Starting phenix.real_space_refine on Sun Apr 7 13:26:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/04_2024/6kph_0746_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/04_2024/6kph_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_0746/04_2024/6kph_0746.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/04_2024/6kph_0746.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/04_2024/6kph_0746_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kph_0746/04_2024/6kph_0746_trim_updated.pdb" } resolution = 2.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.011 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 20.05, per 1000 atoms: 0.32 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: 40.08 Conformation dependent library (CDL) restraints added in 4.6 seconds 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 24 sheets defined 55.9% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.64 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: 21.60 Time building geometry restraints manager: 42.50 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: 26345 17.50 - 34.99: 2624 34.99 - 52.49: 729 52.49 - 69.98: 230 69.98 - 87.48: 60 Dihedral angle restraints: 29988 sinusoidal: 16632 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 29985 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 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.670 Extract box with map and model: 11.240 Check model and map are aligned: 0.680 Set scattering table: 0.430 Process input model: 153.840 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 14.482 77.442 12504 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 % Allowed : 0.75 % Favored : 99.25 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 198 HIS 0.005 0.002 HIS E 253 PHE 0.014 0.002 PHE G 303 TYR 0.012 0.002 TYR F 304 ARG 0.003 0.000 ARG B 130 *********************** 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 : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASP cc_start: 0.7991 (m-30) cc_final: 0.7776 (m-30) REVERT: A 215 LYS cc_start: 0.8726 (mttt) cc_final: 0.8115 (mtmm) REVERT: B 80 ASP cc_start: 0.8110 (m-30) cc_final: 0.7893 (m-30) REVERT: B 281 LYS cc_start: 0.8963 (tttt) cc_final: 0.8677 (tttm) REVERT: C 28 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.7499 (ttt-90) REVERT: C 80 ASP cc_start: 0.8121 (m-30) cc_final: 0.7883 (m-30) REVERT: C 215 LYS cc_start: 0.8723 (mttt) cc_final: 0.8019 (mttm) REVERT: C 281 LYS cc_start: 0.8976 (tttt) cc_final: 0.8686 (tttm) REVERT: D 80 ASP cc_start: 0.8026 (m-30) cc_final: 0.7824 (m-30) REVERT: E 82 VAL cc_start: 0.8306 (t) cc_final: 0.7992 (m) REVERT: E 85 GLU cc_start: 0.8144 (mp0) cc_final: 0.7804 (mp0) REVERT: E 215 LYS cc_start: 0.8695 (mttt) cc_final: 0.7935 (mppt) REVERT: E 281 LYS cc_start: 0.8996 (tttt) cc_final: 0.8721 (tttm) REVERT: F 80 ASP cc_start: 0.8113 (m-30) cc_final: 0.7857 (m-30) REVERT: F 273 ARG cc_start: 0.8318 (ttt90) cc_final: 0.8101 (ttt90) REVERT: F 281 LYS cc_start: 0.8988 (tttt) cc_final: 0.8785 (ttmm) REVERT: G 215 LYS cc_start: 0.8692 (mttt) cc_final: 0.8462 (mppt) REVERT: I 215 LYS cc_start: 0.8716 (mttt) cc_final: 0.8094 (mppt) REVERT: I 281 LYS cc_start: 0.8988 (tttt) cc_final: 0.8718 (tttm) REVERT: J 215 LYS cc_start: 0.8693 (mttt) cc_final: 0.8153 (mptt) REVERT: J 281 LYS cc_start: 0.9080 (tttt) cc_final: 0.8840 (tttp) REVERT: K 28 ARG cc_start: 0.7716 (ttt-90) cc_final: 0.7483 (ttt-90) REVERT: K 80 ASP cc_start: 0.8022 (m-30) cc_final: 0.7795 (m-30) REVERT: K 215 LYS cc_start: 0.8684 (mttt) cc_final: 0.8077 (mtmm) REVERT: L 28 ARG cc_start: 0.7787 (ttt-90) cc_final: 0.7520 (ttt-90) REVERT: L 80 ASP cc_start: 0.8098 (m-30) cc_final: 0.7867 (m-30) REVERT: L 273 ARG cc_start: 0.8381 (ttt90) cc_final: 0.8176 (ttt90) REVERT: L 281 LYS cc_start: 0.9031 (tttt) cc_final: 0.8811 (ttmm) outliers start: 0 outliers final: 2 residues processed: 721 average time/residue: 3.6884 time to fit residues: 2997.0156 Evaluate side-chains 365 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 363 time to evaluate : 3.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain E residue 249 GLN 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: 0.7980 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: 1.9588 ------------------------------------------------------------------------------- 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 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 278 ASN E 25 ASN ** E 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 45 ASN H 96 GLN H 110 ASN H 278 ASN I 25 ASN I 45 ASN I 96 GLN I 110 ASN I 278 ASN J 25 ASN 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 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32280 Z= 0.241 Angle : 0.722 11.997 43704 Z= 0.365 Chirality : 0.149 1.705 4764 Planarity : 0.004 0.067 5484 Dihedral : 7.299 59.608 5058 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.03 % Allowed : 8.83 % Favored : 89.14 % 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: -2.08 (0.12), residues: 3912 helix: -0.27 (0.10), residues: 2280 sheet: -1.65 (0.23), residues: 456 loop : -3.38 (0.15), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 198 HIS 0.003 0.001 HIS J 196 PHE 0.009 0.001 PHE K 303 TYR 0.011 0.001 TYR K 300 ARG 0.007 0.001 ARG H 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 392 time to evaluate : 4.194 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: A 85 GLU cc_start: 0.8056 (mp0) cc_final: 0.7811 (mp0) REVERT: B 215 LYS cc_start: 0.8735 (mttm) cc_final: 0.8041 (mtmm) REVERT: C 28 ARG cc_start: 0.7848 (ttt-90) cc_final: 0.7618 (ttt-90) REVERT: C 85 GLU cc_start: 0.8018 (mp0) cc_final: 0.7766 (mp0) REVERT: D 85 GLU cc_start: 0.8091 (mp0) cc_final: 0.7846 (mp0) REVERT: E 85 GLU cc_start: 0.8114 (mp0) cc_final: 0.7899 (mp0) REVERT: G 83 MET cc_start: 0.8550 (ptm) cc_final: 0.8304 (ptp) REVERT: G 85 GLU cc_start: 0.8099 (mp0) cc_final: 0.7845 (mp0) REVERT: H 85 GLU cc_start: 0.8088 (mp0) cc_final: 0.7861 (mp0) REVERT: J 85 GLU cc_start: 0.8055 (mp0) cc_final: 0.7810 (mp0) REVERT: K 28 ARG cc_start: 0.7796 (ttt-90) cc_final: 0.7520 (ttt-90) REVERT: K 85 GLU cc_start: 0.8044 (mp0) cc_final: 0.7802 (mp0) REVERT: L 28 ARG cc_start: 0.7889 (ttt-90) cc_final: 0.7651 (ttt-90) REVERT: L 130 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.6662 (mpt180) outliers start: 65 outliers final: 29 residues processed: 436 average time/residue: 2.8617 time to fit residues: 1453.6820 Evaluate side-chains 344 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 314 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 329 LYS Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 255 THR Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 329 LYS Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 329 LYS Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 349 optimal weight: 3.9990 chunk 377 optimal weight: 3.9990 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** ** 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** ** 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: 0.8562 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 32280 Z= 0.438 Angle : 0.760 11.405 43704 Z= 0.394 Chirality : 0.149 1.727 4764 Planarity : 0.005 0.075 5484 Dihedral : 6.974 56.117 5052 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.90 % Allowed : 10.74 % Favored : 87.36 % 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: -1.53 (0.13), residues: 3912 helix: -0.02 (0.10), residues: 2388 sheet: -1.42 (0.23), residues: 456 loop : -2.96 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 198 HIS 0.012 0.003 HIS E 196 PHE 0.014 0.002 PHE A 288 TYR 0.013 0.002 TYR I 300 ARG 0.007 0.001 ARG H 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 319 time to evaluate : 3.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8114 (mp0) cc_final: 0.7824 (mp0) REVERT: C 28 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7637 (ttt-90) REVERT: C 85 GLU cc_start: 0.8097 (mp0) cc_final: 0.7828 (mp0) REVERT: D 85 GLU cc_start: 0.8119 (mp0) cc_final: 0.7864 (mp0) REVERT: E 85 GLU cc_start: 0.8152 (mp0) cc_final: 0.7933 (mp0) REVERT: G 85 GLU cc_start: 0.8110 (mp0) cc_final: 0.7856 (mp0) REVERT: H 85 GLU cc_start: 0.8135 (mp0) cc_final: 0.7885 (mp0) REVERT: K 85 GLU cc_start: 0.8109 (mp0) cc_final: 0.7839 (mp0) REVERT: L 28 ARG cc_start: 0.8054 (ttt-90) cc_final: 0.7710 (ttt-90) REVERT: L 130 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.6646 (mpt180) outliers start: 61 outliers final: 34 residues processed: 358 average time/residue: 2.8425 time to fit residues: 1198.3109 Evaluate side-chains 311 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 276 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 149 LEU Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 329 LYS Chi-restraints excluded: chain H residue 149 LEU Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain J residue 149 LEU Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 329 LYS Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 329 LYS Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 137 MET Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 0.6980 chunk 262 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 350 optimal weight: 0.9980 chunk 371 optimal weight: 0.6980 chunk 183 optimal weight: 4.9990 chunk 332 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 253 HIS ** B 30 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 253 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32280 Z= 0.186 Angle : 0.661 11.409 43704 Z= 0.333 Chirality : 0.147 1.679 4764 Planarity : 0.003 0.080 5484 Dihedral : 6.236 58.635 5052 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.56 % Allowed : 11.17 % Favored : 87.27 % 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: -0.78 (0.13), residues: 3912 helix: 0.63 (0.10), residues: 2400 sheet: -0.55 (0.27), residues: 324 loop : -2.93 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 198 HIS 0.004 0.001 HIS I 253 PHE 0.007 0.001 PHE F 303 TYR 0.011 0.001 TYR J 300 ARG 0.008 0.001 ARG K 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 361 time to evaluate : 3.687 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: B 85 GLU cc_start: 0.8049 (mp0) cc_final: 0.7587 (mp0) REVERT: C 28 ARG cc_start: 0.7888 (ttt-90) cc_final: 0.7666 (ttt-90) REVERT: D 85 GLU cc_start: 0.8040 (mp0) cc_final: 0.7583 (mp0) REVERT: E 85 GLU cc_start: 0.8058 (mp0) cc_final: 0.7567 (mp0) REVERT: H 85 GLU cc_start: 0.8052 (mp0) cc_final: 0.7598 (mp0) REVERT: I 85 GLU cc_start: 0.8039 (mp0) cc_final: 0.7493 (mp0) REVERT: K 85 GLU cc_start: 0.8025 (mp0) cc_final: 0.7548 (mp0) outliers start: 50 outliers final: 22 residues processed: 391 average time/residue: 2.9257 time to fit residues: 1329.7362 Evaluate side-chains 340 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 318 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 329 LYS Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 329 LYS Chi-restraints excluded: chain H residue 250 MET Chi-restraints excluded: chain H residue 329 LYS Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain J residue 137 MET Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 329 LYS Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 329 LYS Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 329 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 316 optimal weight: 2.9990 chunk 256 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN D 110 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 32280 Z= 0.339 Angle : 0.707 11.374 43704 Z= 0.362 Chirality : 0.148 1.708 4764 Planarity : 0.004 0.100 5484 Dihedral : 6.665 57.205 5052 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.22 % Allowed : 11.86 % Favored : 85.92 % 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: -0.72 (0.13), residues: 3912 helix: 0.60 (0.10), residues: 2400 sheet: -1.04 (0.23), residues: 456 loop : -2.68 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 198 HIS 0.009 0.003 HIS B 196 PHE 0.013 0.002 PHE C 288 TYR 0.012 0.001 TYR E 300 ARG 0.011 0.001 ARG G 70 *********************** 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: 71 poor density : 304 time to evaluate : 3.742 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: B 130 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8275 (mpt90) REVERT: C 28 ARG cc_start: 0.7958 (ttt-90) cc_final: 0.7717 (ttt-90) REVERT: C 130 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8290 (mpt90) REVERT: L 130 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7765 (mpt180) outliers start: 71 outliers final: 36 residues processed: 345 average time/residue: 2.9717 time to fit residues: 1191.4925 Evaluate side-chains 343 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 304 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 329 LYS Chi-restraints excluded: chain H residue 11 ASP Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain J residue 11 ASP Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain J residue 329 LYS Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain K residue 329 LYS Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 2.9990 chunk 334 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 0.9990 chunk 308 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** 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** ** 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: 0.8522 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 32280 Z= 0.246 Angle : 0.678 11.423 43704 Z= 0.343 Chirality : 0.148 1.690 4764 Planarity : 0.004 0.093 5484 Dihedral : 6.339 57.861 5052 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.69 % Allowed : 12.55 % Favored : 85.77 % 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: -0.42 (0.13), residues: 3912 helix: 0.87 (0.10), residues: 2388 sheet: -0.29 (0.27), residues: 324 loop : -2.67 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 198 HIS 0.005 0.002 HIS B 196 PHE 0.009 0.001 PHE B 288 TYR 0.012 0.001 TYR A 300 ARG 0.011 0.001 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 344 time to evaluate : 4.247 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: B 130 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8244 (mpt90) REVERT: C 28 ARG cc_start: 0.7920 (ttt-90) cc_final: 0.7623 (ttt-90) REVERT: C 130 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8275 (mpt90) REVERT: L 130 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7946 (mpt180) outliers start: 54 outliers final: 25 residues processed: 373 average time/residue: 3.0597 time to fit residues: 1320.1178 Evaluate side-chains 347 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 319 time to evaluate : 3.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 329 LYS Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 329 LYS Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 257 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 271 optimal weight: 0.0770 chunk 210 optimal weight: 1.9990 chunk 312 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 370 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 225 optimal weight: 7.9990 chunk 170 optimal weight: 7.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 32280 Z= 0.318 Angle : 0.699 11.343 43704 Z= 0.355 Chirality : 0.149 1.699 4764 Planarity : 0.004 0.097 5484 Dihedral : 6.501 57.085 5052 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.72 % Allowed : 13.42 % Favored : 84.86 % 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: -0.44 (0.13), residues: 3912 helix: 0.84 (0.10), residues: 2388 sheet: -0.95 (0.24), residues: 456 loop : -2.53 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 198 HIS 0.006 0.002 HIS F 196 PHE 0.012 0.002 PHE C 288 TYR 0.011 0.001 TYR G 300 ARG 0.011 0.001 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 316 time to evaluate : 6.169 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: B 130 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8246 (mpt90) REVERT: C 28 ARG cc_start: 0.7953 (ttt-90) cc_final: 0.7636 (ttt-90) REVERT: C 130 ARG cc_start: 0.9002 (OUTLIER) cc_final: 0.8316 (mpt90) REVERT: L 130 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8044 (mpt180) outliers start: 55 outliers final: 39 residues processed: 342 average time/residue: 3.2246 time to fit residues: 1297.2168 Evaluate side-chains 339 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 297 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 329 LYS Chi-restraints excluded: chain H residue 88 GLU Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain J residue 88 GLU Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 285 ASP 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: 2.9990 chunk 221 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 290 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 32280 Z= 0.332 Angle : 0.714 12.312 43704 Z= 0.363 Chirality : 0.150 1.692 4764 Planarity : 0.004 0.085 5484 Dihedral : 6.568 56.509 5052 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.59 % Allowed : 13.95 % Favored : 84.46 % 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: -0.43 (0.13), residues: 3912 helix: 0.82 (0.10), residues: 2388 sheet: -0.94 (0.24), residues: 456 loop : -2.47 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 198 HIS 0.006 0.002 HIS B 196 PHE 0.012 0.002 PHE C 288 TYR 0.012 0.001 TYR G 300 ARG 0.011 0.000 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 316 time to evaluate : 3.775 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: B 130 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8308 (mpt90) REVERT: C 28 ARG cc_start: 0.7963 (ttt-90) cc_final: 0.7585 (ttt-90) REVERT: C 130 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8322 (mpt90) REVERT: F 314 GLU cc_start: 0.8131 (mp0) cc_final: 0.7896 (mp0) REVERT: J 314 GLU cc_start: 0.8139 (mp0) cc_final: 0.7910 (mp0) REVERT: L 130 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8170 (mpt180) outliers start: 51 outliers final: 40 residues processed: 336 average time/residue: 3.0274 time to fit residues: 1182.6871 Evaluate side-chains 339 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 296 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 329 LYS Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain E residue 329 LYS Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain G residue 329 LYS Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain I residue 329 LYS Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain L residue 88 GLU Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 8.9990 chunk 354 optimal weight: 5.9990 chunk 323 optimal weight: 6.9990 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 270 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 311 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 343 optimal weight: 1.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32280 Z= 0.294 Angle : 0.702 12.197 43704 Z= 0.355 Chirality : 0.149 1.690 4764 Planarity : 0.004 0.081 5484 Dihedral : 6.461 56.617 5052 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.50 % Allowed : 14.39 % Favored : 84.11 % 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: -0.33 (0.13), residues: 3912 helix: 0.89 (0.10), residues: 2388 sheet: -0.88 (0.24), residues: 456 loop : -2.43 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 198 HIS 0.005 0.002 HIS K 196 PHE 0.010 0.001 PHE C 288 TYR 0.011 0.001 TYR I 300 ARG 0.010 0.000 ARG I 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 309 time to evaluate : 4.120 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: B 130 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8280 (mpt90) REVERT: C 130 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8388 (mpt90) REVERT: L 130 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8094 (mpt180) outliers start: 48 outliers final: 33 residues processed: 330 average time/residue: 3.0580 time to fit residues: 1172.2212 Evaluate side-chains 331 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 295 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 285 ASP Chi-restraints excluded: chain B residue 88 GLU Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain B residue 285 ASP Chi-restraints excluded: chain B residue 329 LYS Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 285 ASP Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 250 MET Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 285 ASP Chi-restraints excluded: chain F residue 88 GLU Chi-restraints excluded: chain F residue 250 MET Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain H residue 285 ASP Chi-restraints excluded: chain I residue 285 ASP Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 285 ASP Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 285 ASP Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 257 SER Chi-restraints excluded: chain L residue 285 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 6.9990 chunk 364 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 382 optimal weight: 2.9990 chunk 352 optimal weight: 9.9990 chunk 304 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 235 optimal weight: 0.7980 chunk 186 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8513 moved from start: 0.5014 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= 0.228 Angle : 0.691 12.275 43704 Z= 0.347 Chirality : 0.149 1.689 4764 Planarity : 0.003 0.075 5484 Dihedral : 6.183 57.339 5052 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.15 % Allowed : 14.95 % Favored : 83.90 % 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: -0.14 (0.13), residues: 3912 helix: 1.04 (0.10), residues: 2400 sheet: -0.09 (0.27), residues: 324 loop : -2.49 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 198 HIS 0.004 0.001 HIS J 196 PHE 0.008 0.001 PHE D 288 TYR 0.011 0.001 TYR A 300 ARG 0.010 0.000 ARG I 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7824 Ramachandran restraints generated. 3912 Oldfield, 0 Emsley, 3912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 327 time to evaluate : 3.666 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: B 130 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8318 (mpt90) REVERT: C 28 ARG cc_start: 0.7838 (ttt-90) cc_final: 0.7620 (ttt-90) REVERT: C 314 GLU cc_start: 0.8173 (mp0) cc_final: 0.7958 (mp0) REVERT: K 314 GLU cc_start: 0.8167 (mp0) cc_final: 0.7953 (mp0) outliers start: 37 outliers final: 13 residues processed: 341 average time/residue: 2.9537 time to fit residues: 1173.0356 Evaluate side-chains 338 residues out of total 3204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 324 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain B residue 130 ARG Chi-restraints excluded: chain C residue 250 MET Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 250 MET Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 285 ASP Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain L residue 257 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 305 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 313 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.100414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.072724 restraints weight = 192541.608| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 2.63 r_work: 0.2764 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.5063 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= 0.303 Angle : 0.710 11.645 43704 Z= 0.360 Chirality : 0.149 1.684 4764 Planarity : 0.004 0.108 5484 Dihedral : 6.422 56.451 5052 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.84 % Allowed : 15.26 % Favored : 83.90 % 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: 0.96 (0.10), residues: 2388 sheet: -0.86 (0.23), residues: 456 loop : -2.33 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 198 HIS 0.005 0.002 HIS E 196 PHE 0.012 0.002 PHE C 288 TYR 0.011 0.001 TYR I 300 ARG 0.012 0.000 ARG B 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21375.90 seconds wall clock time: 365 minutes 49.67 seconds (21949.67 seconds total)