Starting phenix.real_space_refine on Fri Aug 9 10:22:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/08_2024/8ukm_42355.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/08_2024/8ukm_42355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/08_2024/8ukm_42355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/08_2024/8ukm_42355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/08_2024/8ukm_42355.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/08_2024/8ukm_42355.cif" } resolution = 4.2 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= 0.003 sd= 0.030 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 17004 2.51 5 N 4464 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E ASP 118": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G ASP 137": "OD1" <-> "OD2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "I ASP 38": "OD1" <-> "OD2" Residue "I ASP 118": "OD1" <-> "OD2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I ASP 184": "OD1" <-> "OD2" Residue "I ASP 188": "OD1" <-> "OD2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "K ASP 38": "OD1" <-> "OD2" Residue "K ASP 118": "OD1" <-> "OD2" Residue "K ASP 137": "OD1" <-> "OD2" Residue "K ASP 184": "OD1" <-> "OD2" Residue "K ASP 188": "OD1" <-> "OD2" Residue "L PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "M ASP 38": "OD1" <-> "OD2" Residue "M ASP 118": "OD1" <-> "OD2" Residue "M ASP 137": "OD1" <-> "OD2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "M ASP 188": "OD1" <-> "OD2" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "O ASP 38": "OD1" <-> "OD2" Residue "O ASP 118": "OD1" <-> "OD2" Residue "O ASP 137": "OD1" <-> "OD2" Residue "O ASP 184": "OD1" <-> "OD2" Residue "O ASP 188": "OD1" <-> "OD2" Residue "P PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 97": "OE1" <-> "OE2" Residue "Q ASP 38": "OD1" <-> "OD2" Residue "Q ASP 118": "OD1" <-> "OD2" Residue "Q ASP 137": "OD1" <-> "OD2" Residue "Q ASP 184": "OD1" <-> "OD2" Residue "Q ASP 188": "OD1" <-> "OD2" Residue "R PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "S ASP 38": "OD1" <-> "OD2" Residue "S ASP 118": "OD1" <-> "OD2" Residue "S ASP 137": "OD1" <-> "OD2" Residue "S ASP 184": "OD1" <-> "OD2" Residue "S ASP 188": "OD1" <-> "OD2" Residue "T PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "U ASP 38": "OD1" <-> "OD2" Residue "U ASP 118": "OD1" <-> "OD2" Residue "U ASP 137": "OD1" <-> "OD2" Residue "U ASP 184": "OD1" <-> "OD2" Residue "U ASP 188": "OD1" <-> "OD2" Residue "V PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 97": "OE1" <-> "OE2" Residue "W ASP 38": "OD1" <-> "OD2" Residue "W ASP 118": "OD1" <-> "OD2" Residue "W ASP 137": "OD1" <-> "OD2" Residue "W ASP 184": "OD1" <-> "OD2" Residue "W ASP 188": "OD1" <-> "OD2" Residue "X PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 97": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 26184 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "B" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "C" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "D" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "E" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "F" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "G" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "H" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "I" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "J" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "K" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "M" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "N" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "O" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "P" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "Q" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "R" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "S" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "T" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "U" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "V" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "W" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "X" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Time building chain proxies: 14.87, per 1000 atoms: 0.57 Number of scatterers: 26184 At special positions: 0 Unit cell: (144.1, 141.9, 137.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 4668 8.00 N 4464 7.00 C 17004 6.00 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: 11.03 Conformation dependent library (CDL) restraints added in 5.5 seconds 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 48 sheets defined 43.5% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'B' and resid 13 through 33 Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 73 through 93 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 100 through 107 removed outlier: 3.682A pdb=" N PHE C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'D' and resid 13 through 33 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 73 through 93 Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 66 through 82 Processing helix chain 'E' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 143 Processing helix chain 'E' and resid 167 through 183 Processing helix chain 'F' and resid 13 through 33 Processing helix chain 'F' and resid 35 through 39 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 73 through 93 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 66 through 82 Processing helix chain 'G' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 107 " --> pdb=" O PRO G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 143 Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'H' and resid 13 through 33 Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 47 through 50 Processing helix chain 'H' and resid 73 through 93 Processing helix chain 'H' and resid 95 through 97 No H-bonds generated for 'chain 'H' and resid 95 through 97' Processing helix chain 'I' and resid 29 through 44 Processing helix chain 'I' and resid 66 through 82 Processing helix chain 'I' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU I 107 " --> pdb=" O PRO I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 143 Processing helix chain 'I' and resid 167 through 183 Processing helix chain 'J' and resid 13 through 33 Processing helix chain 'J' and resid 35 through 39 Processing helix chain 'J' and resid 47 through 50 Processing helix chain 'J' and resid 73 through 93 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'K' and resid 29 through 44 Processing helix chain 'K' and resid 66 through 82 Processing helix chain 'K' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 107 " --> pdb=" O PRO K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 167 through 183 Processing helix chain 'L' and resid 13 through 33 Processing helix chain 'L' and resid 35 through 39 Processing helix chain 'L' and resid 47 through 50 Processing helix chain 'L' and resid 73 through 93 Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'M' and resid 29 through 44 Processing helix chain 'M' and resid 66 through 82 Processing helix chain 'M' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU M 107 " --> pdb=" O PRO M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 143 Processing helix chain 'M' and resid 167 through 183 Processing helix chain 'N' and resid 13 through 33 Processing helix chain 'N' and resid 35 through 39 Processing helix chain 'N' and resid 47 through 50 Processing helix chain 'N' and resid 73 through 93 Processing helix chain 'N' and resid 95 through 97 No H-bonds generated for 'chain 'N' and resid 95 through 97' Processing helix chain 'O' and resid 29 through 44 Processing helix chain 'O' and resid 66 through 82 Processing helix chain 'O' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE O 104 " --> pdb=" O ALA O 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU O 107 " --> pdb=" O PRO O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 143 Processing helix chain 'O' and resid 167 through 183 Processing helix chain 'P' and resid 13 through 33 Processing helix chain 'P' and resid 35 through 39 Processing helix chain 'P' and resid 47 through 50 Processing helix chain 'P' and resid 73 through 93 Processing helix chain 'P' and resid 95 through 97 No H-bonds generated for 'chain 'P' and resid 95 through 97' Processing helix chain 'Q' and resid 29 through 44 Processing helix chain 'Q' and resid 66 through 82 Processing helix chain 'Q' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE Q 104 " --> pdb=" O ALA Q 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU Q 107 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 143 Processing helix chain 'Q' and resid 167 through 183 Processing helix chain 'R' and resid 13 through 33 Processing helix chain 'R' and resid 35 through 39 Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 73 through 93 Processing helix chain 'R' and resid 95 through 97 No H-bonds generated for 'chain 'R' and resid 95 through 97' Processing helix chain 'S' and resid 29 through 44 Processing helix chain 'S' and resid 66 through 82 Processing helix chain 'S' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU S 107 " --> pdb=" O PRO S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 143 Processing helix chain 'S' and resid 167 through 183 Processing helix chain 'T' and resid 13 through 33 Processing helix chain 'T' and resid 35 through 39 Processing helix chain 'T' and resid 47 through 50 Processing helix chain 'T' and resid 73 through 93 Processing helix chain 'T' and resid 95 through 97 No H-bonds generated for 'chain 'T' and resid 95 through 97' Processing helix chain 'U' and resid 29 through 44 Processing helix chain 'U' and resid 66 through 82 Processing helix chain 'U' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU U 107 " --> pdb=" O PRO U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 143 Processing helix chain 'U' and resid 167 through 183 Processing helix chain 'V' and resid 13 through 33 Processing helix chain 'V' and resid 35 through 39 Processing helix chain 'V' and resid 47 through 50 Processing helix chain 'V' and resid 73 through 93 Processing helix chain 'V' and resid 95 through 97 No H-bonds generated for 'chain 'V' and resid 95 through 97' Processing helix chain 'W' and resid 29 through 44 Processing helix chain 'W' and resid 66 through 82 Processing helix chain 'W' and resid 100 through 107 removed outlier: 3.682A pdb=" N PHE W 104 " --> pdb=" O ALA W 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU W 107 " --> pdb=" O PRO W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 143 Processing helix chain 'W' and resid 167 through 183 Processing helix chain 'X' and resid 13 through 33 Processing helix chain 'X' and resid 35 through 39 Processing helix chain 'X' and resid 47 through 50 Processing helix chain 'X' and resid 73 through 93 Processing helix chain 'X' and resid 95 through 97 No H-bonds generated for 'chain 'X' and resid 95 through 97' Processing sheet with id=1, first strand: chain 'A' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU A 48 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 64 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 50 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 90 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU A 147 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 165 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 149 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 160 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 126 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 162 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 124 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 121 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE A 191 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 123 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE A 189 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A 125 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU B 4 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 44 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL B 6 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR B 46 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 8 " --> pdb=" O TYR B 46 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=5, first strand: chain 'C' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU C 48 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR C 64 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 50 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 90 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU C 147 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 165 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 149 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C 160 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C 126 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE C 162 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 124 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 121 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE C 191 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE C 123 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE C 189 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU C 125 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU D 4 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR D 44 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL D 6 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR D 46 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 8 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=9, first strand: chain 'E' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU E 48 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 64 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 50 " --> pdb=" O MET E 62 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 90 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU E 147 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL E 165 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG E 149 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA E 160 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 126 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE E 162 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL E 124 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU E 121 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE E 191 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE E 123 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE E 189 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU E 125 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU F 4 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR F 44 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL F 6 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR F 46 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 8 " --> pdb=" O TYR F 46 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=13, first strand: chain 'G' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU G 48 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR G 64 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS G 50 " --> pdb=" O MET G 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 90 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU G 147 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL G 165 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG G 149 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA G 160 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL G 126 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE G 162 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL G 124 " --> pdb=" O PHE G 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU G 121 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE G 191 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE G 123 " --> pdb=" O ILE G 189 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE G 189 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU G 125 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU H 4 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR H 44 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL H 6 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR H 46 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL H 8 " --> pdb=" O TYR H 46 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=17, first strand: chain 'I' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU I 48 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR I 64 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS I 50 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 90 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU I 147 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL I 165 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG I 149 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA I 160 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL I 126 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE I 162 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL I 124 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU I 121 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE I 191 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE I 123 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE I 189 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU I 125 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'J' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU J 4 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR J 44 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL J 6 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR J 46 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL J 8 " --> pdb=" O TYR J 46 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=21, first strand: chain 'K' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU K 48 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR K 64 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS K 50 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP K 90 " --> pdb=" O GLU K 26 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'K' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU K 147 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL K 165 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG K 149 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA K 160 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL K 126 " --> pdb=" O ALA K 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE K 162 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL K 124 " --> pdb=" O PHE K 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU K 121 " --> pdb=" O ILE K 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE K 191 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE K 123 " --> pdb=" O ILE K 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE K 189 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU K 125 " --> pdb=" O LEU K 187 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'L' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU L 4 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR L 44 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL L 6 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR L 46 " --> pdb=" O VAL L 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL L 8 " --> pdb=" O TYR L 46 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'L' and resid 52 through 53 Processing sheet with id=25, first strand: chain 'M' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU M 48 " --> pdb=" O THR M 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR M 64 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 50 " --> pdb=" O MET M 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP M 90 " --> pdb=" O GLU M 26 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'M' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU M 147 " --> pdb=" O VAL M 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL M 165 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG M 149 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA M 160 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL M 126 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE M 162 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL M 124 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 121 " --> pdb=" O ILE M 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE M 191 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE M 123 " --> pdb=" O ILE M 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE M 189 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU M 125 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'N' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU N 4 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR N 44 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL N 6 " --> pdb=" O THR N 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR N 46 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL N 8 " --> pdb=" O TYR N 46 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'N' and resid 52 through 53 Processing sheet with id=29, first strand: chain 'O' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU O 48 " --> pdb=" O THR O 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR O 64 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS O 50 " --> pdb=" O MET O 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP O 90 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'O' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU O 147 " --> pdb=" O VAL O 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL O 165 " --> pdb=" O LEU O 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG O 149 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA O 160 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL O 126 " --> pdb=" O ALA O 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE O 162 " --> pdb=" O VAL O 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL O 124 " --> pdb=" O PHE O 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU O 121 " --> pdb=" O ILE O 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE O 191 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE O 123 " --> pdb=" O ILE O 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE O 189 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU O 125 " --> pdb=" O LEU O 187 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'P' and resid 42 through 46 removed outlier: 5.526A pdb=" N LEU P 4 " --> pdb=" O ILE P 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR P 44 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL P 6 " --> pdb=" O THR P 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR P 46 " --> pdb=" O VAL P 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL P 8 " --> pdb=" O TYR P 46 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'P' and resid 52 through 53 Processing sheet with id=33, first strand: chain 'Q' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU Q 48 " --> pdb=" O THR Q 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR Q 64 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS Q 50 " --> pdb=" O MET Q 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP Q 90 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'Q' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU Q 147 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL Q 165 " --> pdb=" O LEU Q 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG Q 149 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA Q 160 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL Q 126 " --> pdb=" O ALA Q 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE Q 162 " --> pdb=" O VAL Q 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL Q 124 " --> pdb=" O PHE Q 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU Q 121 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE Q 191 " --> pdb=" O LEU Q 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE Q 123 " --> pdb=" O ILE Q 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE Q 189 " --> pdb=" O PHE Q 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU Q 125 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'R' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU R 4 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR R 44 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL R 6 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR R 46 " --> pdb=" O VAL R 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL R 8 " --> pdb=" O TYR R 46 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'R' and resid 52 through 53 Processing sheet with id=37, first strand: chain 'S' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU S 48 " --> pdb=" O THR S 64 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR S 64 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS S 50 " --> pdb=" O MET S 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP S 90 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'S' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU S 147 " --> pdb=" O VAL S 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL S 165 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG S 149 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA S 160 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL S 126 " --> pdb=" O ALA S 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE S 162 " --> pdb=" O VAL S 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL S 124 " --> pdb=" O PHE S 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU S 121 " --> pdb=" O ILE S 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE S 191 " --> pdb=" O LEU S 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE S 123 " --> pdb=" O ILE S 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE S 189 " --> pdb=" O PHE S 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU S 125 " --> pdb=" O LEU S 187 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'T' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU T 4 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR T 44 " --> pdb=" O LEU T 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL T 6 " --> pdb=" O THR T 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR T 46 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL T 8 " --> pdb=" O TYR T 46 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'T' and resid 52 through 53 Processing sheet with id=41, first strand: chain 'U' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU U 48 " --> pdb=" O THR U 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR U 64 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS U 50 " --> pdb=" O MET U 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP U 90 " --> pdb=" O GLU U 26 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'U' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU U 147 " --> pdb=" O VAL U 165 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL U 165 " --> pdb=" O LEU U 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG U 149 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA U 160 " --> pdb=" O VAL U 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL U 126 " --> pdb=" O ALA U 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE U 162 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL U 124 " --> pdb=" O PHE U 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU U 121 " --> pdb=" O ILE U 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE U 191 " --> pdb=" O LEU U 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE U 123 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE U 189 " --> pdb=" O PHE U 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU U 125 " --> pdb=" O LEU U 187 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'V' and resid 42 through 46 removed outlier: 5.524A pdb=" N LEU V 4 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR V 44 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL V 6 " --> pdb=" O THR V 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR V 46 " --> pdb=" O VAL V 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL V 8 " --> pdb=" O TYR V 46 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'V' and resid 52 through 53 Processing sheet with id=45, first strand: chain 'W' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU W 48 " --> pdb=" O THR W 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR W 64 " --> pdb=" O LEU W 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS W 50 " --> pdb=" O MET W 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP W 90 " --> pdb=" O GLU W 26 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'W' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU W 147 " --> pdb=" O VAL W 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL W 165 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG W 149 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA W 160 " --> pdb=" O VAL W 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL W 126 " --> pdb=" O ALA W 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE W 162 " --> pdb=" O VAL W 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL W 124 " --> pdb=" O PHE W 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU W 121 " --> pdb=" O ILE W 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE W 191 " --> pdb=" O LEU W 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE W 123 " --> pdb=" O ILE W 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE W 189 " --> pdb=" O PHE W 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU W 125 " --> pdb=" O LEU W 187 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'X' and resid 42 through 46 removed outlier: 5.526A pdb=" N LEU X 4 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR X 44 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL X 6 " --> pdb=" O THR X 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR X 46 " --> pdb=" O VAL X 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL X 8 " --> pdb=" O TYR X 46 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'X' and resid 52 through 53 1512 hydrogen bonds defined for protein. 4284 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: 10.42 Time building geometry restraints manager: 11.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8669 1.34 - 1.46: 4132 1.46 - 1.58: 13755 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 26640 Sorted by residual: bond pdb=" N VAL V 62 " pdb=" CA VAL V 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.27e+00 bond pdb=" N VAL L 62 " pdb=" CA VAL L 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.15e+00 bond pdb=" N VAL N 62 " pdb=" CA VAL N 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.09e+00 bond pdb=" N VAL F 62 " pdb=" CA VAL F 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.05e+00 bond pdb=" N VAL X 62 " pdb=" CA VAL X 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.04e+00 ... (remaining 26635 not shown) Histogram of bond angle deviations from ideal: 100.63 - 106.83: 1260 106.83 - 113.02: 14992 113.02 - 119.21: 7001 119.21 - 125.40: 12843 125.40 - 131.59: 324 Bond angle restraints: 36420 Sorted by residual: angle pdb=" N GLY M 201 " pdb=" CA GLY M 201 " pdb=" C GLY M 201 " ideal model delta sigma weight residual 115.08 110.47 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N GLY K 201 " pdb=" CA GLY K 201 " pdb=" C GLY K 201 " ideal model delta sigma weight residual 115.08 110.47 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N GLY Q 201 " pdb=" CA GLY Q 201 " pdb=" C GLY Q 201 " ideal model delta sigma weight residual 115.08 110.49 4.59 1.19e+00 7.06e-01 1.49e+01 angle pdb=" N GLY I 201 " pdb=" CA GLY I 201 " pdb=" C GLY I 201 " ideal model delta sigma weight residual 115.08 110.49 4.59 1.19e+00 7.06e-01 1.49e+01 angle pdb=" N GLY C 201 " pdb=" CA GLY C 201 " pdb=" C GLY C 201 " ideal model delta sigma weight residual 115.08 110.50 4.58 1.19e+00 7.06e-01 1.48e+01 ... (remaining 36415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 15080 17.47 - 34.93: 1276 34.93 - 52.40: 168 52.40 - 69.87: 36 69.87 - 87.34: 12 Dihedral angle restraints: 16572 sinusoidal: 6348 harmonic: 10224 Sorted by residual: dihedral pdb=" CA LEU O 152 " pdb=" C LEU O 152 " pdb=" N SER O 153 " pdb=" CA SER O 153 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LEU G 152 " pdb=" C LEU G 152 " pdb=" N SER G 153 " pdb=" CA SER G 153 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU C 152 " pdb=" C LEU C 152 " pdb=" N SER C 153 " pdb=" CA SER C 153 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 16569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3100 0.042 - 0.083: 932 0.083 - 0.125: 448 0.125 - 0.166: 72 0.166 - 0.208: 20 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CA ILE P 64 " pdb=" N ILE P 64 " pdb=" C ILE P 64 " pdb=" CB ILE P 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE J 64 " pdb=" N ILE J 64 " pdb=" C ILE J 64 " pdb=" CB ILE J 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 4569 not shown) Planarity restraints: 4680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 19 " 0.179 9.50e-02 1.11e+02 8.05e-02 4.18e+00 pdb=" NE ARG G 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG G 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 19 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 19 " 0.179 9.50e-02 1.11e+02 8.04e-02 4.17e+00 pdb=" NE ARG A 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 19 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 19 " 0.179 9.50e-02 1.11e+02 8.05e-02 4.17e+00 pdb=" NE ARG Q 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG Q 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 19 " 0.009 2.00e-02 2.50e+03 ... (remaining 4677 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3740 2.76 - 3.29: 27993 3.29 - 3.83: 44337 3.83 - 4.36: 48519 4.36 - 4.90: 82777 Nonbonded interactions: 207366 Sorted by model distance: nonbonded pdb=" O GLU J 97 " pdb=" NH1 ARG J 100 " model vdw 2.220 3.120 nonbonded pdb=" O GLU R 97 " pdb=" NH1 ARG R 100 " model vdw 2.220 3.120 nonbonded pdb=" O GLU F 97 " pdb=" NH1 ARG F 100 " model vdw 2.220 3.120 nonbonded pdb=" O GLU T 97 " pdb=" NH1 ARG T 100 " model vdw 2.220 3.120 nonbonded pdb=" O GLU H 97 " pdb=" NH1 ARG H 100 " model vdw 2.220 3.120 ... (remaining 207361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } 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 group one per residue 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.280 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 72.740 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.170 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:3.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 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 : 0.004 0.039 26640 Z= 0.261 Angle : 0.752 6.988 36420 Z= 0.394 Chirality : 0.050 0.208 4572 Planarity : 0.007 0.081 4680 Dihedral : 13.153 87.335 9924 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.17 (0.14), residues: 3480 helix: 1.21 (0.13), residues: 1308 sheet: -1.51 (0.15), residues: 876 loop : 0.44 (0.21), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS U 196 PHE 0.013 0.002 PHE K 162 TYR 0.009 0.002 TYR I 30 ARG 0.008 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.892 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: B 12 TYR cc_start: 0.8819 (m-10) cc_final: 0.8590 (m-10) REVERT: B 17 LYS cc_start: 0.9096 (pttm) cc_final: 0.8799 (pttm) REVERT: B 90 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 75 LYS cc_start: 0.9336 (pttm) cc_final: 0.9115 (ptmm) REVERT: C 150 MET cc_start: 0.8584 (tmm) cc_final: 0.8324 (tmm) REVERT: D 90 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 75 LYS cc_start: 0.9303 (pttm) cc_final: 0.9040 (ptmm) REVERT: H 90 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8276 (tm-30) REVERT: I 150 MET cc_start: 0.8576 (tmm) cc_final: 0.8283 (tmm) REVERT: J 90 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8265 (tm-30) REVERT: L 7 TYR cc_start: 0.8913 (m-10) cc_final: 0.8710 (m-10) REVERT: L 90 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8404 (tm-30) REVERT: M 75 LYS cc_start: 0.9363 (pttm) cc_final: 0.9133 (ptmm) REVERT: M 150 MET cc_start: 0.8491 (tmm) cc_final: 0.8217 (tmm) REVERT: N 90 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8399 (tm-30) REVERT: O 75 LYS cc_start: 0.9366 (pttm) cc_final: 0.9141 (ptmm) REVERT: P 90 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8379 (tm-30) REVERT: Q 75 LYS cc_start: 0.9265 (pttm) cc_final: 0.9041 (ptmm) REVERT: Q 150 MET cc_start: 0.8464 (tmm) cc_final: 0.8005 (tmm) REVERT: R 7 TYR cc_start: 0.9016 (m-10) cc_final: 0.8766 (m-10) REVERT: R 90 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8178 (tm-30) REVERT: T 12 TYR cc_start: 0.8788 (m-10) cc_final: 0.8534 (m-10) REVERT: T 17 LYS cc_start: 0.9073 (pttm) cc_final: 0.8776 (pttm) REVERT: T 90 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8361 (tm-30) REVERT: U 75 LYS cc_start: 0.9305 (pttm) cc_final: 0.9072 (ptmm) REVERT: U 150 MET cc_start: 0.8473 (tmm) cc_final: 0.8254 (tmm) REVERT: V 90 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8382 (tm-30) REVERT: W 75 LYS cc_start: 0.9403 (pttm) cc_final: 0.9149 (ptmm) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.3429 time to fit residues: 273.4188 Evaluate side-chains 416 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 10.0000 chunk 254 optimal weight: 0.3980 chunk 141 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: