Starting phenix.real_space_refine (version: dev) on Mon Dec 12 23:15:14 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/12_2022/6kqk_0753_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/12_2022/6kqk_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_0753/12_2022/6kqk_0753.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/12_2022/6kqk_0753.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/12_2022/6kqk_0753_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kqk_0753/12_2022/6kqk_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 21.65, per 1000 atoms: 0.34 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: 38.12 Conformation dependent library (CDL) restraints added in 3.7 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 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: 2.47 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: 20.59 Time building geometry restraints manager: 40.16 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.690 Extract box with map and model: 12.850 Check model and map are aligned: 0.690 Convert atoms to be neutral: 0.420 Process input model: 142.700 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.090 ------------------------------------------------------------------------------- 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 : 3.957 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: 2.5196 time to fit residues: 2142.0414 Evaluate side-chains 457 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 3.759 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.6617 ------------------------------------------------------------------------------- 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 : 3.821 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: 2.3787 time to fit residues: 1521.9014 Evaluate side-chains 456 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 446 time to evaluate : 3.827 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 5 average time/residue: 0.5783 time to fit residues: 9.9157 ------------------------------------------------------------------------------- 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: 8.9990 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: 2.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** B 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** C 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 296 GLN ** E 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 GLN ** H 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 32856 Z= 0.394 Angle : 0.734 18.602 44580 Z= 0.377 Chirality : 0.122 1.815 4860 Planarity : 0.005 0.049 5520 Dihedral : 6.928 85.630 4584 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 2.00 % 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: -1.40 (0.13), residues: 3912 helix: 0.19 (0.10), residues: 2424 sheet: -1.90 (0.21), residues: 504 loop : -3.04 (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 571 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 507 time to evaluate : 3.935 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 outliers start: 64 outliers final: 33 residues processed: 535 average time/residue: 2.4622 time to fit residues: 1566.6956 Evaluate side-chains 493 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 460 time to evaluate : 3.745 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 13 residues processed: 20 average time/residue: 1.5053 time to fit residues: 43.8684 ------------------------------------------------------------------------------- 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: 3.9990 chunk 262 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 0.9990 chunk 371 optimal weight: 0.3980 chunk 183 optimal weight: 5.9990 chunk 332 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 GLN D 296 GLN E 296 GLN F 296 GLN G 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 32856 Z= 0.199 Angle : 0.665 20.050 44580 Z= 0.336 Chirality : 0.123 1.779 4860 Planarity : 0.004 0.040 5520 Dihedral : 6.360 83.669 4584 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 3912 helix: 0.83 (0.11), residues: 2400 sheet: -1.58 (0.21), residues: 504 loop : -2.73 (0.16), residues: 1008 *********************** 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 520 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 496 time to evaluate : 3.898 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: 24 outliers final: 15 residues processed: 510 average time/residue: 2.4569 time to fit residues: 1507.0340 Evaluate side-chains 474 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 459 time to evaluate : 3.784 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 6 average time/residue: 0.8432 time to fit residues: 12.6243 ------------------------------------------------------------------------------- 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: 2.9990 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 1.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 189 optimal weight: 2.9990 chunk 333 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 32856 Z= 0.293 Angle : 0.699 19.554 44580 Z= 0.356 Chirality : 0.124 1.827 4860 Planarity : 0.004 0.044 5520 Dihedral : 6.872 75.648 4584 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 3912 helix: 0.82 (0.10), residues: 2400 sheet: -1.45 (0.21), residues: 504 loop : -2.57 (0.16), 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 516 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 477 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 39 outliers final: 31 residues processed: 491 average time/residue: 2.5556 time to fit residues: 1487.1749 Evaluate side-chains 473 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 442 time to evaluate : 3.765 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 13 residues processed: 18 average time/residue: 1.5751 time to fit residues: 41.2712 ------------------------------------------------------------------------------- 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: 3.9990 chunk 334 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 371 optimal weight: 0.4980 chunk 308 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN H 296 GLN J 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4608 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= 0.178 Angle : 0.662 20.158 44580 Z= 0.332 Chirality : 0.124 1.813 4860 Planarity : 0.003 0.038 5520 Dihedral : 6.137 70.540 4584 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 3912 helix: 1.22 (0.11), residues: 2400 sheet: -1.23 (0.23), residues: 444 loop : -2.22 (0.17), residues: 1068 *********************** 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 517 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 496 time to evaluate : 4.199 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 outliers start: 21 outliers final: 15 residues processed: 510 average time/residue: 2.5096 time to fit residues: 1518.9888 Evaluate side-chains 464 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 449 time to evaluate : 3.798 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 5 average time/residue: 0.6408 time to fit residues: 10.3754 ------------------------------------------------------------------------------- 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: 0.8980 chunk 41 optimal weight: 5.9990 chunk 211 optimal weight: 2.9990 chunk 271 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 370 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 225 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN D 296 GLN F 37 ASN F 296 GLN G 26 GLN G 312 GLN I 296 GLN J 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 32856 Z= 0.289 Angle : 0.704 19.579 44580 Z= 0.358 Chirality : 0.124 1.790 4860 Planarity : 0.004 0.042 5520 Dihedral : 6.879 58.639 4584 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 1.12 % 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: -0.15 (0.13), residues: 3912 helix: 1.07 (0.10), residues: 2400 sheet: -1.21 (0.21), residues: 504 loop : -2.29 (0.17), residues: 1008 *********************** 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 498 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 462 time to evaluate : 4.473 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 outliers start: 36 outliers final: 25 residues processed: 476 average time/residue: 2.6133 time to fit residues: 1468.5128 Evaluate side-chains 456 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 431 time to evaluate : 3.778 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 15 residues processed: 14 average time/residue: 1.3849 time to fit residues: 30.6223 ------------------------------------------------------------------------------- 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: 3.9990 chunk 147 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 290 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 GLN D 26 GLN E 296 GLN G 26 GLN G 296 GLN J 26 GLN K 296 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 32856 Z= 0.301 Angle : 0.713 19.756 44580 Z= 0.361 Chirality : 0.125 1.797 4860 Planarity : 0.004 0.045 5520 Dihedral : 7.026 63.485 4584 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 0.91 % 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: -0.21 (0.13), residues: 3912 helix: 1.00 (0.10), residues: 2400 sheet: -1.20 (0.21), residues: 504 loop : -2.30 (0.17), residues: 1008 *********************** 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 490 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 461 time to evaluate : 4.150 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: 29 outliers final: 20 residues processed: 474 average time/residue: 2.6298 time to fit residues: 1481.2306 Evaluate side-chains 454 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 434 time to evaluate : 3.755 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 10 average time/residue: 1.0404 time to fit residues: 19.8879 ------------------------------------------------------------------------------- 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: 8.9990 chunk 354 optimal weight: 9.9990 chunk 323 optimal weight: 5.9990 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 150 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 311 optimal weight: 6.9990 chunk 326 optimal weight: 5.9990 chunk 343 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 G 26 GLN H 26 GLN I 26 GLN J 26 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 32856 Z= 0.237 Angle : 0.692 20.034 44580 Z= 0.349 Chirality : 0.124 1.786 4860 Planarity : 0.003 0.041 5520 Dihedral : 6.855 66.570 4584 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.13), residues: 3912 helix: 1.13 (0.10), residues: 2400 sheet: -1.18 (0.23), residues: 444 loop : -2.16 (0.17), residues: 1068 *********************** 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 485 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 459 time to evaluate : 3.794 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: 26 outliers final: 16 residues processed: 471 average time/residue: 2.6922 time to fit residues: 1515.1539 Evaluate side-chains 448 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 432 time to evaluate : 3.791 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 6 average time/residue: 0.6888 time to fit residues: 12.1419 ------------------------------------------------------------------------------- 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: 9.9990 chunk 364 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 F 296 GLN G 26 GLN H 26 GLN I 26 GLN J 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.5079 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= 0.202 Angle : 0.687 20.174 44580 Z= 0.344 Chirality : 0.124 1.784 4860 Planarity : 0.003 0.039 5520 Dihedral : 6.650 68.680 4584 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.13), residues: 3912 helix: 1.21 (0.10), residues: 2424 sheet: -1.05 (0.23), residues: 444 loop : -2.05 (0.18), residues: 1044 ********************** 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 474 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 453 time to evaluate : 3.799 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 outliers start: 21 outliers final: 13 residues processed: 468 average time/residue: 2.5529 time to fit residues: 1418.3067 Evaluate side-chains 455 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 442 time to evaluate : 3.800 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 4 average time/residue: 0.5870 time to fit residues: 8.9062 ------------------------------------------------------------------------------- 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: 0.0980 chunk 324 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 313 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN E 26 GLN G 26 GLN H 26 GLN I 26 GLN J 26 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.127564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.083114 restraints weight = 183052.699| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.95 r_work: 0.2872 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3882 r_free = 0.3882 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 = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 32856 Z= 0.198 Angle : 0.685 20.172 44580 Z= 0.343 Chirality : 0.124 1.781 4860 Planarity : 0.003 0.040 5520 Dihedral : 6.626 70.154 4584 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 3912 helix: 1.28 (0.10), residues: 2424 sheet: -0.98 (0.23), residues: 444 loop : -2.01 (0.18), residues: 1044 =============================================================================== Job complete usr+sys time: 23373.56 seconds wall clock time: 400 minutes 15.32 seconds (24015.32 seconds total)