Starting phenix.real_space_refine (version: dev) on Fri Feb 24 06:57:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/02_2023/6kph_0746_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/02_2023/6kph_0746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/02_2023/6kph_0746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/02_2023/6kph_0746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/02_2023/6kph_0746_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/02_2023/6kph_0746_trim_updated.pdb" } resolution = 2.41 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= -0.011 sd= 0.366 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 314": "OE1" <-> "OE2" Residue "B ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 314": "OE1" <-> "OE2" Residue "C ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 314": "OE1" <-> "OE2" Residue "D ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 314": "OE1" <-> "OE2" Residue "E ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 314": "OE1" <-> "OE2" Residue "F ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 155": "OD1" <-> "OD2" Residue "F ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 314": "OE1" <-> "OE2" Residue "G ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 314": "OE1" <-> "OE2" Residue "H ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 314": "OE1" <-> "OE2" Residue "I ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 52": "OE1" <-> "OE2" Residue "I ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 314": "OE1" <-> "OE2" Residue "J ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 52": "OE1" <-> "OE2" Residue "J ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 155": "OD1" <-> "OD2" Residue "J ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 314": "OE1" <-> "OE2" Residue "K ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 52": "OE1" <-> "OE2" Residue "K ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 314": "OE1" <-> "OE2" Residue "L ARG 35": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 52": "OE1" <-> "OE2" Residue "L ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 155": "OD1" <-> "OD2" Residue "L ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 314": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 62832 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: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "C" 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: "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: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "G" 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: "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: 5181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5181 Classifications: {'peptide': 328} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 316} Chain: "L" 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: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 55 Unusual residues: {' MG': 2, '9TY': 1, 'NAI': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 22.29, per 1000 atoms: 0.35 Number of scatterers: 62832 At special positions: 0 Unit cell: (140.28, 140.28, 140.28, 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 24 15.00 Mg 24 11.99 O 5976 8.00 N 5160 7.00 C 20316 6.00 H 31212 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 42.88 Conformation dependent library (CDL) restraints added in 3.9 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 24 sheets defined 55.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.50 Creating SS restraints... Processing helix chain 'A' and resid 25 through 37 removed outlier: 4.064A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 Processing helix chain 'A' and resid 64 through 70 Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.591A pdb=" N LYS A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 95 No H-bonds generated for 'chain 'A' and resid 92 through 95' 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 136 through 142 Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL A 199 " --> pdb=" O GLU A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 233 through 243 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 25 through 37 removed outlier: 4.064A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 Processing helix chain 'B' and resid 64 through 70 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS B 89 " --> pdb=" O GLU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 95 No H-bonds generated for 'chain 'B' and resid 92 through 95' 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 136 through 142 Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 184 through 216 removed outlier: 3.880A pdb=" N TRP B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 233 through 243 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 25 through 37 removed outlier: 4.064A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 Processing helix chain 'C' and resid 64 through 70 Processing helix chain 'C' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 95 No H-bonds generated for 'chain 'C' and resid 92 through 95' 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 136 through 142 Processing helix chain 'C' and resid 160 through 171 Processing helix chain 'C' and resid 184 through 216 removed outlier: 3.882A pdb=" N TRP C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 233 through 243 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 25 through 37 removed outlier: 4.063A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 57 Processing helix chain 'D' and resid 64 through 70 Processing helix chain 'D' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS D 89 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 95 No H-bonds generated for 'chain 'D' and resid 92 through 95' 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 136 through 142 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 184 through 217 removed outlier: 3.881A pdb=" N TRP D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix removed outlier: 3.559A 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 243 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 25 through 37 removed outlier: 4.063A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 57 Processing helix chain 'E' and resid 64 through 70 Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS E 89 " --> pdb=" O GLU E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' 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 136 through 142 Processing helix chain 'E' and resid 160 through 171 Processing helix chain 'E' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL E 199 " --> pdb=" O GLU E 195 " (cutoff:3.500A) Proline residue: E 200 - end of helix Processing helix chain 'E' and resid 221 through 228 Processing helix chain 'E' and resid 233 through 243 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 25 through 37 removed outlier: 4.064A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 57 Processing helix chain 'F' and resid 64 through 70 Processing helix chain 'F' and resid 85 through 90 removed outlier: 3.591A pdb=" N LYS F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 95 No H-bonds generated for 'chain 'F' and resid 92 through 95' 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 136 through 142 Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 184 through 217 removed outlier: 3.881A pdb=" N TRP F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Proline residue: F 200 - end of helix removed outlier: 3.559A 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 243 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 25 through 37 removed outlier: 4.064A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 57 Processing helix chain 'G' and resid 64 through 70 Processing helix chain 'G' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 95 No H-bonds generated for 'chain 'G' and resid 92 through 95' 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 136 through 142 Processing helix chain 'G' and resid 160 through 171 Processing helix chain 'G' and resid 184 through 216 removed outlier: 3.882A pdb=" N TRP G 198 " --> pdb=" O SER G 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL G 199 " --> pdb=" O GLU G 195 " (cutoff:3.500A) Proline residue: G 200 - end of helix Processing helix chain 'G' and resid 221 through 228 Processing helix chain 'G' and resid 233 through 243 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 25 through 37 removed outlier: 4.063A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 57 Processing helix chain 'H' and resid 64 through 70 Processing helix chain 'H' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS H 89 " --> pdb=" O GLU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 95 No H-bonds generated for 'chain 'H' and resid 92 through 95' 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 136 through 142 Processing helix chain 'H' and resid 160 through 171 Processing helix chain 'H' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL H 199 " --> pdb=" O GLU H 195 " (cutoff:3.500A) Proline residue: H 200 - end of helix Processing helix chain 'H' and resid 221 through 228 Processing helix chain 'H' and resid 233 through 243 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 25 through 37 removed outlier: 4.063A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 57 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS I 89 " --> pdb=" O GLU I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 95 No H-bonds generated for 'chain 'I' and resid 92 through 95' 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 136 through 142 Processing helix chain 'I' and resid 160 through 171 Processing helix chain 'I' and resid 184 through 217 removed outlier: 3.880A pdb=" N TRP I 198 " --> pdb=" O SER I 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL I 199 " --> pdb=" O GLU I 195 " (cutoff:3.500A) Proline residue: I 200 - end of helix removed outlier: 3.558A 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 243 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 25 through 37 removed outlier: 4.064A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 64 through 70 Processing helix chain 'J' and resid 85 through 90 removed outlier: 3.591A pdb=" N LYS J 89 " --> pdb=" O GLU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 95 No H-bonds generated for 'chain 'J' and resid 92 through 95' 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 136 through 142 Processing helix chain 'J' and resid 160 through 171 Processing helix chain 'J' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP J 198 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL J 199 " --> pdb=" O GLU J 195 " (cutoff:3.500A) Proline residue: J 200 - end of helix Processing helix chain 'J' and resid 221 through 228 Processing helix chain 'J' and resid 233 through 243 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 25 through 37 removed outlier: 4.064A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 57 Processing helix chain 'K' and resid 64 through 70 Processing helix chain 'K' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS K 89 " --> pdb=" O GLU K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 95 No H-bonds generated for 'chain 'K' and resid 92 through 95' 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 136 through 142 Processing helix chain 'K' and resid 160 through 171 Processing helix chain 'K' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP K 198 " --> pdb=" O SER K 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL K 199 " --> pdb=" O GLU K 195 " (cutoff:3.500A) Proline residue: K 200 - end of helix Processing helix chain 'K' and resid 221 through 228 Processing helix chain 'K' and resid 233 through 243 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 25 through 37 removed outlier: 4.063A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 57 Processing helix chain 'L' and resid 64 through 70 Processing helix chain 'L' and resid 85 through 90 removed outlier: 3.590A pdb=" N LYS L 89 " --> pdb=" O GLU L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 95 No H-bonds generated for 'chain 'L' and resid 92 through 95' 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 136 through 142 Processing helix chain 'L' and resid 160 through 171 Processing helix chain 'L' and resid 184 through 216 removed outlier: 3.881A pdb=" N TRP L 198 " --> pdb=" O SER L 194 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL L 199 " --> pdb=" O GLU L 195 " (cutoff:3.500A) Proline residue: L 200 - end of helix Processing helix chain 'L' and resid 221 through 228 Processing helix chain 'L' and resid 233 through 243 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: 6.175A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL A 73 " --> pdb=" O GLY A 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE A 21 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU A 75 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL A 102 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU A 76 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP A 104 " --> pdb=" O LEU A 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL A 148 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 73 " --> pdb=" O GLY B 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE B 21 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 75 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL B 102 " --> pdb=" O ALA B 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU B 76 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP B 104 " --> pdb=" O LEU B 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL B 148 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE C 18 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY C 44 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 20 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL C 73 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE C 21 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU C 75 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 102 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU C 76 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP C 104 " --> pdb=" O LEU C 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL C 148 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE D 18 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY D 44 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL D 20 " --> pdb=" O GLY D 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL D 73 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE D 21 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 75 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL D 102 " --> pdb=" O ALA D 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU D 76 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP D 104 " --> pdb=" O LEU D 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'D' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL D 148 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.176A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL E 73 " --> pdb=" O GLY E 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE E 21 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU E 75 " --> pdb=" O ILE E 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL E 102 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU E 76 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP E 104 " --> pdb=" O LEU E 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL E 148 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE F 18 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY F 44 " --> pdb=" O ILE F 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL F 20 " --> pdb=" O GLY F 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL F 73 " --> pdb=" O GLY F 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE F 21 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU F 75 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL F 102 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU F 76 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP F 104 " --> pdb=" O LEU F 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'F' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL F 148 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL G 73 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE G 21 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU G 75 " --> pdb=" O ILE G 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL G 102 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU G 76 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP G 104 " --> pdb=" O LEU G 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'G' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL G 148 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.176A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL H 73 " --> pdb=" O GLY H 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE H 21 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU H 75 " --> pdb=" O ILE H 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL H 102 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU H 76 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP H 104 " --> pdb=" O LEU H 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL H 148 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL I 73 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE I 21 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU I 75 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL I 102 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU I 76 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP I 104 " --> pdb=" O LEU I 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'I' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL I 148 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL J 73 " --> pdb=" O GLY J 19 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE J 21 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU J 75 " --> pdb=" O ILE J 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL J 102 " --> pdb=" O ALA J 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU J 76 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP J 104 " --> pdb=" O LEU J 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'J' and resid 179 through 181 removed outlier: 6.963A pdb=" N VAL J 148 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 41 through 44 removed outlier: 6.176A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL K 73 " --> pdb=" O GLY K 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE K 21 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU K 75 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL K 102 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N LEU K 76 " --> pdb=" O VAL K 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP K 104 " --> pdb=" O LEU K 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'K' and resid 179 through 181 removed outlier: 6.964A pdb=" N VAL K 148 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 41 through 44 removed outlier: 6.175A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL L 73 " --> pdb=" O GLY L 19 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE L 21 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU L 75 " --> pdb=" O ILE L 21 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL L 102 " --> pdb=" O ALA L 74 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N LEU L 76 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASP L 104 " --> pdb=" O LEU L 76 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 179 through 181 removed outlier: 6.965A pdb=" N VAL L 148 " --> pdb=" O VAL L 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) 1368 hydrogen bonds defined for protein. 4032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 21.19 Time building geometry restraints manager: 44.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 31199 1.03 - 1.22: 25 1.22 - 1.41: 13314 1.41 - 1.61: 18654 1.61 - 1.80: 300 Bond restraints: 63492 Sorted by residual: bond pdb=" C1B NAI D 403 " pdb=" C2B NAI D 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI I 403 " pdb=" C2B NAI I 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI C 403 " pdb=" C2B NAI C 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI H 403 " pdb=" C2B NAI H 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1B NAI L 403 " pdb=" C2B NAI L 403 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 ... (remaining 63487 not shown) Histogram of bond angle deviations from ideal: 59.76 - 74.66: 47 74.66 - 89.55: 262 89.55 - 104.45: 411 104.45 - 119.35: 88288 119.35 - 134.25: 25988 Bond angle restraints: 114996 Sorted by residual: angle pdb=" CG1 VAL H 46 " pdb=" CB VAL H 46 " pdb=" HB VAL H 46 " ideal model delta sigma weight residual 108.00 69.66 38.34 3.00e+00 1.11e-01 1.63e+02 angle pdb=" CG2 VAL H 46 " pdb=" CB VAL H 46 " pdb=" HB VAL H 46 " ideal model delta sigma weight residual 108.00 71.60 36.40 3.00e+00 1.11e-01 1.47e+02 angle pdb=" OG1 THR I 17 " pdb=" CB THR I 17 " pdb=" HB THR I 17 " ideal model delta sigma weight residual 109.00 73.42 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" OG1 THR K 17 " pdb=" CB THR K 17 " pdb=" HB THR K 17 " ideal model delta sigma weight residual 109.00 73.42 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" OG1 THR G 17 " pdb=" CB THR G 17 " pdb=" HB THR G 17 " ideal model delta sigma weight residual 109.00 73.43 35.57 3.00e+00 1.11e-01 1.41e+02 ... (remaining 114991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 22567 17.50 - 34.99: 1902 34.99 - 52.49: 393 52.49 - 69.98: 86 69.98 - 87.48: 60 Dihedral angle restraints: 25008 sinusoidal: 11652 harmonic: 13356 Sorted by residual: dihedral pdb=" CA ARG C 70 " pdb=" C ARG C 70 " pdb=" N SER C 71 " pdb=" CA SER C 71 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG E 70 " pdb=" C ARG E 70 " pdb=" N SER E 71 " pdb=" CA SER E 71 " ideal model delta harmonic sigma weight residual 180.00 -162.34 -17.66 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ARG J 70 " pdb=" C ARG J 70 " pdb=" N SER J 71 " pdb=" CA SER J 71 " ideal model delta harmonic sigma weight residual -180.00 -162.35 -17.65 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 25005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 4728 0.347 - 0.694: 0 0.694 - 1.040: 0 1.040 - 1.387: 0 1.387 - 1.734: 36 Chirality restraints: 4764 Sorted by residual: chirality pdb=" CG LEU I 75 " pdb=" CB LEU I 75 " pdb=" CD1 LEU I 75 " pdb=" CD2 LEU I 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.52e+01 chirality pdb=" CG LEU D 75 " pdb=" CB LEU D 75 " pdb=" CD1 LEU D 75 " pdb=" CD2 LEU D 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CG LEU E 75 " pdb=" CB LEU E 75 " pdb=" CD1 LEU E 75 " pdb=" CD2 LEU E 75 " both_signs ideal model delta sigma weight residual False -2.59 -0.86 -1.73 2.00e-01 2.50e+01 7.50e+01 ... (remaining 4761 not shown) Planarity restraints: 9264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 284 " -0.006 2.00e-02 2.50e+03 7.30e-03 2.13e+00 pdb=" CG TRP G 284 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP G 284 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP G 284 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 284 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 284 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP G 284 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 284 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 284 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP G 284 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP G 284 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP G 284 " 0.019 2.00e-02 2.50e+03 pdb=" HE3 TRP G 284 " 0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP G 284 " -0.011 2.00e-02 2.50e+03 pdb=" HZ3 TRP G 284 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP G 284 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 284 " -0.006 2.00e-02 2.50e+03 7.07e-03 2.00e+00 pdb=" CG TRP L 284 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP L 284 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP L 284 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP L 284 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 284 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP L 284 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 284 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 284 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP L 284 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP L 284 " -0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP L 284 " 0.018 2.00e-02 2.50e+03 pdb=" HE3 TRP L 284 " 0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 284 " -0.010 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 284 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP L 284 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 284 " -0.006 2.00e-02 2.50e+03 6.73e-03 1.81e+00 pdb=" CG TRP D 284 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP D 284 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP D 284 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 284 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 284 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP D 284 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 284 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 284 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 284 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP D 284 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP D 284 " 0.019 2.00e-02 2.50e+03 pdb=" HE3 TRP D 284 " 0.006 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 284 " -0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 284 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP D 284 " -0.002 2.00e-02 2.50e+03 ... (remaining 9261 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 3042 2.15 - 2.77: 123403 2.77 - 3.38: 172303 3.38 - 3.99: 229560 3.99 - 4.60: 373570 Nonbonded interactions: 901878 Sorted by model distance: nonbonded pdb=" O MET A 193 " pdb=" HG1 THR A 197 " model vdw 1.543 1.850 nonbonded pdb=" O MET G 193 " pdb=" HG1 THR G 197 " model vdw 1.545 1.850 nonbonded pdb=" O MET D 193 " pdb=" HG1 THR D 197 " model vdw 1.545 1.850 nonbonded pdb=" O MET K 193 " pdb=" HG1 THR K 197 " model vdw 1.546 1.850 nonbonded pdb=" O MET J 193 " pdb=" HG1 THR J 197 " model vdw 1.546 1.850 ... (remaining 901873 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 24 5.49 5 Mg 24 5.21 5 S 120 5.16 5 C 20316 2.51 5 N 5160 2.21 5 O 5976 1.98 5 H 31212 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=1.00 max=1.00 mean=1.00 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: 3.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.440 Extract box with map and model: 12.690 Check model and map are aligned: 0.700 Process input model: 151.340 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Set scattering table: 0.430 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:11.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 : 0.014 0.241 32280 Z= 0.881 Angle : 1.032 13.401 43704 Z= 0.479 Chirality : 0.147 1.734 4764 Planarity : 0.004 0.033 5484 Dihedral : 13.222 77.442 11904 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.10), residues: 3912 helix: -2.16 (0.08), residues: 2292 sheet: -2.31 (0.21), residues: 456 loop : -4.07 (0.14), residues: 1164 *********************** 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 721 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 721 time to evaluate : 3.784 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 outliers start: 0 outliers final: 2 residues processed: 721 average time/residue: 3.7163 time to fit residues: 3026.1643 Evaluate side-chains 355 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 353 time to evaluate : 3.775 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 4.6681 ------------------------------------------------------------------------------- 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: 1.9990 chunk 291 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 99 optimal weight: 8.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 224 optimal weight: 8.9990 chunk 348 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 45 ASN A 96 GLN A 110 ASN A 278 ASN B 25 ASN B 45 ASN B 96 GLN B 110 ASN B 278 ASN C 25 ASN C 45 ASN C 96 GLN C 110 ASN C 278 ASN D 25 ASN D 45 ASN D 96 GLN D 110 ASN D 278 ASN E 25 ASN E 45 ASN E 96 GLN E 110 ASN E 278 ASN F 25 ASN F 45 ASN F 96 GLN F 110 ASN F 278 ASN G 25 ASN G 45 ASN G 96 GLN G 110 ASN G 278 ASN H 25 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 ASN H 96 GLN H 110 ASN ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 278 ASN I 25 ASN ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 ASN I 96 GLN I 110 ASN I 278 ASN J 25 ASN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN J 96 GLN J 110 ASN ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 278 ASN K 25 ASN K 45 ASN K 96 GLN K 110 ASN K 278 ASN L 25 ASN L 45 ASN L 96 GLN L 110 ASN L 142 GLN L 278 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 32280 Z= 0.243 Angle : 0.729 12.264 43704 Z= 0.367 Chirality : 0.150 1.693 4764 Planarity : 0.005 0.073 5484 Dihedral : 6.720 59.971 4452 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 3912 helix: -0.20 (0.10), residues: 2292 sheet: 0.07 (0.35), residues: 180 loop : -3.50 (0.13), residues: 1440 *********************** 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 457 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 387 time to evaluate : 3.811 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 outliers start: 70 outliers final: 29 residues processed: 431 average time/residue: 2.8978 time to fit residues: 1463.8841 Evaluate side-chains 348 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 319 time to evaluate : 3.795 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 19 residues processed: 10 average time/residue: 1.0745 time to fit residues: 20.1364 ------------------------------------------------------------------------------- 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: 9.9990 chunk 108 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.044 32280 Z= 0.438 Angle : 0.753 11.383 43704 Z= 0.390 Chirality : 0.149 1.730 4764 Planarity : 0.005 0.070 5484 Dihedral : 5.987 57.567 4452 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3912 helix: 0.05 (0.10), residues: 2388 sheet: -1.47 (0.23), residues: 456 loop : -2.87 (0.17), residues: 1068 *********************** 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 387 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 318 time to evaluate : 3.882 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: 69 outliers final: 40 residues processed: 359 average time/residue: 2.9665 time to fit residues: 1260.1902 Evaluate side-chains 318 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 278 time to evaluate : 3.847 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 19 residues processed: 21 average time/residue: 1.4008 time to fit residues: 45.1562 ------------------------------------------------------------------------------- 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: 0.0470 chunk 262 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 234 optimal weight: 4.9990 chunk 350 optimal weight: 0.8980 chunk 371 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 332 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 253 HIS ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 HIS ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 HIS ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 253 HIS ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 253 HIS ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 253 HIS ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 253 HIS ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 32280 Z= 0.220 Angle : 0.670 11.411 43704 Z= 0.339 Chirality : 0.148 1.683 4764 Planarity : 0.003 0.078 5484 Dihedral : 5.705 59.066 4452 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 3912 helix: 0.59 (0.10), residues: 2400 sheet: -0.66 (0.26), residues: 324 loop : -2.84 (0.16), residues: 1188 *********************** 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 408 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 353 time to evaluate : 3.886 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: 55 outliers final: 20 residues processed: 387 average time/residue: 2.9782 time to fit residues: 1344.9965 Evaluate side-chains 327 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 307 time to evaluate : 3.845 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 19 residues processed: 1 average time/residue: 1.7334 time to fit residues: 6.9684 ------------------------------------------------------------------------------- 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: 5.9990 chunk 5 optimal weight: 10.0000 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 chunk 333 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 32280 Z= 0.284 Angle : 0.689 11.374 43704 Z= 0.350 Chirality : 0.149 1.699 4764 Planarity : 0.004 0.085 5484 Dihedral : 5.660 58.102 4452 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 3912 helix: 0.72 (0.10), residues: 2400 sheet: -0.43 (0.27), residues: 324 loop : -2.78 (0.16), residues: 1188 *********************** 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 375 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 315 time to evaluate : 5.720 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 outliers start: 60 outliers final: 31 residues processed: 352 average time/residue: 3.0747 time to fit residues: 1263.8367 Evaluate side-chains 325 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 294 time to evaluate : 3.777 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 20 residues processed: 12 average time/residue: 0.6682 time to fit residues: 18.6193 ------------------------------------------------------------------------------- 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: 3.9990 chunk 73 optimal weight: 0.0870 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 371 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 6.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 32280 Z= 0.195 Angle : 0.663 11.366 43704 Z= 0.332 Chirality : 0.148 1.686 4764 Planarity : 0.003 0.078 5484 Dihedral : 5.464 59.357 4452 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.13), residues: 3912 helix: 1.02 (0.10), residues: 2400 sheet: -0.15 (0.27), residues: 324 loop : -2.65 (0.16), residues: 1188 *********************** 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 372 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 330 time to evaluate : 3.861 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 outliers start: 42 outliers final: 23 residues processed: 356 average time/residue: 3.1042 time to fit residues: 1286.1398 Evaluate side-chains 335 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 312 time to evaluate : 3.875 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 3 average time/residue: 0.6805 time to fit residues: 8.2298 ------------------------------------------------------------------------------- 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: 5.9990 chunk 41 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 271 optimal weight: 10.0000 chunk 210 optimal weight: 2.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 9.9990 chunk 370 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 170 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 32280 Z= 0.448 Angle : 0.742 11.467 43704 Z= 0.381 Chirality : 0.151 1.709 4764 Planarity : 0.004 0.108 5484 Dihedral : 5.785 55.014 4452 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3912 helix: 0.67 (0.10), residues: 2400 sheet: -0.95 (0.24), residues: 456 loop : -2.55 (0.17), residues: 1056 *********************** 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 364 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 299 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 outliers start: 65 outliers final: 37 residues processed: 330 average time/residue: 3.0385 time to fit residues: 1166.4291 Evaluate side-chains 322 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 3.758 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 19 residues processed: 18 average time/residue: 1.1211 time to fit residues: 33.2948 ------------------------------------------------------------------------------- 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: 9.9990 chunk 147 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 154 GLN ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 32280 Z= 0.186 Angle : 0.672 12.364 43704 Z= 0.335 Chirality : 0.149 1.678 4764 Planarity : 0.003 0.077 5484 Dihedral : 5.468 57.407 4452 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.13), residues: 3912 helix: 1.11 (0.10), residues: 2400 sheet: -0.13 (0.27), residues: 324 loop : -2.56 (0.16), residues: 1188 *********************** 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 366 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 331 time to evaluate : 3.889 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 outliers start: 35 outliers final: 19 residues processed: 352 average time/residue: 3.1012 time to fit residues: 1283.0105 Evaluate side-chains 331 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 312 time to evaluate : 3.760 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 1.4415 time to fit residues: 8.6534 ------------------------------------------------------------------------------- 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: 0.0050 chunk 354 optimal weight: 5.9990 chunk 323 optimal weight: 0.8980 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 311 optimal weight: 5.9990 chunk 326 optimal weight: 0.3980 chunk 343 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 32280 Z= 0.175 Angle : 0.665 11.630 43704 Z= 0.328 Chirality : 0.149 1.705 4764 Planarity : 0.004 0.108 5484 Dihedral : 5.139 59.078 4452 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3912 helix: 1.58 (0.11), residues: 2352 sheet: 0.21 (0.28), residues: 324 loop : -2.10 (0.17), residues: 1236 *********************** 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 355 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 331 time to evaluate : 3.852 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 outliers start: 24 outliers final: 18 residues processed: 349 average time/residue: 3.0272 time to fit residues: 1236.0283 Evaluate side-chains 333 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 315 time to evaluate : 3.777 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 1 average time/residue: 0.7078 time to fit residues: 5.8249 ------------------------------------------------------------------------------- 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: 5.9990 chunk 364 optimal weight: 2.9990 chunk 222 optimal weight: 0.4980 chunk 173 optimal weight: 6.9990 chunk 253 optimal weight: 0.8980 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 9.9990 chunk 304 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 0.1980 chunk 186 optimal weight: 1.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 32280 Z= 0.178 Angle : 0.667 11.676 43704 Z= 0.329 Chirality : 0.149 1.693 4764 Planarity : 0.003 0.102 5484 Dihedral : 4.991 59.163 4452 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3912 helix: 1.69 (0.11), residues: 2352 sheet: 0.33 (0.28), residues: 324 loop : -2.01 (0.17), residues: 1236 ********************** 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 345 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 325 time to evaluate : 3.850 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 outliers start: 20 outliers final: 15 residues processed: 342 average time/residue: 2.9685 time to fit residues: 1186.3189 Evaluate side-chains 337 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 322 time to evaluate : 3.846 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 3 average time/residue: 1.1502 time to fit residues: 9.5881 ------------------------------------------------------------------------------- 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: 2.9990 chunk 324 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.100735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073054 restraints weight = 193554.480| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.65 r_work: 0.2757 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2652 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 32280 Z= 0.319 Angle : 0.715 11.571 43704 Z= 0.362 Chirality : 0.150 1.686 4764 Planarity : 0.004 0.107 5484 Dihedral : 5.354 55.750 4452 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 3912 helix: 1.22 (0.10), residues: 2400 sheet: -0.65 (0.24), residues: 456 loop : -2.27 (0.17), residues: 1056 =============================================================================== Job complete usr+sys time: 21467.97 seconds wall clock time: 368 minutes 39.34 seconds (22119.34 seconds total)