Starting phenix.real_space_refine (version: dev) on Fri Feb 24 14:02:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/02_2023/6kqk_0753_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/02_2023/6kqk_0753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/02_2023/6kqk_0753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/02_2023/6kqk_0753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/02_2023/6kqk_0753_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/02_2023/6kqk_0753_trim_updated.pdb" } resolution = 2.17 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.014 sd= 0.407 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned 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-4877/modules/chem_data/mon_lib" Total number of atoms: 63373 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "B" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "D" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "E" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "F" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" Number of atoms: 5185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5185 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "H" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "I" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "J" Number of atoms: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "K" Number of atoms: 5184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5184 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" Number of atoms: 5180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5180 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "A" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "B" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "C" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "D" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "E" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "F" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "G" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "H" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "I" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "J" Number of atoms: 99 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 9 Chain: "K" Number of atoms: 98 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Conformer: "B" Number of residues, atoms: 3, 54 Unusual residues: {' MG': 1, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} bond proxies already assigned to first conformer: 9 Chain: "L" Number of atoms: 100 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Conformer: "B" Number of residues, atoms: 5, 56 Unusual residues: {' MG': 3, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} bond proxies already assigned to first conformer: 9 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" C1BANAI A 402 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI A 402 " occ=0.54 residue: pdb=" C1BANAI B 403 " occ=0.47 ... (86 atoms not shown) pdb=" PN BNAI B 403 " occ=0.53 residue: pdb=" C1BANAI C 402 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI C 402 " occ=0.54 residue: pdb=" C1BANAI D 403 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI D 403 " occ=0.54 residue: pdb=" C1BANAI E 402 " occ=0.47 ... (86 atoms not shown) pdb=" PN BNAI E 402 " occ=0.53 residue: pdb=" C1BANAI F 403 " occ=0.45 ... (86 atoms not shown) pdb=" PN BNAI F 403 " occ=0.55 residue: pdb=" C1BANAI G 402 " occ=0.47 ... (86 atoms not shown) pdb=" PN BNAI G 402 " occ=0.53 residue: pdb=" C1BANAI H 403 " occ=0.47 ... (86 atoms not shown) pdb=" PN BNAI H 403 " occ=0.53 residue: pdb=" C1BANAI I 402 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI I 402 " occ=0.54 residue: pdb=" C1BANAI J 403 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI J 403 " occ=0.54 residue: pdb=" C1BANAI K 402 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI K 402 " occ=0.54 residue: pdb=" C1BANAI L 404 " occ=0.46 ... (86 atoms not shown) pdb=" PN BNAI L 404 " occ=0.54 Time building chain proxies: 22.08, 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: 45.30 Conformation dependent library (CDL) restraints added in 4.0 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 12 sheets defined 57.0% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 49 through 56 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 109 through 112 No H-bonds generated for 'chain 'A' and resid 109 through 112' Processing helix chain 'A' and resid 134 through 140 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 184 through 217 removed outlier: 3.600A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.571A pdb=" N TYR A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 248 through 252 Processing helix chain 'A' and resid 255 through 267 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 287 through 298 Processing helix chain 'A' and resid 301 through 311 Processing helix chain 'A' and resid 314 through 325 Processing helix chain 'B' and resid 26 through 37 Processing helix chain 'B' and resid 49 through 56 Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 83 through 90 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 109 through 112 No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 184 through 217 removed outlier: 3.601A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.571A pdb=" N TYR B 217 " --> pdb=" O ALA B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 269 through 284 Processing helix chain 'B' and resid 287 through 298 Processing helix chain 'B' and resid 301 through 311 Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 49 through 56 Processing helix chain 'C' and resid 64 through 70 Processing helix chain 'C' and resid 83 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 109 through 112 No H-bonds generated for 'chain 'C' and resid 109 through 112' Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 160 through 171 Processing helix chain 'C' and resid 184 through 217 removed outlier: 3.601A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix removed outlier: 3.572A pdb=" N TYR C 217 " --> pdb=" O ALA C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 255 through 267 Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 287 through 298 Processing helix chain 'C' and resid 301 through 311 Processing helix chain 'C' and resid 314 through 325 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 49 through 56 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 83 through 90 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 109 through 112 No H-bonds generated for 'chain 'D' and resid 109 through 112' Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 184 through 217 removed outlier: 3.601A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix removed outlier: 3.572A pdb=" N TYR D 217 " --> pdb=" O ALA D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'D' and resid 301 through 311 Processing helix chain 'D' and resid 314 through 325 Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 49 through 56 Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 83 through 90 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 109 through 112 No H-bonds generated for 'chain 'E' and resid 109 through 112' Processing helix chain 'E' and resid 134 through 140 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 184 through 217 removed outlier: 3.600A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Proline residue: E 200 - end of helix removed outlier: 3.572A pdb=" N TYR E 217 " --> pdb=" O ALA E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 228 Processing helix chain 'E' and resid 233 through 244 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 287 through 298 Processing helix chain 'E' and resid 301 through 311 Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 49 through 56 Processing helix chain 'F' and resid 64 through 70 Processing helix chain 'F' and resid 83 through 90 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 109 through 112 No H-bonds generated for 'chain 'F' and resid 109 through 112' Processing helix chain 'F' and resid 134 through 140 Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 184 through 217 removed outlier: 3.601A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Proline residue: F 200 - end of helix removed outlier: 3.571A pdb=" N TYR F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 228 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 248 through 252 Processing helix chain 'F' and resid 255 through 267 Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 287 through 298 Processing helix chain 'F' and resid 301 through 311 Processing helix chain 'F' and resid 314 through 325 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 49 through 56 Processing helix chain 'G' and resid 64 through 70 Processing helix chain 'G' and resid 83 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 109 through 112 No H-bonds generated for 'chain 'G' and resid 109 through 112' Processing helix chain 'G' and resid 134 through 140 Processing helix chain 'G' and resid 160 through 171 Processing helix chain 'G' and resid 184 through 217 removed outlier: 3.600A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL G 199 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Proline residue: G 200 - end of helix removed outlier: 3.571A pdb=" N TYR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 228 Processing helix chain 'G' and resid 233 through 244 Processing helix chain 'G' and resid 248 through 252 Processing helix chain 'G' and resid 255 through 267 Processing helix chain 'G' and resid 269 through 284 Processing helix chain 'G' and resid 287 through 298 Processing helix chain 'G' and resid 301 through 311 Processing helix chain 'G' and resid 314 through 325 Processing helix chain 'H' and resid 26 through 37 Processing helix chain 'H' and resid 49 through 56 Processing helix chain 'H' and resid 64 through 70 Processing helix chain 'H' and resid 83 through 90 Processing helix chain 'H' and resid 92 through 97 Processing helix chain 'H' and resid 109 through 112 No H-bonds generated for 'chain 'H' and resid 109 through 112' Processing helix chain 'H' and resid 134 through 140 Processing helix chain 'H' and resid 160 through 171 Processing helix chain 'H' and resid 184 through 217 removed outlier: 3.600A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TRP H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N VAL H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Proline residue: H 200 - end of helix removed outlier: 3.571A pdb=" N TYR H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 228 Processing helix chain 'H' and resid 233 through 244 Processing helix chain 'H' and resid 248 through 252 Processing helix chain 'H' and resid 255 through 267 Processing helix chain 'H' and resid 269 through 284 Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 301 through 311 Processing helix chain 'H' and resid 314 through 325 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 49 through 56 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 83 through 90 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'I' and resid 109 through 112 No H-bonds generated for 'chain 'I' and resid 109 through 112' Processing helix chain 'I' and resid 134 through 140 Processing helix chain 'I' and resid 160 through 171 Processing helix chain 'I' and resid 184 through 217 removed outlier: 3.601A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 200 - end of helix removed outlier: 3.571A pdb=" N TYR I 217 " --> pdb=" O ALA I 213 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 228 Processing helix chain 'I' and resid 233 through 244 Processing helix chain 'I' and resid 248 through 252 Processing helix chain 'I' and resid 255 through 267 Processing helix chain 'I' and resid 269 through 284 Processing helix chain 'I' and resid 287 through 298 Processing helix chain 'I' and resid 301 through 311 Processing helix chain 'I' and resid 314 through 325 Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 49 through 56 Processing helix chain 'J' and resid 64 through 70 Processing helix chain 'J' and resid 83 through 90 Processing helix chain 'J' and resid 92 through 97 Processing helix chain 'J' and resid 109 through 112 No H-bonds generated for 'chain 'J' and resid 109 through 112' Processing helix chain 'J' and resid 134 through 140 Processing helix chain 'J' and resid 160 through 171 Processing helix chain 'J' and resid 184 through 217 removed outlier: 3.600A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Proline residue: J 200 - end of helix removed outlier: 3.572A pdb=" N TYR J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 228 Processing helix chain 'J' and resid 233 through 244 Processing helix chain 'J' and resid 248 through 252 Processing helix chain 'J' and resid 255 through 267 Processing helix chain 'J' and resid 269 through 284 Processing helix chain 'J' and resid 287 through 298 Processing helix chain 'J' and resid 301 through 311 Processing helix chain 'J' and resid 314 through 325 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 49 through 54 Processing helix chain 'K' and resid 64 through 70 Processing helix chain 'K' and resid 83 through 90 Processing helix chain 'K' and resid 92 through 97 Processing helix chain 'K' and resid 109 through 112 No H-bonds generated for 'chain 'K' and resid 109 through 112' Processing helix chain 'K' and resid 134 through 140 Processing helix chain 'K' and resid 160 through 171 Processing helix chain 'K' and resid 184 through 217 removed outlier: 3.601A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Proline residue: K 200 - end of helix removed outlier: 3.572A pdb=" N TYR K 217 " --> pdb=" O ALA K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 228 Processing helix chain 'K' and resid 233 through 244 Processing helix chain 'K' and resid 248 through 252 Processing helix chain 'K' and resid 255 through 267 Processing helix chain 'K' and resid 269 through 284 Processing helix chain 'K' and resid 287 through 298 Processing helix chain 'K' and resid 301 through 311 Processing helix chain 'K' and resid 314 through 325 Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 49 through 56 Processing helix chain 'L' and resid 64 through 70 Processing helix chain 'L' and resid 83 through 90 Processing helix chain 'L' and resid 92 through 97 Processing helix chain 'L' and resid 109 through 112 No H-bonds generated for 'chain 'L' and resid 109 through 112' Processing helix chain 'L' and resid 134 through 140 Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 184 through 217 removed outlier: 3.601A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TRP L 198 " --> pdb=" O SER L 194 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix removed outlier: 3.571A pdb=" N TYR L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 228 Processing helix chain 'L' and resid 233 through 244 Processing helix chain 'L' and resid 248 through 252 Processing helix chain 'L' and resid 255 through 267 Processing helix chain 'L' and resid 269 through 284 Processing helix chain 'L' and resid 287 through 298 Processing helix chain 'L' and resid 301 through 311 Processing helix chain 'L' and resid 314 through 325 Processing sheet with id= A, first strand: chain 'A' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 73 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE A 21 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 75 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL A 102 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP A 104 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE A 105 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET A 126 " --> pdb=" O VAL A 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL A 152 " --> pdb=" O MET A 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA A 128 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU A 150 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 73 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE B 21 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU B 75 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N VAL B 102 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP B 104 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 105 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET B 126 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL B 152 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA B 128 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU B 150 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.522A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 73 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE C 21 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU C 75 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL C 102 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP C 104 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 105 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET C 126 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL C 152 " --> pdb=" O MET C 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA C 128 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU C 150 " --> pdb=" O ALA C 128 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL D 73 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE D 21 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU D 75 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL D 102 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU D 76 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP D 104 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE D 105 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET D 126 " --> pdb=" O VAL D 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL D 152 " --> pdb=" O MET D 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA D 128 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU D 150 " --> pdb=" O ALA D 128 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL E 73 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE E 21 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU E 75 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL E 102 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU E 76 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP E 104 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE E 105 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET E 126 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL E 152 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA E 128 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU E 150 " --> pdb=" O ALA E 128 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL F 73 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE F 21 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU F 75 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL F 102 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU F 76 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP F 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE F 105 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET F 126 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL F 152 " --> pdb=" O MET F 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA F 128 " --> pdb=" O LEU F 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU F 150 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL G 73 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE G 21 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU G 75 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL G 102 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU G 76 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP G 104 " --> pdb=" O LEU G 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE G 105 " --> pdb=" O ILE G 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL G 152 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA G 128 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU G 150 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 73 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE H 21 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU H 75 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU H 76 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP H 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET H 126 " --> pdb=" O VAL H 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL H 152 " --> pdb=" O MET H 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA H 128 " --> pdb=" O LEU H 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU H 150 " --> pdb=" O ALA H 128 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.520A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL I 73 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE I 21 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU I 75 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL I 102 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU I 76 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP I 104 " --> pdb=" O LEU I 76 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE I 105 " --> pdb=" O ILE I 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL I 152 " --> pdb=" O MET I 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA I 128 " --> pdb=" O LEU I 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU I 150 " --> pdb=" O ALA I 128 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL J 73 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE J 21 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU J 75 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL J 102 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU J 76 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP J 104 " --> pdb=" O LEU J 76 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE J 105 " --> pdb=" O ILE J 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET J 126 " --> pdb=" O VAL J 152 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL J 152 " --> pdb=" O MET J 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA J 128 " --> pdb=" O LEU J 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU J 150 " --> pdb=" O ALA J 128 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL K 73 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE K 21 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU K 75 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL K 102 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU K 76 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP K 104 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE K 105 " --> pdb=" O ILE K 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET K 126 " --> pdb=" O VAL K 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL K 152 " --> pdb=" O MET K 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA K 128 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N LEU K 150 " --> pdb=" O ALA K 128 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.521A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL L 73 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE L 21 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU L 75 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL L 102 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU L 76 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASP L 104 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE L 105 " --> pdb=" O ILE L 125 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET L 126 " --> pdb=" O VAL L 152 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL L 152 " --> pdb=" O MET L 126 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ALA L 128 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU L 150 " --> pdb=" O ALA L 128 " (cutoff:3.500A) 1426 hydrogen bonds defined for protein. 4206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.64 Time building geometry restraints manager: 47.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 31211 1.02 - 1.22: 38 1.22 - 1.41: 13392 1.41 - 1.61: 19068 1.61 - 1.81: 372 Bond restraints: 64081 Sorted by residual: bond pdb=" C1BANAI F 403 " pdb=" C2BANAI F 403 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1BANAI D 403 " pdb=" C2BANAI D 403 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1BANAI G 402 " pdb=" C2BANAI G 402 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1BANAI J 403 " pdb=" C2BANAI J 403 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1BANAI A 402 " pdb=" C2BANAI A 402 " ideal model delta sigma weight residual 1.528 1.286 0.242 2.00e-02 2.50e+03 1.46e+02 ... (remaining 64076 not shown) Histogram of bond angle deviations from ideal: 55.67 - 77.84: 208 77.84 - 100.01: 247 100.01 - 122.19: 105494 122.19 - 144.36: 9953 144.36 - 166.53: 4 Bond angle restraints: 115906 Sorted by residual: angle pdb=" C ASP J 48 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 124.96 65.90 59.06 3.00e+00 1.11e-01 3.88e+02 angle pdb=" CA ALA K 31 " pdb=" N ALA K 31 " pdb=" H ALA K 31 " ideal model delta sigma weight residual 114.63 55.67 58.96 3.00e+00 1.11e-01 3.86e+02 angle pdb=" CA ALA L 31 " pdb=" N ALA L 31 " pdb=" H ALA L 31 " ideal model delta sigma weight residual 114.63 55.78 58.85 3.00e+00 1.11e-01 3.85e+02 angle pdb=" CA LYS J 49 " pdb=" N LYS J 49 " pdb=" H LYS J 49 " ideal model delta sigma weight residual 114.66 55.88 58.78 3.00e+00 1.11e-01 3.84e+02 angle pdb=" C LYS K 55 " pdb=" N LYS K 56 " pdb=" H LYS K 56 " ideal model delta sigma weight residual 124.83 66.05 58.77 3.00e+00 1.11e-01 3.84e+02 ... (remaining 115901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 22627 17.96 - 35.93: 2023 35.93 - 53.89: 387 53.89 - 71.85: 73 71.85 - 89.82: 27 Dihedral angle restraints: 25137 sinusoidal: 11784 harmonic: 13353 Sorted by residual: dihedral pdb=" CA MET C 126 " pdb=" C MET C 126 " pdb=" N VAL C 127 " pdb=" CA VAL C 127 " ideal model delta harmonic sigma weight residual 180.00 143.97 36.03 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA MET E 126 " pdb=" C MET E 126 " pdb=" N VAL E 127 " pdb=" CA VAL E 127 " ideal model delta harmonic sigma weight residual 180.00 143.99 36.01 0 5.00e+00 4.00e-02 5.19e+01 dihedral pdb=" CA MET F 126 " pdb=" C MET F 126 " pdb=" N VAL F 127 " pdb=" CA VAL F 127 " ideal model delta harmonic sigma weight residual 180.00 144.00 36.00 0 5.00e+00 4.00e-02 5.18e+01 ... (remaining 25134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3863 0.067 - 0.133: 809 0.133 - 0.200: 116 0.200 - 0.267: 36 0.267 - 0.334: 36 Chirality restraints: 4860 Sorted by residual: chirality pdb=" CG LEU E 95 " pdb=" CB LEU E 95 " pdb=" CD1 LEU E 95 " pdb=" CD2 LEU E 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU C 95 " pdb=" CB LEU C 95 " pdb=" CD1 LEU C 95 " pdb=" CD2 LEU C 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CG LEU L 95 " pdb=" CB LEU L 95 " pdb=" CD1 LEU L 95 " pdb=" CD2 LEU L 95 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 4857 not shown) Planarity restraints: 9304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 9 " 0.006 2.00e-02 2.50e+03 2.72e-02 1.11e+01 pdb=" CG ASN F 9 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN F 9 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN F 9 " 0.020 2.00e-02 2.50e+03 pdb="HD21 ASN F 9 " 0.020 2.00e-02 2.50e+03 pdb="HD22 ASN F 9 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 9 " 0.007 2.00e-02 2.50e+03 2.71e-02 1.10e+01 pdb=" CG ASN J 9 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN J 9 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN J 9 " 0.024 2.00e-02 2.50e+03 pdb="HD21 ASN J 9 " 0.017 2.00e-02 2.50e+03 pdb="HD22 ASN J 9 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 9 " -0.014 2.00e-02 2.50e+03 2.63e-02 1.04e+01 pdb=" CG ASN I 9 " 0.056 2.00e-02 2.50e+03 pdb=" OD1 ASN I 9 " -0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN I 9 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN I 9 " -0.001 2.00e-02 2.50e+03 pdb="HD22 ASN I 9 " -0.012 2.00e-02 2.50e+03 ... (remaining 9301 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 1056 2.01 - 2.66: 90409 2.66 - 3.30: 184532 3.30 - 3.95: 238501 3.95 - 4.60: 386472 Nonbonded interactions: 900970 Sorted by model distance: nonbonded pdb=" H PHE K 59 " pdb=" HA PHE K 59 " model vdw 1.358 1.816 nonbonded pdb=" H GLY G 232 " pdb=" HA2 GLY G 232 " model vdw 1.406 1.816 nonbonded pdb=" O LEU I 150 " pdb=" H SER I 182 " model vdw 1.415 1.850 nonbonded pdb=" H LEU I 150 " pdb=" O VAL I 180 " model vdw 1.415 1.850 nonbonded pdb=" O LEU A 150 " pdb=" H SER A 182 " model vdw 1.418 1.850 ... (remaining 900965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'B' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'C' and (resid 2 through 329 or resid 401)) selection = (chain 'D' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'E' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'F' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 195 or (re \ sid 196 and (name N or name CA or name C or name O or name CB or name CG or name \ ND1 or name CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or nam \ e HB3 or name HD2 or name HE1 or name HE2)) or resid 197 through 329 or resid 40 \ 1)) selection = (chain 'H' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'I' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'J' and (resid 2 through 195 or (resid 196 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 197 through 329 or resid 401)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 3 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name HA or \ name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE2 \ or name HE3 or name HZ1 or name HZ2 or name HZ3)) or resid 4 through 329 or res \ id 401)) selection = (chain 'L' and (resid 2 through 329 or resid 401)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 1.450 Extract box with map and model: 12.980 Check model and map are aligned: 0.720 Process input model: 159.780 Find NCS groups from input model: 3.050 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.450 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.018 0.242 32856 Z= 1.143 Angle : 1.172 14.690 44580 Z= 0.511 Chirality : 0.063 0.334 4860 Planarity : 0.005 0.045 5520 Dihedral : 14.726 89.817 12036 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.10), residues: 3912 helix: -2.32 (0.08), residues: 2448 sheet: -2.62 (0.20), residues: 480 loop : -4.01 (0.13), residues: 984 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 719 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 719 average time/residue: 2.9201 time to fit residues: 2446.8248 Evaluate side-chains 457 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 3.977 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 224 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN A 312 GLN B 40 ASN B 278 ASN B 296 GLN B 312 GLN C 25 ASN C 278 ASN ** C 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 ASN D 40 ASN D 278 ASN D 312 GLN E 249 GLN E 278 ASN E 296 GLN E 312 GLN F 37 ASN F 40 ASN F 278 ASN F 296 GLN G 26 GLN G 278 ASN G 296 GLN G 312 GLN H 37 ASN H 278 ASN I 37 ASN I 40 ASN I 278 ASN I 296 GLN J 37 ASN J 40 ASN J 278 ASN J 312 GLN K 37 ASN K 40 ASN K 278 ASN K 296 GLN K 312 GLN L 26 GLN L 278 ASN ** L 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 32856 Z= 0.311 Angle : 0.731 19.172 44580 Z= 0.372 Chirality : 0.120 1.632 4860 Planarity : 0.005 0.051 5520 Dihedral : 7.037 63.892 4584 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 3912 helix: -0.33 (0.10), residues: 2436 sheet: -2.11 (0.20), residues: 504 loop : -3.25 (0.16), residues: 972 *********************** 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 557 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 509 time to evaluate : 4.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 10 residues processed: 534 average time/residue: 2.6986 time to fit residues: 1700.5492 Evaluate side-chains 456 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 446 time to evaluate : 3.907 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 5 average time/residue: 0.5945 time to fit residues: 10.0987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 290 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 349 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 346 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 ASN A 312 GLN B 40 ASN B 312 GLN C 40 ASN ** D 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN E 40 ASN E 296 GLN F 40 ASN F 296 GLN G 296 GLN G 312 GLN H 40 ASN I 40 ASN K 40 ASN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 32856 Z= 0.324 Angle : 0.707 18.916 44580 Z= 0.362 Chirality : 0.122 1.857 4860 Planarity : 0.004 0.046 5520 Dihedral : 6.679 85.497 4584 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.13), residues: 3912 helix: 0.34 (0.10), residues: 2424 sheet: -1.86 (0.21), residues: 504 loop : -2.98 (0.16), residues: 984 *********************** 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 584 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 512 time to evaluate : 4.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 28 residues processed: 540 average time/residue: 2.7940 time to fit residues: 1773.1610 Evaluate side-chains 489 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 461 time to evaluate : 3.945 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 12 residues processed: 16 average time/residue: 1.5507 time to fit residues: 37.2778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 234 optimal weight: 6.9990 chunk 350 optimal weight: 2.9990 chunk 371 optimal weight: 0.3980 chunk 183 optimal weight: 6.9990 chunk 332 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN B 312 GLN D 296 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 296 GLN K 296 GLN ** L 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 32856 Z= 0.170 Angle : 0.653 20.149 44580 Z= 0.328 Chirality : 0.123 1.778 4860 Planarity : 0.004 0.037 5520 Dihedral : 6.046 84.754 4584 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.13), residues: 3912 helix: 0.92 (0.11), residues: 2436 sheet: -1.52 (0.21), residues: 504 loop : -2.59 (0.17), residues: 972 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 506 time to evaluate : 4.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 520 average time/residue: 2.7408 time to fit residues: 1693.0740 Evaluate side-chains 465 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 451 time to evaluate : 3.942 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 10 residues processed: 4 average time/residue: 0.6531 time to fit residues: 9.4479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 3.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 3.9990 chunk 256 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 296 GLN D 37 ASN G 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 32856 Z= 0.306 Angle : 0.705 19.529 44580 Z= 0.359 Chirality : 0.125 1.812 4860 Planarity : 0.004 0.043 5520 Dihedral : 6.880 76.433 4584 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 1.28 % 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: -0.45 (0.13), residues: 3912 helix: 0.88 (0.10), residues: 2400 sheet: -1.41 (0.21), residues: 504 loop : -2.52 (0.17), residues: 1008 *********************** 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 527 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 486 time to evaluate : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 29 residues processed: 499 average time/residue: 2.9523 time to fit residues: 1733.8767 Evaluate side-chains 475 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 446 time to evaluate : 3.987 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 13 residues processed: 16 average time/residue: 1.8014 time to fit residues: 42.6479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.9980 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN G 296 GLN J 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 32856 Z= 0.223 Angle : 0.677 19.852 44580 Z= 0.341 Chirality : 0.124 1.790 4860 Planarity : 0.004 0.041 5520 Dihedral : 6.427 72.534 4584 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 0.97 % 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: -0.10 (0.13), residues: 3912 helix: 1.08 (0.10), residues: 2424 sheet: -1.23 (0.21), residues: 504 loop : -2.25 (0.18), residues: 984 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 479 time to evaluate : 4.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 493 average time/residue: 2.9180 time to fit residues: 1680.2833 Evaluate side-chains 469 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 450 time to evaluate : 4.051 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 7 average time/residue: 0.8449 time to fit residues: 14.0807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN E 296 GLN F 296 GLN I 296 GLN K 296 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 32856 Z= 0.388 Angle : 0.739 19.089 44580 Z= 0.377 Chirality : 0.125 1.791 4860 Planarity : 0.004 0.047 5520 Dihedral : 7.418 72.380 4584 Min Nonbonded Distance : 1.675 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3912 helix: 0.82 (0.10), residues: 2388 sheet: -1.29 (0.21), residues: 504 loop : -2.48 (0.16), residues: 1020 *********************** 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 510 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 465 time to evaluate : 3.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 34 residues processed: 481 average time/residue: 3.0106 time to fit residues: 1698.3581 Evaluate side-chains 475 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 441 time to evaluate : 3.953 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 16 residues processed: 21 average time/residue: 1.5554 time to fit residues: 48.0734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 10.0000 chunk 147 optimal weight: 0.6980 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 290 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN D 26 GLN H 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 32856 Z= 0.193 Angle : 0.678 20.153 44580 Z= 0.340 Chirality : 0.124 1.781 4860 Planarity : 0.003 0.040 5520 Dihedral : 6.575 61.976 4584 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.13), residues: 3912 helix: 1.11 (0.10), residues: 2424 sheet: -1.19 (0.22), residues: 444 loop : -2.12 (0.17), residues: 1044 *********************** 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 495 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 472 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 19 residues processed: 486 average time/residue: 3.0781 time to fit residues: 1776.5450 Evaluate side-chains 462 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 443 time to evaluate : 3.927 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 16 residues processed: 7 average time/residue: 0.7083 time to fit residues: 13.7042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 326 optimal weight: 6.9990 chunk 343 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 26 GLN E 26 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 32856 Z= 0.306 Angle : 0.716 19.677 44580 Z= 0.363 Chirality : 0.125 1.790 4860 Planarity : 0.004 0.042 5520 Dihedral : 7.113 69.081 4584 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 3912 helix: 1.04 (0.10), residues: 2388 sheet: -1.20 (0.21), residues: 504 loop : -2.32 (0.17), residues: 1020 *********************** 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 476 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 449 time to evaluate : 3.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 463 average time/residue: 2.9731 time to fit residues: 1602.8836 Evaluate side-chains 450 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 432 time to evaluate : 3.998 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 14 residues processed: 6 average time/residue: 0.8630 time to fit residues: 13.0322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 10.0000 chunk 364 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 253 optimal weight: 0.9980 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 304 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN D 26 GLN E 26 GLN K 26 GLN L 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 32856 Z= 0.214 Angle : 0.690 20.029 44580 Z= 0.347 Chirality : 0.124 1.780 4860 Planarity : 0.003 0.039 5520 Dihedral : 6.800 70.807 4584 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 3912 helix: 1.17 (0.10), residues: 2412 sheet: -1.13 (0.23), residues: 444 loop : -2.10 (0.18), residues: 1056 ********************** 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 478 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 458 time to evaluate : 4.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 19 residues processed: 473 average time/residue: 3.0101 time to fit residues: 1674.6101 Evaluate side-chains 458 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 439 time to evaluate : 3.973 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 6 average time/residue: 0.6486 time to fit residues: 11.8403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 26 GLN D 296 GLN E 26 GLN E 296 GLN F 296 GLN I 296 GLN K 26 GLN K 296 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.127574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.083085 restraints weight = 192342.544| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.00 r_work: 0.2872 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3881 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3881 r_free = 0.3881 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 32856 Z= 0.191 Angle : 0.684 20.191 44580 Z= 0.342 Chirality : 0.124 1.781 4860 Planarity : 0.003 0.039 5520 Dihedral : 6.597 72.162 4584 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.69 % 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: 0.23 (0.13), residues: 3912 helix: 1.30 (0.10), residues: 2424 sheet: -1.01 (0.23), residues: 444 loop : -2.00 (0.18), residues: 1044 =============================================================================== Job complete usr+sys time: 25480.11 seconds wall clock time: 436 minutes 31.88 seconds (26191.88 seconds total)