 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: 9.9990 chunk 181 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 234 optimal weight: 3.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 332 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32856 Z= 0.284 Angle : 0.689 20.040 44580 Z= 0.351 Chirality : 0.124 1.735 4860 Planarity : 0.004 0.049 5520 Dihedral : 8.403 88.395 5784 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.69 % Allowed : 11.70 % Favored : 86.61 % 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: -0.83 (0.13), residues: 3912 helix: 0.64 (0.10), residues: 2388 sheet: -1.44 (0.21), residues: 504 loop : -2.86 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 198 HIS 0.004 0.001 HIS J 196 PHE 0.009 0.002 PHE F 228 TYR 0.015 0.001 TYR I 23 ARG 0.004 0.000 ARG F 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 334 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 280 time to evaluate : 4.048 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: A 131 MET cc_start: 0.3995 (OUTLIER) cc_final: 0.3708 (mtt) REVERT: B 76 LEU cc_start: 0.8898 (tt) cc_final: 0.8663 (tt) REVERT: B 131 MET cc_start: 0.3551 (OUTLIER) cc_final: 0.2959 (mtt) REVERT: C 131 MET cc_start: 0.3524 (OUTLIER) cc_final: 0.3153 (mtm) REVERT: D 131 MET cc_start: 0.3715 (OUTLIER) cc_final: 0.3343 (mtt) REVERT: E 76 LEU cc_start: 0.8882 (tt) cc_final: 0.8609 (tt) REVERT: E 131 MET cc_start: 0.3978 (OUTLIER) cc_final: 0.3649 (mtt) REVERT: F 131 MET cc_start: 0.3896 (OUTLIER) cc_final: 0.3619 (mtt) REVERT: G 131 MET cc_start: 0.3848 (OUTLIER) cc_final: 0.3646 (mtt) REVERT: H 131 MET cc_start: 0.3421 (OUTLIER) cc_final: 0.3126 (mtt) REVERT: I 131 MET cc_start: 0.3749 (OUTLIER) cc_final: 0.3359 (mtm) REVERT: J 131 MET cc_start: 0.4053 (OUTLIER) cc_final: 0.3775 (mtt) REVERT: K 131 MET cc_start: 0.3678 (OUTLIER) cc_final: 0.3316 (mtt) REVERT: L 26 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6991 (mp10) REVERT: L 131 MET cc_start: 0.3864 (OUTLIER) cc_final: 0.3509 (mtt) outliers start: 54 outliers final: 22 residues processed: 306 average time/residue: 2.3267 time to fit residues: 859.2663 Evaluate side-chains 286 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 251 time to evaluate : 3.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 251 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 0.8980 chunk 333 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 32856 Z= 0.299 Angle : 0.692 19.814 44580 Z= 0.353 Chirality : 0.124 1.761 4860 Planarity : 0.004 0.048 5520 Dihedral : 8.522 83.696 5784 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.81 % Allowed : 12.70 % Favored : 85.49 % 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: -0.44 (0.13), residues: 3912 helix: 0.88 (0.10), residues: 2400 sheet: -1.25 (0.21), residues: 540 loop : -2.61 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 198 HIS 0.006 0.002 HIS D 196 PHE 0.010 0.002 PHE F 288 TYR 0.013 0.001 TYR K 23 ARG 0.002 0.000 ARG J 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 345 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 287 time to evaluate : 3.848 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: A 131 MET cc_start: 0.4159 (OUTLIER) cc_final: 0.3803 (mtt) REVERT: B 131 MET cc_start: 0.3613 (OUTLIER) cc_final: 0.3212 (mtt) REVERT: C 131 MET cc_start: 0.3620 (OUTLIER) cc_final: 0.3207 (mtm) REVERT: D 131 MET cc_start: 0.3815 (OUTLIER) cc_final: 0.3377 (mtt) REVERT: D 249 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9155 (pp30) REVERT: E 131 MET cc_start: 0.4168 (OUTLIER) cc_final: 0.3803 (mtt) REVERT: F 131 MET cc_start: 0.4166 (OUTLIER) cc_final: 0.3789 (mtt) REVERT: G 131 MET cc_start: 0.3983 (OUTLIER) cc_final: 0.3621 (mtt) REVERT: H 131 MET cc_start: 0.3651 (OUTLIER) cc_final: 0.3308 (mtt) REVERT: I 131 MET cc_start: 0.3956 (OUTLIER) cc_final: 0.3563 (mtm) REVERT: J 53 LEU cc_start: 0.8657 (tp) cc_final: 0.8384 (tp) REVERT: J 131 MET cc_start: 0.4180 (OUTLIER) cc_final: 0.3886 (mtt) REVERT: K 131 MET cc_start: 0.3708 (OUTLIER) cc_final: 0.3297 (mtt) REVERT: L 26 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: L 131 MET cc_start: 0.3976 (OUTLIER) cc_final: 0.3662 (mtt) outliers start: 58 outliers final: 18 residues processed: 315 average time/residue: 2.3930 time to fit residues: 911.9640 Evaluate side-chains 299 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 267 time to evaluate : 3.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 251 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32856 Z= 0.296 Angle : 0.693 19.951 44580 Z= 0.352 Chirality : 0.124 1.749 4860 Planarity : 0.004 0.046 5520 Dihedral : 8.496 89.472 5784 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.78 % Allowed : 14.04 % Favored : 84.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.13), residues: 3912 helix: 1.00 (0.11), residues: 2400 sheet: -1.09 (0.21), residues: 540 loop : -2.48 (0.18), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 198 HIS 0.004 0.001 HIS G 196 PHE 0.010 0.001 PHE A 228 TYR 0.027 0.001 TYR D 23 ARG 0.002 0.000 ARG H 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 333 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 276 time to evaluate : 4.531 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: A 131 MET cc_start: 0.3903 (OUTLIER) cc_final: 0.3612 (mtt) REVERT: B 26 GLN cc_start: 0.6925 (mp10) cc_final: 0.6600 (mp10) REVERT: B 131 MET cc_start: 0.3551 (OUTLIER) cc_final: 0.3298 (mtt) REVERT: C 131 MET cc_start: 0.3680 (OUTLIER) cc_final: 0.2939 (mtt) REVERT: D 131 MET cc_start: 0.3734 (OUTLIER) cc_final: 0.3475 (mtt) REVERT: E 131 MET cc_start: 0.3892 (OUTLIER) cc_final: 0.3674 (mtt) REVERT: G 131 MET cc_start: 0.3929 (OUTLIER) cc_final: 0.3718 (mtt) REVERT: H 53 LEU cc_start: 0.8716 (tp) cc_final: 0.8382 (tp) REVERT: H 131 MET cc_start: 0.3637 (OUTLIER) cc_final: 0.3392 (mtt) REVERT: I 131 MET cc_start: 0.3863 (OUTLIER) cc_final: 0.3587 (mtt) REVERT: I 249 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9158 (pp30) REVERT: J 53 LEU cc_start: 0.8675 (tp) cc_final: 0.8418 (tp) REVERT: J 131 MET cc_start: 0.4009 (OUTLIER) cc_final: 0.3790 (mtt) REVERT: K 131 MET cc_start: 0.3625 (OUTLIER) cc_final: 0.3391 (mtt) REVERT: L 26 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: L 131 MET cc_start: 0.3927 (OUTLIER) cc_final: 0.3617 (mtt) outliers start: 57 outliers final: 28 residues processed: 302 average time/residue: 2.3306 time to fit residues: 854.4990 Evaluate side-chains 311 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 270 time to evaluate : 3.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 250 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 131 MET Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 211 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 370 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 32856 Z= 0.313 Angle : 0.704 19.894 44580 Z= 0.358 Chirality : 0.125 1.755 4860 Planarity : 0.004 0.048 5520 Dihedral : 8.697 88.606 5784 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.94 % Allowed : 14.70 % Favored : 83.36 % 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: -0.15 (0.13), residues: 3912 helix: 1.03 (0.11), residues: 2400 sheet: -0.90 (0.22), residues: 504 loop : -2.39 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 198 HIS 0.005 0.001 HIS B 196 PHE 0.010 0.002 PHE L 288 TYR 0.026 0.001 TYR I 23 ARG 0.002 0.000 ARG F 28 *********************** 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 348 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 286 time to evaluate : 3.859 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: A 131 MET cc_start: 0.4099 (OUTLIER) cc_final: 0.3755 (mtt) REVERT: B 26 GLN cc_start: 0.6918 (mp10) cc_final: 0.6589 (mp10) REVERT: B 131 MET cc_start: 0.3743 (OUTLIER) cc_final: 0.3456 (mtt) REVERT: C 131 MET cc_start: 0.3709 (OUTLIER) cc_final: 0.3164 (mtt) REVERT: D 131 MET cc_start: 0.3757 (OUTLIER) cc_final: 0.3370 (mtt) REVERT: D 249 GLN cc_start: 0.9555 (OUTLIER) cc_final: 0.9163 (pp30) REVERT: E 131 MET cc_start: 0.3887 (OUTLIER) cc_final: 0.3645 (mtt) REVERT: F 53 LEU cc_start: 0.8674 (tp) cc_final: 0.8427 (tp) REVERT: F 131 MET cc_start: 0.3531 (OUTLIER) cc_final: 0.3317 (mtt) REVERT: G 53 LEU cc_start: 0.8667 (tp) cc_final: 0.8382 (tp) REVERT: G 131 MET cc_start: 0.3913 (OUTLIER) cc_final: 0.3467 (mtt) REVERT: H 53 LEU cc_start: 0.8780 (tp) cc_final: 0.8451 (tp) REVERT: H 131 MET cc_start: 0.3612 (OUTLIER) cc_final: 0.3346 (mtt) REVERT: I 131 MET cc_start: 0.4009 (OUTLIER) cc_final: 0.3679 (mtt) REVERT: I 249 GLN cc_start: 0.9570 (OUTLIER) cc_final: 0.9182 (pp30) REVERT: J 53 LEU cc_start: 0.8685 (tp) cc_final: 0.8417 (tp) REVERT: K 131 MET cc_start: 0.3718 (OUTLIER) cc_final: 0.3325 (mtt) REVERT: L 26 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.6931 (mm-40) REVERT: L 131 MET cc_start: 0.4092 (OUTLIER) cc_final: 0.3738 (mtt) outliers start: 62 outliers final: 32 residues processed: 314 average time/residue: 2.3619 time to fit residues: 899.0468 Evaluate side-chains 323 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 277 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 131 MET Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 131 MET Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ASP Chi-restraints excluded: chain L residue 131 MET Chi-restraints excluded: chain L residue 162 ASP Chi-restraints excluded: chain L residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 290 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32856 Z= 0.268 Angle : 0.691 20.073 44580 Z= 0.348 Chirality : 0.125 1.743 4860 Planarity : 0.004 0.045 5520 Dihedral : 8.501 87.913 5784 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.69 % Allowed : 15.17 % Favored : 83.15 % 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: 0.01 (0.13), residues: 3912 helix: 1.14 (0.11), residues: 2400 sheet: -0.84 (0.22), residues: 504 loop : -2.26 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 198 HIS 0.003 0.001 HIS G 196 PHE 0.009 0.001 PHE A 228 TYR 0.026 0.001 TYR K 23 ARG 0.002 0.000 ARG J 28 *********************** 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 341 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 287 time to evaluate : 3.885 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: B 26 GLN cc_start: 0.6877 (mp10) cc_final: 0.6543 (mp10) REVERT: C 131 MET cc_start: 0.3952 (OUTLIER) cc_final: 0.3488 (mtt) REVERT: D 131 MET cc_start: 0.3771 (OUTLIER) cc_final: 0.3538 (mtt) REVERT: D 249 GLN cc_start: 0.9557 (OUTLIER) cc_final: 0.9155 (pp30) REVERT: E 131 MET cc_start: 0.3876 (OUTLIER) cc_final: 0.3669 (mtt) REVERT: F 53 LEU cc_start: 0.8680 (tp) cc_final: 0.8439 (tp) REVERT: G 53 LEU cc_start: 0.8668 (tp) cc_final: 0.8388 (tp) REVERT: G 131 MET cc_start: 0.3857 (OUTLIER) cc_final: 0.3630 (mtt) REVERT: H 53 LEU cc_start: 0.8783 (tp) cc_final: 0.8449 (tp) REVERT: H 131 MET cc_start: 0.3583 (OUTLIER) cc_final: 0.3378 (mtt) REVERT: I 249 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.9162 (pp30) REVERT: J 53 LEU cc_start: 0.8703 (tp) cc_final: 0.8447 (tp) REVERT: K 131 MET cc_start: 0.3730 (OUTLIER) cc_final: 0.3492 (mtt) REVERT: K 249 GLN cc_start: 0.9551 (OUTLIER) cc_final: 0.9160 (pp30) outliers start: 54 outliers final: 32 residues processed: 312 average time/residue: 2.2822 time to fit residues: 864.3499 Evaluate side-chains 315 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 274 time to evaluate : 3.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain L residue 83 MET Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ASP 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: 8.9990 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 6.9990 chunk 343 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 32856 Z= 0.388 Angle : 0.738 19.807 44580 Z= 0.376 Chirality : 0.125 1.752 4860 Planarity : 0.004 0.050 5520 Dihedral : 9.087 87.301 5784 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.53 % Allowed : 15.64 % Favored : 82.83 % 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: -0.21 (0.13), residues: 3912 helix: 0.94 (0.10), residues: 2400 sheet: -0.78 (0.23), residues: 504 loop : -2.36 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 284 HIS 0.005 0.001 HIS L 196 PHE 0.012 0.002 PHE E 288 TYR 0.028 0.002 TYR I 23 ARG 0.002 0.000 ARG I 28 *********************** 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 330 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 281 time to evaluate : 3.939 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: A 53 LEU cc_start: 0.8633 (tp) cc_final: 0.8374 (tp) REVERT: B 26 GLN cc_start: 0.6872 (mp10) cc_final: 0.6532 (mp10) REVERT: B 53 LEU cc_start: 0.8578 (tp) cc_final: 0.8317 (tp) REVERT: B 131 MET cc_start: 0.3355 (mtt) cc_final: 0.3026 (mtt) REVERT: C 131 MET cc_start: 0.3834 (OUTLIER) cc_final: 0.3306 (mtt) REVERT: D 131 MET cc_start: 0.3885 (OUTLIER) cc_final: 0.3503 (mtt) REVERT: D 249 GLN cc_start: 0.9583 (OUTLIER) cc_final: 0.9198 (pp30) REVERT: E 131 MET cc_start: 0.3898 (OUTLIER) cc_final: 0.3474 (mtt) REVERT: F 53 LEU cc_start: 0.8701 (tp) cc_final: 0.8454 (tp) REVERT: G 53 LEU cc_start: 0.8663 (tp) cc_final: 0.8404 (tp) REVERT: G 131 MET cc_start: 0.3930 (OUTLIER) cc_final: 0.3519 (mtt) REVERT: H 131 MET cc_start: 0.3670 (OUTLIER) cc_final: 0.3391 (mtt) REVERT: I 249 GLN cc_start: 0.9584 (OUTLIER) cc_final: 0.9203 (pp30) REVERT: J 53 LEU cc_start: 0.8745 (tp) cc_final: 0.8476 (tp) REVERT: K 131 MET cc_start: 0.3873 (OUTLIER) cc_final: 0.3487 (mtt) REVERT: K 249 GLN cc_start: 0.9567 (OUTLIER) cc_final: 0.9188 (pp30) REVERT: L 26 GLN cc_start: 0.6857 (OUTLIER) cc_final: 0.6063 (mm110) REVERT: L 53 LEU cc_start: 0.8618 (tp) cc_final: 0.8367 (tp) outliers start: 49 outliers final: 33 residues processed: 304 average time/residue: 2.2888 time to fit residues: 845.1575 Evaluate side-chains 317 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 274 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 250 MET Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 250 MET Chi-restraints excluded: chain L residue 26 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ASP 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: 6.9990 chunk 253 optimal weight: 3.9990 chunk 382 optimal weight: 0.4980 chunk 352 optimal weight: 9.9990 chunk 304 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 32856 Z= 0.345 Angle : 0.812 59.200 44580 Z= 0.435 Chirality : 0.125 1.746 4860 Planarity : 0.004 0.050 5520 Dihedral : 9.078 87.311 5784 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.65 % Allowed : 15.61 % Favored : 82.74 % 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: -0.22 (0.13), residues: 3912 helix: 0.93 (0.10), residues: 2400 sheet: -0.79 (0.23), residues: 504 loop : -2.35 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 284 HIS 0.004 0.001 HIS A 196 PHE 0.012 0.002 PHE K 288 TYR 0.023 0.001 TYR I 23 ARG 0.001 0.000 ARG H 28 ********************** 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 327 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 274 time to evaluate : 4.549 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: A 53 LEU cc_start: 0.8631 (tp) cc_final: 0.8370 (tp) REVERT: B 26 GLN cc_start: 0.6878 (mp10) cc_final: 0.6534 (mp10) REVERT: B 53 LEU cc_start: 0.8577 (tp) cc_final: 0.8314 (tp) REVERT: B 131 MET cc_start: 0.3347 (mtt) cc_final: 0.3017 (mtt) REVERT: C 131 MET cc_start: 0.3823 (OUTLIER) cc_final: 0.3295 (mtt) REVERT: D 131 MET cc_start: 0.3875 (OUTLIER) cc_final: 0.3493 (mtt) REVERT: D 249 GLN cc_start: 0.9579 (OUTLIER) cc_final: 0.9193 (pp30) REVERT: E 131 MET cc_start: 0.3839 (OUTLIER) cc_final: 0.3415 (mtt) REVERT: F 53 LEU cc_start: 0.8695 (tp) cc_final: 0.8450 (tp) REVERT: G 53 LEU cc_start: 0.8663 (tp) cc_final: 0.8401 (tp) REVERT: G 131 MET cc_start: 0.3974 (OUTLIER) cc_final: 0.3558 (mtt) REVERT: H 131 MET cc_start: 0.3651 (OUTLIER) cc_final: 0.3372 (mtt) REVERT: I 249 GLN cc_start: 0.9582 (OUTLIER) cc_final: 0.9200 (pp30) REVERT: J 53 LEU cc_start: 0.8744 (tp) cc_final: 0.8473 (tp) REVERT: K 131 MET cc_start: 0.3862 (OUTLIER) cc_final: 0.3476 (mtt) REVERT: K 249 GLN cc_start: 0.9564 (OUTLIER) cc_final: 0.9185 (pp30) REVERT: L 53 LEU cc_start: 0.8609 (tp) cc_final: 0.8357 (tp) outliers start: 53 outliers final: 41 residues processed: 298 average time/residue: 2.2401 time to fit residues: 811.6698 Evaluate side-chains 323 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 273 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain C residue 99 LYS Chi-restraints excluded: chain C residue 131 MET Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 249 GLN Chi-restraints excluded: chain D residue 250 MET Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 131 MET Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 4 THR Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 131 MET Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain H residue 99 LYS Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain H residue 162 ASP Chi-restraints excluded: chain H residue 250 MET Chi-restraints excluded: chain I residue 23 TYR Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 162 ASP Chi-restraints excluded: chain I residue 249 GLN Chi-restraints excluded: chain J residue 103 LEU Chi-restraints excluded: chain J residue 162 ASP Chi-restraints excluded: chain K residue 99 LYS Chi-restraints excluded: chain K residue 131 MET Chi-restraints excluded: chain K residue 162 ASP Chi-restraints excluded: chain K residue 249 GLN Chi-restraints excluded: chain K residue 250 MET Chi-restraints excluded: chain L residue 99 LYS Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 104 ASP 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: 3.9990 chunk 324 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.098151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.068890 restraints weight = 256437.221| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.40 r_work: 0.2832 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.141 32856 Z= 0.345 Angle : 0.812 59.200 44580 Z= 0.435 Chirality : 0.125 1.746 4860 Planarity : 0.004 0.050 5520 Dihedral : 9.078 87.311 5784 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.56 % Allowed : 15.70 % Favored : 82.74 % 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: -0.22 (0.13), residues: 3912 helix: 0.93 (0.10), residues: 2400 sheet: -0.79 (0.23), residues: 504 loop : -2.35 (0.16), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 284 HIS 0.004 0.001 HIS A 196 PHE 0.012 0.002 PHE K 288 TYR 0.023 0.001 TYR I 23 ARG 0.001 0.000 ARG H 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16707.57 seconds wall clock time: 287 minutes 12.31 seconds (17232.31 seconds total)