Starting phenix.real_space_refine on Wed Jul 24 12:18:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui2_42286/07_2024/8ui2_42286.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui2_42286/07_2024/8ui2_42286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui2_42286/07_2024/8ui2_42286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui2_42286/07_2024/8ui2_42286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui2_42286/07_2024/8ui2_42286.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ui2_42286/07_2024/8ui2_42286.cif" } resolution = 2.73 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= 0.008 sd= 0.147 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 17052 2.51 5 N 4668 2.21 5 O 4800 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 GLU 79": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E GLU 79": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G GLU 184": "OE1" <-> "OE2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 38": "OD1" <-> "OD2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 184": "OE1" <-> "OE2" Residue "I ASP 188": "OD1" <-> "OD2" Residue "J ASP 85": "OD1" <-> "OD2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 38": "OD1" <-> "OD2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "K GLU 184": "OE1" <-> "OE2" Residue "K ASP 188": "OD1" <-> "OD2" Residue "L ASP 85": "OD1" <-> "OD2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 38": "OD1" <-> "OD2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M GLU 184": "OE1" <-> "OE2" Residue "M ASP 188": "OD1" <-> "OD2" Residue "N ASP 85": "OD1" <-> "OD2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 38": "OD1" <-> "OD2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O GLU 184": "OE1" <-> "OE2" Residue "O ASP 188": "OD1" <-> "OD2" Residue "P ASP 85": "OD1" <-> "OD2" Residue "P GLU 87": "OE1" <-> "OE2" Residue "P TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 38": "OD1" <-> "OD2" Residue "Q GLU 79": "OE1" <-> "OE2" Residue "Q GLU 184": "OE1" <-> "OE2" Residue "Q ASP 188": "OD1" <-> "OD2" Residue "R ASP 85": "OD1" <-> "OD2" Residue "R GLU 87": "OE1" <-> "OE2" Residue "R TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 38": "OD1" <-> "OD2" Residue "S GLU 79": "OE1" <-> "OE2" Residue "S GLU 184": "OE1" <-> "OE2" Residue "S ASP 188": "OD1" <-> "OD2" Residue "T ASP 85": "OD1" <-> "OD2" Residue "T GLU 87": "OE1" <-> "OE2" Residue "T TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 38": "OD1" <-> "OD2" Residue "U GLU 79": "OE1" <-> "OE2" Residue "U GLU 184": "OE1" <-> "OE2" Residue "U ASP 188": "OD1" <-> "OD2" Residue "V ASP 85": "OD1" <-> "OD2" Residue "V GLU 87": "OE1" <-> "OE2" Residue "V TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 38": "OD1" <-> "OD2" Residue "W GLU 79": "OE1" <-> "OE2" Residue "W GLU 184": "OE1" <-> "OE2" Residue "W ASP 188": "OD1" <-> "OD2" Residue "X ASP 85": "OD1" <-> "OD2" Residue "X GLU 87": "OE1" <-> "OE2" Residue "X TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 26568 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "B" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "C" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "D" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "E" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "F" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "G" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "H" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "I" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "J" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "K" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "M" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "N" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "O" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "P" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "Q" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "S" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "T" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "U" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "V" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Chain: "W" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1398 Classifications: {'peptide': 188} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 174} Chain: "X" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 7, 'TRANS': 95} Time building chain proxies: 14.76, per 1000 atoms: 0.56 Number of scatterers: 26568 At special positions: 0 Unit cell: (135.3, 138.6, 133.1, 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 4800 8.00 N 4668 7.00 C 17052 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: 9.77 Conformation dependent library (CDL) restraints added in 5.5 seconds 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6600 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 36 sheets defined 40.9% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 11 No H-bonds generated for 'chain 'B' and resid 9 through 11' Processing helix chain 'B' and resid 12 through 23 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 90 through 101 Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 128 through 143 Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'C' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 11 No H-bonds generated for 'chain 'D' and resid 9 through 11' Processing helix chain 'D' and resid 12 through 23 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'E' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 106 Processing helix chain 'E' and resid 128 through 143 Processing helix chain 'E' and resid 167 through 183 Processing helix chain 'E' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG E 202 " --> pdb=" O ALA E 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 11 No H-bonds generated for 'chain 'F' and resid 9 through 11' Processing helix chain 'F' and resid 12 through 23 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.645A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 106 Processing helix chain 'G' and resid 128 through 143 Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'G' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY G 201 " --> pdb=" O GLU G 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 11 No H-bonds generated for 'chain 'H' and resid 9 through 11' Processing helix chain 'H' and resid 12 through 23 Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 90 through 101 Processing helix chain 'I' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 106 Processing helix chain 'I' and resid 128 through 143 Processing helix chain 'I' and resid 167 through 183 Processing helix chain 'I' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG I 202 " --> pdb=" O ALA I 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 11 No H-bonds generated for 'chain 'J' and resid 9 through 11' Processing helix chain 'J' and resid 12 through 23 Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 90 through 101 Processing helix chain 'K' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 106 Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 167 through 183 Processing helix chain 'K' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY K 201 " --> pdb=" O GLU K 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG K 202 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 11 No H-bonds generated for 'chain 'L' and resid 9 through 11' Processing helix chain 'L' and resid 12 through 23 Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 90 through 101 Processing helix chain 'M' and resid 29 through 44 removed outlier: 3.645A pdb=" N ALA M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS M 82 " --> pdb=" O LEU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 106 Processing helix chain 'M' and resid 128 through 143 Processing helix chain 'M' and resid 167 through 183 Processing helix chain 'M' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY M 201 " --> pdb=" O GLU M 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG M 202 " --> pdb=" O ALA M 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 11 No H-bonds generated for 'chain 'N' and resid 9 through 11' Processing helix chain 'N' and resid 12 through 23 Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 90 through 101 Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS O 82 " --> pdb=" O LEU O 78 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 106 Processing helix chain 'O' and resid 128 through 143 Processing helix chain 'O' and resid 167 through 183 Processing helix chain 'O' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY O 201 " --> pdb=" O GLU O 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG O 202 " --> pdb=" O ALA O 198 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 11 No H-bonds generated for 'chain 'P' and resid 9 through 11' Processing helix chain 'P' and resid 12 through 23 Processing helix chain 'P' and resid 60 through 70 Processing helix chain 'P' and resid 90 through 101 Processing helix chain 'Q' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA Q 44 " --> pdb=" O ALA Q 40 " (cutoff:3.500A) Processing helix chain 'Q' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS Q 82 " --> pdb=" O LEU Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 106 Processing helix chain 'Q' and resid 128 through 143 Processing helix chain 'Q' and resid 167 through 183 Processing helix chain 'Q' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY Q 201 " --> pdb=" O GLU Q 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG Q 202 " --> pdb=" O ALA Q 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 11 No H-bonds generated for 'chain 'R' and resid 9 through 11' Processing helix chain 'R' and resid 12 through 23 Processing helix chain 'R' and resid 60 through 70 Processing helix chain 'R' and resid 90 through 101 Processing helix chain 'S' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS S 82 " --> pdb=" O LEU S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 106 Processing helix chain 'S' and resid 128 through 143 Processing helix chain 'S' and resid 167 through 183 Processing helix chain 'S' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY S 201 " --> pdb=" O GLU S 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG S 202 " --> pdb=" O ALA S 198 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 11 No H-bonds generated for 'chain 'T' and resid 9 through 11' Processing helix chain 'T' and resid 12 through 23 Processing helix chain 'T' and resid 60 through 70 Processing helix chain 'T' and resid 90 through 101 Processing helix chain 'U' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 82 removed outlier: 3.658A pdb=" N LYS U 82 " --> pdb=" O LEU U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 101 through 106 Processing helix chain 'U' and resid 128 through 143 Processing helix chain 'U' and resid 167 through 183 Processing helix chain 'U' and resid 196 through 204 removed outlier: 3.568A pdb=" N GLY U 201 " --> pdb=" O GLU U 197 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG U 202 " --> pdb=" O ALA U 198 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 11 No H-bonds generated for 'chain 'V' and resid 9 through 11' Processing helix chain 'V' and resid 12 through 23 Processing helix chain 'V' and resid 60 through 70 Processing helix chain 'V' and resid 90 through 101 Processing helix chain 'W' and resid 29 through 44 removed outlier: 3.646A pdb=" N ALA W 44 " --> pdb=" O ALA W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 82 removed outlier: 3.657A pdb=" N LYS W 82 " --> pdb=" O LEU W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 101 through 106 Processing helix chain 'W' and resid 128 through 143 Processing helix chain 'W' and resid 167 through 183 Processing helix chain 'W' and resid 196 through 204 removed outlier: 3.569A pdb=" N GLY W 201 " --> pdb=" O GLU W 197 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG W 202 " --> pdb=" O ALA W 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 11 No H-bonds generated for 'chain 'X' and resid 9 through 11' Processing helix chain 'X' and resid 12 through 23 Processing helix chain 'X' and resid 60 through 70 Processing helix chain 'X' and resid 90 through 101 Processing sheet with id=1, first strand: chain 'A' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET A 62 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS A 51 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 60 " --> pdb=" O CYS A 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS A 58 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 22 " --> pdb=" O PHE A 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE A 93 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 24 " --> pdb=" O HIS A 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS A 91 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU A 26 " --> pdb=" O ILE A 89 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU A 147 " --> pdb=" O ALA A 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA A 165 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 149 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL A 121 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 191 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL A 123 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU A 189 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU A 125 " --> pdb=" O ILE A 187 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU B 28 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR B 38 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 3 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'C' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET C 62 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS C 51 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU C 60 " --> pdb=" O CYS C 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS C 58 " --> pdb=" O PRO C 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU C 22 " --> pdb=" O PHE C 93 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE C 93 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 24 " --> pdb=" O HIS C 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS C 91 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU C 26 " --> pdb=" O ILE C 89 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU C 147 " --> pdb=" O ALA C 165 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 165 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 149 " --> pdb=" O VAL C 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL C 121 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE C 191 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 123 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU C 189 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU C 125 " --> pdb=" O ILE C 187 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'D' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU D 28 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 38 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 3 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'E' and resid 47 through 54 removed outlier: 5.955A pdb=" N MET E 62 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS E 51 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU E 60 " --> pdb=" O CYS E 51 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS E 58 " --> pdb=" O PRO E 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU E 22 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE E 93 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL E 24 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS E 91 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU E 26 " --> pdb=" O ILE E 89 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'E' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU E 147 " --> pdb=" O ALA E 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA E 165 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG E 149 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL E 121 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE E 191 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 123 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU E 189 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU E 125 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'F' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU F 28 " --> pdb=" O LEU F 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR F 38 " --> pdb=" O ARG F 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE F 3 " --> pdb=" O LEU F 82 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'G' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET G 62 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS G 51 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU G 60 " --> pdb=" O CYS G 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS G 58 " --> pdb=" O PRO G 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU G 22 " --> pdb=" O PHE G 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE G 93 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL G 24 " --> pdb=" O HIS G 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS G 91 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU G 26 " --> pdb=" O ILE G 89 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'G' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU G 147 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA G 165 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG G 149 " --> pdb=" O VAL G 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL G 121 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE G 191 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL G 123 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU G 189 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU G 125 " --> pdb=" O ILE G 187 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'H' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU H 28 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR H 38 " --> pdb=" O ARG H 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE H 3 " --> pdb=" O LEU H 82 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'I' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET I 62 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS I 51 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU I 60 " --> pdb=" O CYS I 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS I 58 " --> pdb=" O PRO I 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU I 22 " --> pdb=" O PHE I 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE I 93 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL I 24 " --> pdb=" O HIS I 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS I 91 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU I 26 " --> pdb=" O ILE I 89 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'I' and resid 146 through 152 removed outlier: 5.577A pdb=" N LEU I 147 " --> pdb=" O ALA I 165 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA I 165 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG I 149 " --> pdb=" O VAL I 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL I 121 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE I 191 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL I 123 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU I 189 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU I 125 " --> pdb=" O ILE I 187 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'J' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU J 28 " --> pdb=" O LEU J 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR J 38 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE J 3 " --> pdb=" O LEU J 82 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'K' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET K 62 " --> pdb=" O LEU K 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS K 51 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU K 60 " --> pdb=" O CYS K 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS K 58 " --> pdb=" O PRO K 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU K 22 " --> pdb=" O PHE K 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE K 93 " --> pdb=" O LEU K 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL K 24 " --> pdb=" O HIS K 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS K 91 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU K 26 " --> pdb=" O ILE K 89 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'K' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU K 147 " --> pdb=" O ALA K 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA K 165 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG K 149 " --> pdb=" O VAL K 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL K 121 " --> pdb=" O ILE K 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE K 191 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL K 123 " --> pdb=" O LEU K 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU K 189 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU K 125 " --> pdb=" O ILE K 187 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'L' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU L 28 " --> pdb=" O LEU L 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR L 38 " --> pdb=" O ARG L 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE L 3 " --> pdb=" O LEU L 82 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'M' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET M 62 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS M 51 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU M 60 " --> pdb=" O CYS M 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS M 58 " --> pdb=" O PRO M 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU M 22 " --> pdb=" O PHE M 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE M 93 " --> pdb=" O LEU M 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL M 24 " --> pdb=" O HIS M 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS M 91 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU M 26 " --> pdb=" O ILE M 89 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'M' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU M 147 " --> pdb=" O ALA M 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA M 165 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG M 149 " --> pdb=" O VAL M 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL M 121 " --> pdb=" O ILE M 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE M 191 " --> pdb=" O VAL M 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL M 123 " --> pdb=" O LEU M 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU M 189 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU M 125 " --> pdb=" O ILE M 187 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'N' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU N 28 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR N 38 " --> pdb=" O ARG N 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE N 3 " --> pdb=" O LEU N 82 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'O' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET O 62 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS O 51 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU O 60 " --> pdb=" O CYS O 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS O 58 " --> pdb=" O PRO O 53 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU O 22 " --> pdb=" O PHE O 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE O 93 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL O 24 " --> pdb=" O HIS O 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS O 91 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU O 26 " --> pdb=" O ILE O 89 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'O' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU O 147 " --> pdb=" O ALA O 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA O 165 " --> pdb=" O LEU O 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG O 149 " --> pdb=" O VAL O 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL O 121 " --> pdb=" O ILE O 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE O 191 " --> pdb=" O VAL O 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL O 123 " --> pdb=" O LEU O 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU O 189 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU O 125 " --> pdb=" O ILE O 187 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'P' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU P 28 " --> pdb=" O LEU P 55 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR P 38 " --> pdb=" O ARG P 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE P 3 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'Q' and resid 47 through 54 removed outlier: 5.955A pdb=" N MET Q 62 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS Q 51 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU Q 60 " --> pdb=" O CYS Q 51 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS Q 58 " --> pdb=" O PRO Q 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU Q 22 " --> pdb=" O PHE Q 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE Q 93 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL Q 24 " --> pdb=" O HIS Q 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS Q 91 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU Q 26 " --> pdb=" O ILE Q 89 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'Q' and resid 146 through 152 removed outlier: 5.577A pdb=" N LEU Q 147 " --> pdb=" O ALA Q 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA Q 165 " --> pdb=" O LEU Q 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG Q 149 " --> pdb=" O VAL Q 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL Q 121 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE Q 191 " --> pdb=" O VAL Q 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL Q 123 " --> pdb=" O LEU Q 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU Q 189 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU Q 125 " --> pdb=" O ILE Q 187 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'R' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU R 28 " --> pdb=" O LEU R 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR R 38 " --> pdb=" O ARG R 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE R 3 " --> pdb=" O LEU R 82 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'S' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET S 62 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS S 51 " --> pdb=" O LEU S 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU S 60 " --> pdb=" O CYS S 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS S 58 " --> pdb=" O PRO S 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU S 22 " --> pdb=" O PHE S 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE S 93 " --> pdb=" O LEU S 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL S 24 " --> pdb=" O HIS S 91 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS S 91 " --> pdb=" O VAL S 24 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU S 26 " --> pdb=" O ILE S 89 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'S' and resid 146 through 152 removed outlier: 5.577A pdb=" N LEU S 147 " --> pdb=" O ALA S 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA S 165 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG S 149 " --> pdb=" O VAL S 163 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL S 121 " --> pdb=" O ILE S 191 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE S 191 " --> pdb=" O VAL S 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL S 123 " --> pdb=" O LEU S 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU S 189 " --> pdb=" O VAL S 123 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU S 125 " --> pdb=" O ILE S 187 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'T' and resid 28 through 40 removed outlier: 3.600A pdb=" N GLU T 28 " --> pdb=" O LEU T 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR T 38 " --> pdb=" O ARG T 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE T 3 " --> pdb=" O LEU T 82 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'U' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET U 62 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS U 51 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU U 60 " --> pdb=" O CYS U 51 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYS U 58 " --> pdb=" O PRO U 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU U 22 " --> pdb=" O PHE U 93 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE U 93 " --> pdb=" O LEU U 22 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL U 24 " --> pdb=" O HIS U 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS U 91 " --> pdb=" O VAL U 24 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU U 26 " --> pdb=" O ILE U 89 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'U' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU U 147 " --> pdb=" O ALA U 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA U 165 " --> pdb=" O LEU U 147 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG U 149 " --> pdb=" O VAL U 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL U 121 " --> pdb=" O ILE U 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE U 191 " --> pdb=" O VAL U 121 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL U 123 " --> pdb=" O LEU U 189 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU U 189 " --> pdb=" O VAL U 123 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLU U 125 " --> pdb=" O ILE U 187 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'V' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU V 28 " --> pdb=" O LEU V 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR V 38 " --> pdb=" O ARG V 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE V 3 " --> pdb=" O LEU V 82 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'W' and resid 47 through 54 removed outlier: 5.956A pdb=" N MET W 62 " --> pdb=" O LEU W 49 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N CYS W 51 " --> pdb=" O LEU W 60 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU W 60 " --> pdb=" O CYS W 51 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS W 58 " --> pdb=" O PRO W 53 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU W 22 " --> pdb=" O PHE W 93 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE W 93 " --> pdb=" O LEU W 22 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL W 24 " --> pdb=" O HIS W 91 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N HIS W 91 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU W 26 " --> pdb=" O ILE W 89 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'W' and resid 146 through 152 removed outlier: 5.576A pdb=" N LEU W 147 " --> pdb=" O ALA W 165 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA W 165 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG W 149 " --> pdb=" O VAL W 163 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL W 121 " --> pdb=" O ILE W 191 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE W 191 " --> pdb=" O VAL W 121 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL W 123 " --> pdb=" O LEU W 189 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LEU W 189 " --> pdb=" O VAL W 123 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU W 125 " --> pdb=" O ILE W 187 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'X' and resid 28 through 40 removed outlier: 3.601A pdb=" N GLU X 28 " --> pdb=" O LEU X 55 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR X 38 " --> pdb=" O ARG X 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE X 3 " --> pdb=" O LEU X 82 " (cutoff:3.500A) 1452 hydrogen bonds defined for protein. 4140 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: 8.30 Time building geometry restraints manager: 10.82 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: 9072 1.34 - 1.46: 4075 1.46 - 1.58: 13805 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 27036 Sorted by residual: bond pdb=" C ARG M 96 " pdb=" N ILE M 97 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 7.12e-01 bond pdb=" C ARG C 96 " pdb=" N ILE C 97 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 6.99e-01 bond pdb=" C ARG I 96 " pdb=" N ILE I 97 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 6.92e-01 bond pdb=" C ARG Q 96 " pdb=" N ILE Q 97 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 6.91e-01 bond pdb=" C ARG G 96 " pdb=" N ILE G 97 " ideal model delta sigma weight residual 1.334 1.323 0.010 1.29e-02 6.01e+03 6.61e-01 ... (remaining 27031 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.39: 1248 107.39 - 114.03: 15646 114.03 - 120.68: 10669 120.68 - 127.33: 8929 127.33 - 133.98: 300 Bond angle restraints: 36792 Sorted by residual: angle pdb=" C HIS H 72 " pdb=" N PRO H 73 " pdb=" CA PRO H 73 " ideal model delta sigma weight residual 118.97 120.62 -1.65 1.04e+00 9.25e-01 2.53e+00 angle pdb=" C HIS P 72 " pdb=" N PRO P 73 " pdb=" CA PRO P 73 " ideal model delta sigma weight residual 118.97 120.62 -1.65 1.04e+00 9.25e-01 2.51e+00 angle pdb=" C HIS R 72 " pdb=" N PRO R 73 " pdb=" CA PRO R 73 " ideal model delta sigma weight residual 118.97 120.61 -1.64 1.04e+00 9.25e-01 2.49e+00 angle pdb=" C HIS T 72 " pdb=" N PRO T 73 " pdb=" CA PRO T 73 " ideal model delta sigma weight residual 118.97 120.61 -1.64 1.04e+00 9.25e-01 2.48e+00 angle pdb=" C HIS F 72 " pdb=" N PRO F 73 " pdb=" CA PRO F 73 " ideal model delta sigma weight residual 118.97 120.60 -1.63 1.04e+00 9.25e-01 2.45e+00 ... (remaining 36787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.02: 14393 17.02 - 34.03: 1534 34.03 - 51.05: 657 51.05 - 68.06: 180 68.06 - 85.08: 36 Dihedral angle restraints: 16800 sinusoidal: 6660 harmonic: 10140 Sorted by residual: dihedral pdb=" CA ARG L 35 " pdb=" C ARG L 35 " pdb=" N ARG L 36 " pdb=" CA ARG L 36 " ideal model delta harmonic sigma weight residual -180.00 -164.39 -15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CB GLU G 134 " pdb=" CG GLU G 134 " pdb=" CD GLU G 134 " pdb=" OE1 GLU G 134 " ideal model delta sinusoidal sigma weight residual 0.00 -85.08 85.08 1 3.00e+01 1.11e-03 9.75e+00 dihedral pdb=" CB GLU M 134 " pdb=" CG GLU M 134 " pdb=" CD GLU M 134 " pdb=" OE1 GLU M 134 " ideal model delta sinusoidal sigma weight residual 0.00 -85.03 85.03 1 3.00e+01 1.11e-03 9.74e+00 ... (remaining 16797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2388 0.027 - 0.053: 1274 0.053 - 0.080: 297 0.080 - 0.107: 223 0.107 - 0.133: 222 Chirality restraints: 4404 Sorted by residual: chirality pdb=" CA VAL C 124 " pdb=" N VAL C 124 " pdb=" C VAL C 124 " pdb=" CB VAL C 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA VAL O 124 " pdb=" N VAL O 124 " pdb=" C VAL O 124 " pdb=" CB VAL O 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA VAL E 124 " pdb=" N VAL E 124 " pdb=" C VAL E 124 " pdb=" CB VAL E 124 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 4401 not shown) Planarity restraints: 4788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU F 14 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO F 15 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 15 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 15 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 14 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO D 15 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 15 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 15 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 14 " 0.023 5.00e-02 4.00e+02 3.45e-02 1.91e+00 pdb=" N PRO J 15 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO J 15 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 15 " 0.020 5.00e-02 4.00e+02 ... (remaining 4785 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1226 2.73 - 3.27: 23700 3.27 - 3.81: 41074 3.81 - 4.36: 50133 4.36 - 4.90: 93374 Nonbonded interactions: 209507 Sorted by model distance: nonbonded pdb=" OE2 GLU K 125 " pdb=" OG SER M 29 " model vdw 2.187 2.440 nonbonded pdb=" OG SER G 29 " pdb=" OE2 GLU Q 125 " model vdw 2.187 2.440 nonbonded pdb=" OE2 GLU M 125 " pdb=" OG SER U 29 " model vdw 2.187 2.440 nonbonded pdb=" OG SER O 29 " pdb=" OE2 GLU S 125 " model vdw 2.187 2.440 nonbonded pdb=" OG SER K 29 " pdb=" OE2 GLU U 125 " model vdw 2.187 2.440 ... (remaining 209502 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 '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 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: 0.400 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: 0.040 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 69.940 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.190 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:11.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 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 0.023 27036 Z= 0.264 Angle : 0.516 5.142 36792 Z= 0.256 Chirality : 0.044 0.133 4404 Planarity : 0.005 0.035 4788 Dihedral : 17.613 85.075 10200 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.35 % Allowed : 24.32 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.39 (0.14), residues: 3444 helix: -0.36 (0.13), residues: 1380 sheet: 0.67 (0.18), residues: 972 loop : -0.75 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 67 HIS 0.003 0.001 HIS W 196 PHE 0.017 0.002 PHE E 93 TYR 0.008 0.002 TYR K 161 ARG 0.003 0.000 ARG N 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 302 time to evaluate : 3.000 Fit side-chains REVERT: A 150 MET cc_start: 0.8854 (tpt) cc_final: 0.8401 (tpp) REVERT: A 185 LYS cc_start: 0.8918 (mttm) cc_final: 0.8396 (mptt) REVERT: B 58 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7580 (mtp180) REVERT: B 90 ASN cc_start: 0.8779 (t160) cc_final: 0.8558 (t0) REVERT: C 150 MET cc_start: 0.8741 (tpt) cc_final: 0.8433 (tpp) REVERT: D 58 ARG cc_start: 0.7771 (mtp-110) cc_final: 0.7563 (mtp180) REVERT: E 62 MET cc_start: 0.9072 (mtt) cc_final: 0.8851 (mtm) REVERT: E 150 MET cc_start: 0.8796 (tpt) cc_final: 0.8522 (tpp) REVERT: E 185 LYS cc_start: 0.8874 (mttm) cc_final: 0.8528 (mmtp) REVERT: F 58 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7584 (mtp180) REVERT: G 185 LYS cc_start: 0.8965 (mttm) cc_final: 0.8620 (mmtp) REVERT: H 58 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.7608 (mtp-110) REVERT: H 76 ILE cc_start: 0.6787 (OUTLIER) cc_final: 0.6396 (mt) REVERT: I 185 LYS cc_start: 0.8895 (mttm) cc_final: 0.8654 (mttp) REVERT: K 185 LYS cc_start: 0.8951 (mttm) cc_final: 0.8646 (mmtm) REVERT: O 74 MET cc_start: 0.8208 (mmm) cc_final: 0.7794 (mmm) REVERT: O 150 MET cc_start: 0.8835 (tpt) cc_final: 0.8042 (tpt) REVERT: O 185 LYS cc_start: 0.9011 (mttm) cc_final: 0.8637 (mttp) REVERT: P 18 ARG cc_start: 0.7943 (mtt90) cc_final: 0.7653 (mtt90) REVERT: P 58 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7795 (mtp180) REVERT: Q 28 LYS cc_start: 0.8479 (mttp) cc_final: 0.8172 (mttp) REVERT: R 58 ARG cc_start: 0.7760 (mtp-110) cc_final: 0.7443 (tpp-160) REVERT: S 185 LYS cc_start: 0.8824 (mttm) cc_final: 0.8277 (mptt) REVERT: U 185 LYS cc_start: 0.8881 (mttm) cc_final: 0.8666 (mmtm) REVERT: V 76 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6532 (mt) REVERT: V 90 ASN cc_start: 0.8700 (t160) cc_final: 0.8468 (t0) REVERT: V 93 TYR cc_start: 0.8664 (t80) cc_final: 0.8437 (t80) REVERT: W 28 LYS cc_start: 0.8539 (mttp) cc_final: 0.8319 (mttp) REVERT: W 185 LYS cc_start: 0.8881 (mttm) cc_final: 0.8669 (mtpt) REVERT: X 18 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7633 (mtt90) REVERT: X 58 ARG cc_start: 0.7777 (mtp-110) cc_final: 0.7491 (mtp180) outliers start: 36 outliers final: 6 residues processed: 335 average time/residue: 1.8108 time to fit residues: 679.2891 Evaluate side-chains 276 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 268 time to evaluate : 2.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain S residue 29 SER Chi-restraints excluded: chain V residue 76 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 171 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 263 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 10.0000 chunk 305 optimal weight: 0.0670 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS B 72 HIS B 90 ASN C 196 HIS D 72 HIS D 90 ASN E 196 HIS F 72 HIS F 90 ASN G 196 HIS H 72 HIS H 90 ASN I 196 HIS J 72 HIS J 90 ASN K 196 HIS L 72 HIS L 90 ASN M 196 HIS N 72 HIS N 90 ASN O 196 HIS P 72 HIS P 90 ASN Q 196 HIS R 72 HIS R 90 ASN S 196 HIS T 72 HIS T 90 ASN U 196 HIS V 72 HIS V 90 ASN W 196 HIS X 72 HIS X 90 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 27036 Z= 0.266 Angle : 0.594 5.700 36792 Z= 0.293 Chirality : 0.045 0.129 4404 Planarity : 0.005 0.035 4788 Dihedral : 4.591 38.952 3852 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.27 % Allowed : 22.07 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 3444 helix: 0.47 (0.13), residues: 1404 sheet: 0.83 (0.18), residues: 984 loop : -0.93 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 67 HIS 0.004 0.001 HIS C 91 PHE 0.015 0.002 PHE M 162 TYR 0.017 0.002 TYR L 93 ARG 0.007 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 282 time to evaluate : 2.778 Fit side-chains REVERT: A 47 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8120 (tt0) REVERT: A 149 ARG cc_start: 0.8116 (ttp80) cc_final: 0.7905 (ttp80) REVERT: A 150 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8381 (tpp) REVERT: C 150 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8511 (tpp) REVERT: D 58 ARG cc_start: 0.7797 (mtp-110) cc_final: 0.7583 (mtp180) REVERT: D 69 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: E 93 PHE cc_start: 0.8943 (t80) cc_final: 0.8577 (t80) REVERT: E 150 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8637 (tpp) REVERT: E 171 VAL cc_start: 0.8268 (t) cc_final: 0.8041 (t) REVERT: E 185 LYS cc_start: 0.8854 (mttm) cc_final: 0.8465 (mmtp) REVERT: G 66 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7682 (mm-30) REVERT: G 185 LYS cc_start: 0.8929 (mttm) cc_final: 0.8575 (mmtp) REVERT: H 39 ARG cc_start: 0.5853 (OUTLIER) cc_final: 0.5635 (ttp-170) REVERT: H 58 ARG cc_start: 0.7859 (mtp-110) cc_final: 0.7568 (mtp180) REVERT: I 149 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7656 (ttm170) REVERT: I 185 LYS cc_start: 0.8894 (mttm) cc_final: 0.8622 (mmtp) REVERT: K 28 LYS cc_start: 0.8523 (mttp) cc_final: 0.8285 (mttp) REVERT: K 52 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7673 (pt0) REVERT: K 185 LYS cc_start: 0.8960 (mttm) cc_final: 0.8665 (mmtm) REVERT: M 66 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: M 90 ASP cc_start: 0.8673 (t0) cc_final: 0.8393 (t0) REVERT: O 52 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: O 150 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8309 (tpt) REVERT: O 185 LYS cc_start: 0.8946 (mttm) cc_final: 0.8562 (mttp) REVERT: P 58 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7767 (mtp180) REVERT: Q 52 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7890 (pt0) REVERT: R 58 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7419 (tpp-160) REVERT: S 184 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7574 (pt0) REVERT: S 185 LYS cc_start: 0.8778 (mttm) cc_final: 0.8224 (mptt) REVERT: U 66 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7610 (mm-30) REVERT: U 185 LYS cc_start: 0.8888 (mttm) cc_final: 0.8626 (mmtm) REVERT: W 28 LYS cc_start: 0.8564 (mttp) cc_final: 0.8306 (mttp) REVERT: W 52 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: X 18 ARG cc_start: 0.7941 (mtt90) cc_final: 0.7730 (mtt90) REVERT: X 58 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7523 (mtp180) outliers start: 87 outliers final: 17 residues processed: 349 average time/residue: 1.9838 time to fit residues: 768.4205 Evaluate side-chains 303 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 270 time to evaluate : 2.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 76 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 149 ARG Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain Q residue 171 VAL Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 171 VAL Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain W residue 29 SER Chi-restraints excluded: chain W residue 52 GLU Chi-restraints excluded: chain W residue 171 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 253 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 0.6980 chunk 330 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 303 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 245 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 27036 Z= 0.174 Angle : 0.491 5.195 36792 Z= 0.246 Chirality : 0.043 0.126 4404 Planarity : 0.005 0.032 4788 Dihedral : 4.094 41.151 3840 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.00 % Allowed : 23.57 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.47 (0.15), residues: 3444 helix: 0.98 (0.14), residues: 1404 sheet: 0.82 (0.18), residues: 972 loop : -0.99 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP J 67 HIS 0.002 0.001 HIS P 102 PHE 0.011 0.001 PHE A 162 TYR 0.012 0.001 TYR J 93 ARG 0.006 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 287 time to evaluate : 3.057 Fit side-chains REVERT: A 150 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8413 (tpp) REVERT: B 69 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: C 38 ASP cc_start: 0.8369 (t0) cc_final: 0.8154 (t0) REVERT: C 150 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8435 (tpp) REVERT: D 58 ARG cc_start: 0.7742 (mtp-110) cc_final: 0.7525 (mtp180) REVERT: D 69 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7048 (mp0) REVERT: E 93 PHE cc_start: 0.8970 (t80) cc_final: 0.8593 (t80) REVERT: E 171 VAL cc_start: 0.8327 (t) cc_final: 0.8105 (t) REVERT: E 184 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7342 (pp20) REVERT: E 185 LYS cc_start: 0.8839 (mttm) cc_final: 0.8562 (mmtp) REVERT: F 69 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: G 47 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: G 74 MET cc_start: 0.8428 (mmm) cc_final: 0.7984 (mmm) REVERT: G 184 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7523 (pt0) REVERT: G 185 LYS cc_start: 0.8880 (mttm) cc_final: 0.8508 (mmtm) REVERT: H 39 ARG cc_start: 0.5775 (OUTLIER) cc_final: 0.5567 (ttp-170) REVERT: H 58 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7575 (mtp180) REVERT: I 90 ASP cc_start: 0.8696 (t0) cc_final: 0.8425 (t0) REVERT: I 185 LYS cc_start: 0.8904 (mttm) cc_final: 0.8373 (mptt) REVERT: K 28 LYS cc_start: 0.8525 (mttp) cc_final: 0.8298 (mttp) REVERT: K 52 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: K 185 LYS cc_start: 0.8909 (mttm) cc_final: 0.8633 (mmtm) REVERT: L 87 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7313 (mp0) REVERT: M 184 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: N 18 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7445 (mtt-85) REVERT: N 85 ASP cc_start: 0.8205 (t70) cc_final: 0.7989 (t70) REVERT: O 150 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8333 (tpt) REVERT: O 184 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7575 (pt0) REVERT: O 185 LYS cc_start: 0.8949 (mttm) cc_final: 0.8606 (mmtp) REVERT: P 58 ARG cc_start: 0.8005 (mtp-110) cc_final: 0.7767 (mtp180) REVERT: Q 52 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: R 58 ARG cc_start: 0.7686 (mtp-110) cc_final: 0.7441 (tpp-160) REVERT: S 52 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7942 (pt0) REVERT: S 184 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: S 185 LYS cc_start: 0.8736 (mttm) cc_final: 0.8176 (mptt) REVERT: U 185 LYS cc_start: 0.8842 (mttm) cc_final: 0.8482 (mmtp) REVERT: V 35 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7881 (ttp80) REVERT: V 69 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: W 47 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: W 90 ASP cc_start: 0.8728 (t0) cc_final: 0.8441 (t0) REVERT: W 184 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7154 (pp20) REVERT: X 58 ARG cc_start: 0.7798 (mtp-110) cc_final: 0.7568 (mtp180) outliers start: 80 outliers final: 13 residues processed: 342 average time/residue: 1.8505 time to fit residues: 706.6776 Evaluate side-chains 304 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 272 time to evaluate : 3.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 39 ARG Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 47 GLU Chi-restraints excluded: chain W residue 184 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 6.9990 chunk 229 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 27036 Z= 0.209 Angle : 0.524 5.348 36792 Z= 0.257 Chirality : 0.044 0.126 4404 Planarity : 0.005 0.032 4788 Dihedral : 4.103 47.569 3840 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.42 % Allowed : 24.14 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.54 (0.14), residues: 3444 helix: 1.08 (0.14), residues: 1404 sheet: 0.83 (0.18), residues: 972 loop : -1.00 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 67 HIS 0.003 0.001 HIS U 91 PHE 0.012 0.002 PHE W 162 TYR 0.013 0.002 TYR I 161 ARG 0.005 0.000 ARG N 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 275 time to evaluate : 2.951 Fit side-chains REVERT: A 150 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8413 (tpp) REVERT: A 184 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: B 69 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: C 38 ASP cc_start: 0.8452 (t0) cc_final: 0.8212 (t0) REVERT: C 150 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8536 (tpp) REVERT: D 69 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: E 93 PHE cc_start: 0.8987 (t80) cc_final: 0.8678 (t80) REVERT: E 171 VAL cc_start: 0.8207 (t) cc_final: 0.7992 (t) REVERT: E 184 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: E 185 LYS cc_start: 0.8871 (mttm) cc_final: 0.8595 (mmtp) REVERT: F 69 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.6710 (mp0) REVERT: G 47 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: G 74 MET cc_start: 0.8395 (mmm) cc_final: 0.8063 (mmm) REVERT: G 185 LYS cc_start: 0.8912 (mttm) cc_final: 0.8559 (mmtp) REVERT: H 58 ARG cc_start: 0.7876 (mtp-110) cc_final: 0.7600 (mtp180) REVERT: I 185 LYS cc_start: 0.8904 (mttm) cc_final: 0.8378 (mptt) REVERT: K 28 LYS cc_start: 0.8520 (mttp) cc_final: 0.8303 (mttp) REVERT: K 52 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: K 185 LYS cc_start: 0.8919 (mttm) cc_final: 0.8636 (mmtm) REVERT: L 87 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7293 (mp0) REVERT: M 66 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: M 184 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7382 (pp20) REVERT: N 18 ARG cc_start: 0.7853 (mtt90) cc_final: 0.7460 (mtt-85) REVERT: O 150 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8300 (tpt) REVERT: O 184 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: O 185 LYS cc_start: 0.8952 (mttm) cc_final: 0.8609 (mmtp) REVERT: P 58 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7792 (mtp180) REVERT: Q 28 LYS cc_start: 0.8473 (mttp) cc_final: 0.8193 (mttp) REVERT: Q 47 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8038 (tt0) REVERT: Q 52 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: R 58 ARG cc_start: 0.7693 (mtp-110) cc_final: 0.7428 (tpp-160) REVERT: S 52 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7938 (pt0) REVERT: S 184 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: S 185 LYS cc_start: 0.8755 (mttm) cc_final: 0.8171 (mptt) REVERT: T 74 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7315 (p0) REVERT: T 87 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7299 (mp0) REVERT: U 169 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6892 (mm-30) REVERT: U 184 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7353 (pp20) REVERT: U 185 LYS cc_start: 0.8874 (mttm) cc_final: 0.8480 (mmtp) REVERT: V 35 ARG cc_start: 0.8120 (ttp80) cc_final: 0.7888 (ttp80) REVERT: V 69 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: W 90 ASP cc_start: 0.8745 (t0) cc_final: 0.8426 (t0) REVERT: X 58 ARG cc_start: 0.7835 (mtp-110) cc_final: 0.7611 (mtp180) outliers start: 91 outliers final: 14 residues processed: 344 average time/residue: 1.7928 time to fit residues: 691.4041 Evaluate side-chains 307 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 272 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain I residue 25 LEU Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain J residue 74 ASP Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain M residue 66 GLU Chi-restraints excluded: chain M residue 184 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 150 MET Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain U residue 169 GLU Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 171 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.4980 chunk 184 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 241 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 0.0370 chunk 291 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 27036 Z= 0.139 Angle : 0.451 5.260 36792 Z= 0.226 Chirality : 0.042 0.129 4404 Planarity : 0.004 0.034 4788 Dihedral : 3.768 47.104 3840 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.19 % Allowed : 24.59 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.83 (0.15), residues: 3444 helix: 1.42 (0.14), residues: 1404 sheet: 1.19 (0.18), residues: 912 loop : -1.11 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 67 HIS 0.002 0.000 HIS X 72 PHE 0.010 0.001 PHE O 162 TYR 0.010 0.001 TYR I 161 ARG 0.005 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 299 time to evaluate : 2.876 Fit side-chains REVERT: A 150 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8277 (tpp) REVERT: A 184 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: B 58 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.7485 (mtp180) REVERT: B 69 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: C 38 ASP cc_start: 0.8456 (t0) cc_final: 0.8229 (t0) REVERT: C 156 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.6238 (pt) REVERT: D 69 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: E 93 PHE cc_start: 0.8955 (t80) cc_final: 0.8667 (t80) REVERT: E 184 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: E 185 LYS cc_start: 0.8809 (mttm) cc_final: 0.8488 (mmtp) REVERT: F 69 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6742 (mp0) REVERT: G 74 MET cc_start: 0.8371 (mmm) cc_final: 0.7871 (mmm) REVERT: G 184 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: G 185 LYS cc_start: 0.8854 (mttm) cc_final: 0.8506 (mmtp) REVERT: H 58 ARG cc_start: 0.7862 (mtp-110) cc_final: 0.7585 (mtp180) REVERT: I 90 ASP cc_start: 0.8642 (t0) cc_final: 0.8273 (t0) REVERT: I 185 LYS cc_start: 0.8850 (mttm) cc_final: 0.8312 (mptt) REVERT: K 28 LYS cc_start: 0.8578 (mttp) cc_final: 0.8370 (mttp) REVERT: K 52 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: K 185 LYS cc_start: 0.8890 (mttm) cc_final: 0.8607 (mmtm) REVERT: L 69 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: L 87 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7331 (mp0) REVERT: M 68 GLU cc_start: 0.7421 (mp0) cc_final: 0.7169 (mp0) REVERT: M 90 ASP cc_start: 0.8726 (t0) cc_final: 0.8261 (t70) REVERT: N 18 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7466 (mtt-85) REVERT: N 28 GLU cc_start: 0.8091 (tt0) cc_final: 0.7882 (tp30) REVERT: O 150 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8360 (tpt) REVERT: O 185 LYS cc_start: 0.8887 (mttm) cc_final: 0.8577 (mmtp) REVERT: P 58 ARG cc_start: 0.8001 (mtp-110) cc_final: 0.7789 (mtp180) REVERT: Q 28 LYS cc_start: 0.8457 (mttp) cc_final: 0.8203 (mttp) REVERT: Q 47 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: Q 52 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: R 28 GLU cc_start: 0.7755 (tt0) cc_final: 0.7531 (tp30) REVERT: R 58 ARG cc_start: 0.7675 (mtp-110) cc_final: 0.7451 (tpp-160) REVERT: S 52 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7823 (pt0) REVERT: S 150 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8291 (tpp) REVERT: S 184 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7516 (pt0) REVERT: S 185 LYS cc_start: 0.8698 (mttm) cc_final: 0.8390 (mmmm) REVERT: T 74 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7272 (p0) REVERT: T 87 GLU cc_start: 0.7505 (mm-30) cc_final: 0.7254 (mp0) REVERT: U 184 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: U 185 LYS cc_start: 0.8810 (mttm) cc_final: 0.8407 (mmtp) REVERT: V 35 ARG cc_start: 0.8083 (ttp80) cc_final: 0.7870 (ttp80) REVERT: V 69 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6818 (mp0) REVERT: W 184 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7130 (pp20) REVERT: X 58 ARG cc_start: 0.7817 (mtp-110) cc_final: 0.7589 (mtp180) outliers start: 85 outliers final: 11 residues processed: 360 average time/residue: 1.7777 time to fit residues: 717.2826 Evaluate side-chains 310 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 279 time to evaluate : 2.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain L residue 76 ILE Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 171 VAL Chi-restraints excluded: chain W residue 184 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 9.9990 chunk 292 optimal weight: 0.0040 chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 80 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 chunk 269 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 27036 Z= 0.264 Angle : 0.568 6.170 36792 Z= 0.274 Chirality : 0.045 0.128 4404 Planarity : 0.005 0.034 4788 Dihedral : 4.077 50.296 3840 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.25 % Allowed : 25.86 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.60 (0.15), residues: 3444 helix: 1.18 (0.14), residues: 1404 sheet: 0.83 (0.17), residues: 972 loop : -1.01 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP T 67 HIS 0.003 0.001 HIS E 91 PHE 0.013 0.002 PHE W 162 TYR 0.014 0.002 TYR I 161 ARG 0.005 0.000 ARG N 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 278 time to evaluate : 2.994 Fit side-chains REVERT: A 47 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: A 150 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8365 (tpp) REVERT: A 184 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7637 (pt0) REVERT: B 69 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: C 38 ASP cc_start: 0.8514 (t0) cc_final: 0.8250 (t0) REVERT: D 69 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7093 (mp0) REVERT: D 93 TYR cc_start: 0.8735 (t80) cc_final: 0.8428 (t80) REVERT: E 93 PHE cc_start: 0.8992 (t80) cc_final: 0.8679 (t80) REVERT: E 185 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8611 (mmtp) REVERT: F 69 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6732 (mp0) REVERT: G 74 MET cc_start: 0.8417 (mmm) cc_final: 0.8093 (mmm) REVERT: G 184 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: G 185 LYS cc_start: 0.8906 (mttm) cc_final: 0.8538 (mmtp) REVERT: H 58 ARG cc_start: 0.7892 (mtp-110) cc_final: 0.7618 (mtp180) REVERT: H 85 ASP cc_start: 0.8683 (t70) cc_final: 0.8272 (t0) REVERT: I 185 LYS cc_start: 0.8904 (mttm) cc_final: 0.8380 (mptt) REVERT: J 39 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.5270 (ttp-170) REVERT: K 28 LYS cc_start: 0.8559 (mttp) cc_final: 0.8341 (mttp) REVERT: K 185 LYS cc_start: 0.8917 (mttm) cc_final: 0.8629 (mmtm) REVERT: L 69 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: L 87 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7339 (mp0) REVERT: M 68 GLU cc_start: 0.7518 (mp0) cc_final: 0.7246 (mp0) REVERT: N 18 ARG cc_start: 0.7870 (mtt90) cc_final: 0.7460 (mtt-85) REVERT: O 150 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8403 (tpt) REVERT: O 185 LYS cc_start: 0.8954 (mttm) cc_final: 0.8621 (mmtp) REVERT: P 58 ARG cc_start: 0.8024 (mtp-110) cc_final: 0.7809 (mtp180) REVERT: P 86 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7935 (mt-10) REVERT: Q 28 LYS cc_start: 0.8465 (mttp) cc_final: 0.8203 (mttp) REVERT: Q 47 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8041 (tt0) REVERT: R 58 ARG cc_start: 0.7667 (mtp-110) cc_final: 0.7424 (tpp-160) REVERT: S 184 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7644 (pt0) REVERT: S 185 LYS cc_start: 0.8759 (mttm) cc_final: 0.8451 (mmtm) REVERT: T 74 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7282 (p0) REVERT: T 87 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7320 (mp0) REVERT: U 184 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7336 (pp20) REVERT: U 185 LYS cc_start: 0.8951 (mttm) cc_final: 0.8490 (mmtp) REVERT: V 35 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7901 (ttp80) REVERT: V 69 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: X 58 ARG cc_start: 0.7836 (mtp-110) cc_final: 0.7615 (mtp180) outliers start: 60 outliers final: 11 residues processed: 319 average time/residue: 1.8644 time to fit residues: 664.9460 Evaluate side-chains 298 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 2.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 185 LYS Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain I residue 171 VAL Chi-restraints excluded: chain J residue 39 ARG Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain P residue 76 ILE Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain S residue 25 LEU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 171 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 237 optimal weight: 0.0370 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 323 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 197 optimal weight: 0.8980 chunk 149 optimal weight: 0.3980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 27036 Z= 0.147 Angle : 0.462 5.219 36792 Z= 0.231 Chirality : 0.042 0.128 4404 Planarity : 0.004 0.034 4788 Dihedral : 3.801 50.672 3840 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.99 % Allowed : 26.31 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.84 (0.15), residues: 3444 helix: 1.45 (0.14), residues: 1404 sheet: 1.17 (0.18), residues: 912 loop : -1.13 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 67 HIS 0.002 0.000 HIS K 91 PHE 0.010 0.001 PHE G 162 TYR 0.010 0.001 TYR I 161 ARG 0.006 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 288 time to evaluate : 3.368 Fit side-chains REVERT: A 47 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8066 (tt0) REVERT: A 150 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8313 (tpp) REVERT: A 184 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: B 58 ARG cc_start: 0.7756 (mtp-110) cc_final: 0.7491 (mtp180) REVERT: B 69 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: C 38 ASP cc_start: 0.8463 (t0) cc_final: 0.8234 (t0) REVERT: D 69 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: E 93 PHE cc_start: 0.8962 (t80) cc_final: 0.8706 (t80) REVERT: E 185 LYS cc_start: 0.8832 (mttm) cc_final: 0.8508 (mmtp) REVERT: F 69 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6748 (mp0) REVERT: G 74 MET cc_start: 0.8384 (mmm) cc_final: 0.7915 (mmm) REVERT: G 184 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7475 (pt0) REVERT: G 185 LYS cc_start: 0.8849 (mttm) cc_final: 0.8498 (mmtp) REVERT: H 58 ARG cc_start: 0.7898 (mtp-110) cc_final: 0.7632 (mtp180) REVERT: I 90 ASP cc_start: 0.8667 (t0) cc_final: 0.8345 (t0) REVERT: I 185 LYS cc_start: 0.8852 (mttm) cc_final: 0.8316 (mptt) REVERT: K 52 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: K 184 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7320 (pp20) REVERT: K 185 LYS cc_start: 0.8893 (mttm) cc_final: 0.8591 (mmtm) REVERT: L 69 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7036 (mp0) REVERT: L 87 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7326 (mp0) REVERT: M 68 GLU cc_start: 0.7402 (mp0) cc_final: 0.7150 (mp0) REVERT: M 90 ASP cc_start: 0.8758 (t0) cc_final: 0.8262 (t70) REVERT: N 18 ARG cc_start: 0.7849 (mtt90) cc_final: 0.7457 (mtt-85) REVERT: N 28 GLU cc_start: 0.8081 (tt0) cc_final: 0.7841 (tp30) REVERT: O 150 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8382 (tpt) REVERT: O 184 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7699 (pt0) REVERT: O 185 LYS cc_start: 0.8879 (mttm) cc_final: 0.8548 (mmtp) REVERT: P 58 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7809 (mtp180) REVERT: P 86 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7856 (mt-10) REVERT: Q 47 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: Q 52 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: R 28 GLU cc_start: 0.7827 (tt0) cc_final: 0.7582 (tp30) REVERT: R 58 ARG cc_start: 0.7652 (mtp-110) cc_final: 0.7425 (tpp-160) REVERT: S 52 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: S 150 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8285 (tpp) REVERT: S 184 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7556 (pt0) REVERT: S 185 LYS cc_start: 0.8700 (mttm) cc_final: 0.8385 (mmmm) REVERT: T 74 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7264 (p0) REVERT: T 87 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7248 (mp0) REVERT: U 184 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: U 185 LYS cc_start: 0.8859 (mttm) cc_final: 0.8435 (mmtp) REVERT: V 35 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7903 (ttp80) REVERT: V 69 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: W 184 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7191 (pp20) REVERT: X 58 ARG cc_start: 0.7827 (mtp-110) cc_final: 0.7603 (mtp180) outliers start: 53 outliers final: 7 residues processed: 325 average time/residue: 1.9071 time to fit residues: 693.9227 Evaluate side-chains 315 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 287 time to evaluate : 2.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 52 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Chi-restraints excluded: chain W residue 184 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 30.0000 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 63 optimal weight: 0.0770 chunk 62 optimal weight: 10.0000 chunk 205 optimal weight: 0.0000 chunk 220 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 254 optimal weight: 6.9990 overall best weight: 2.3146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 27036 Z= 0.221 Angle : 0.533 5.215 36792 Z= 0.259 Chirality : 0.044 0.125 4404 Planarity : 0.005 0.034 4788 Dihedral : 3.957 51.675 3840 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.65 % Allowed : 26.73 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.69 (0.15), residues: 3444 helix: 1.31 (0.14), residues: 1404 sheet: 0.84 (0.18), residues: 972 loop : -1.00 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 67 HIS 0.003 0.001 HIS U 91 PHE 0.012 0.002 PHE W 162 TYR 0.013 0.002 TYR I 161 ARG 0.006 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 286 time to evaluate : 3.196 Fit side-chains REVERT: A 47 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: A 150 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8368 (tpp) REVERT: A 184 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: B 69 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: C 38 ASP cc_start: 0.8477 (t0) cc_final: 0.8230 (t0) REVERT: D 69 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: D 93 TYR cc_start: 0.8726 (t80) cc_final: 0.8417 (t80) REVERT: E 93 PHE cc_start: 0.8984 (t80) cc_final: 0.8687 (t80) REVERT: E 185 LYS cc_start: 0.8905 (mttm) cc_final: 0.8593 (mmtp) REVERT: F 69 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: G 184 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7457 (pt0) REVERT: G 185 LYS cc_start: 0.8933 (mttm) cc_final: 0.8532 (mmtp) REVERT: H 58 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7667 (mtp180) REVERT: I 52 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: I 90 ASP cc_start: 0.8682 (t0) cc_final: 0.8384 (t0) REVERT: I 185 LYS cc_start: 0.8898 (mttm) cc_final: 0.8359 (mptt) REVERT: K 52 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: K 184 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7409 (pp20) REVERT: K 185 LYS cc_start: 0.8906 (mttm) cc_final: 0.8592 (mmtm) REVERT: L 69 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6980 (mp0) REVERT: L 87 GLU cc_start: 0.7553 (mm-30) cc_final: 0.7315 (mp0) REVERT: M 68 GLU cc_start: 0.7495 (mp0) cc_final: 0.7251 (mp0) REVERT: M 90 ASP cc_start: 0.8805 (t0) cc_final: 0.8310 (t70) REVERT: N 18 ARG cc_start: 0.7864 (mtt90) cc_final: 0.7457 (mtt-85) REVERT: N 28 GLU cc_start: 0.8129 (tt0) cc_final: 0.7922 (tp30) REVERT: N 85 ASP cc_start: 0.8237 (t70) cc_final: 0.7986 (t70) REVERT: O 150 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8383 (tpt) REVERT: O 184 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: O 185 LYS cc_start: 0.8916 (mttm) cc_final: 0.8578 (mmtp) REVERT: P 58 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7810 (mtp180) REVERT: Q 47 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: R 58 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7428 (tpp-160) REVERT: S 184 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7633 (pt0) REVERT: S 185 LYS cc_start: 0.8756 (mttm) cc_final: 0.8462 (mmtm) REVERT: T 74 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.7262 (p0) REVERT: T 87 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7266 (mp0) REVERT: U 184 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7326 (pp20) REVERT: U 185 LYS cc_start: 0.8924 (mttm) cc_final: 0.8669 (mmtm) REVERT: V 35 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7881 (ttp80) REVERT: V 69 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: X 58 ARG cc_start: 0.7752 (mtp-110) cc_final: 0.7530 (mtp180) outliers start: 44 outliers final: 6 residues processed: 315 average time/residue: 1.8945 time to fit residues: 669.0183 Evaluate side-chains 305 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 281 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 9.9990 chunk 310 optimal weight: 0.9990 chunk 283 optimal weight: 0.0970 chunk 301 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 272 optimal weight: 10.0000 chunk 285 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 27036 Z= 0.181 Angle : 0.497 5.221 36792 Z= 0.245 Chirality : 0.043 0.125 4404 Planarity : 0.004 0.034 4788 Dihedral : 3.898 52.972 3840 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.43 % Allowed : 27.06 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.74 (0.15), residues: 3444 helix: 1.39 (0.14), residues: 1404 sheet: 0.82 (0.18), residues: 972 loop : -0.99 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 67 HIS 0.002 0.001 HIS C 91 PHE 0.011 0.001 PHE O 162 TYR 0.012 0.001 TYR I 161 ARG 0.006 0.000 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 286 time to evaluate : 3.244 Fit side-chains REVERT: A 47 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: A 184 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7614 (pt0) REVERT: B 69 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: C 38 ASP cc_start: 0.8472 (t0) cc_final: 0.8237 (t0) REVERT: D 69 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: E 93 PHE cc_start: 0.8971 (t80) cc_final: 0.8666 (t80) REVERT: E 184 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7403 (pp20) REVERT: E 185 LYS cc_start: 0.8858 (mttm) cc_final: 0.8526 (mmtp) REVERT: F 69 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6785 (mp0) REVERT: G 74 MET cc_start: 0.8397 (mmm) cc_final: 0.7977 (mmm) REVERT: G 184 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7446 (pt0) REVERT: G 185 LYS cc_start: 0.8913 (mttm) cc_final: 0.8521 (mmtp) REVERT: H 58 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7647 (mtp180) REVERT: I 52 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6866 (pm20) REVERT: I 90 ASP cc_start: 0.8692 (t0) cc_final: 0.8384 (t0) REVERT: I 185 LYS cc_start: 0.8879 (mttm) cc_final: 0.8335 (mptt) REVERT: K 52 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: K 184 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7368 (pp20) REVERT: K 185 LYS cc_start: 0.8914 (mttm) cc_final: 0.8641 (mmtm) REVERT: L 69 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: L 87 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7311 (mp0) REVERT: M 68 GLU cc_start: 0.7467 (mp0) cc_final: 0.7204 (mp0) REVERT: N 18 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7457 (mtt-85) REVERT: N 85 ASP cc_start: 0.8229 (t70) cc_final: 0.7993 (t70) REVERT: O 150 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.8343 (tpt) REVERT: O 184 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7708 (pt0) REVERT: O 185 LYS cc_start: 0.8902 (mttm) cc_final: 0.8558 (mmtp) REVERT: P 58 ARG cc_start: 0.8017 (mtp-110) cc_final: 0.7807 (mtp180) REVERT: Q 47 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8040 (tt0) REVERT: Q 52 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: R 58 ARG cc_start: 0.7653 (mtp-110) cc_final: 0.7430 (tpp-160) REVERT: S 184 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7635 (pt0) REVERT: S 185 LYS cc_start: 0.8738 (mttm) cc_final: 0.8449 (mmtm) REVERT: T 74 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7251 (p0) REVERT: T 87 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7272 (mp0) REVERT: U 184 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7329 (pp20) REVERT: U 185 LYS cc_start: 0.8926 (mttm) cc_final: 0.8669 (mmtm) REVERT: V 35 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7885 (ttp80) REVERT: V 69 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: X 58 ARG cc_start: 0.7761 (mtp-110) cc_final: 0.7535 (mtp180) outliers start: 38 outliers final: 13 residues processed: 311 average time/residue: 1.8532 time to fit residues: 644.3591 Evaluate side-chains 312 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 280 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain E residue 141 ASP Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain G residue 184 GLU Chi-restraints excluded: chain H residue 35 ARG Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain K residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 10.0000 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 151 optimal weight: 8.9990 chunk 221 optimal weight: 5.9990 chunk 334 optimal weight: 0.8980 chunk 308 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 205 optimal weight: 6.9990 chunk 163 optimal weight: 0.0270 overall best weight: 4.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 27036 Z= 0.347 Angle : 0.636 8.148 36792 Z= 0.304 Chirality : 0.047 0.135 4404 Planarity : 0.005 0.039 4788 Dihedral : 4.282 56.006 3840 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.35 % Allowed : 27.06 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.42 (0.14), residues: 3444 helix: 1.00 (0.14), residues: 1404 sheet: 0.79 (0.17), residues: 972 loop : -1.11 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 67 HIS 0.004 0.001 HIS U 91 PHE 0.017 0.002 PHE W 162 TYR 0.016 0.002 TYR I 161 ARG 0.005 0.000 ARG L 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6888 Ramachandran restraints generated. 3444 Oldfield, 0 Emsley, 3444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 2.982 Fit side-chains REVERT: A 47 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8164 (tt0) REVERT: A 184 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7680 (pt0) REVERT: B 69 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: C 38 ASP cc_start: 0.8492 (t0) cc_final: 0.8251 (t0) REVERT: D 69 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: E 93 PHE cc_start: 0.9014 (t80) cc_final: 0.8802 (t80) REVERT: E 185 LYS cc_start: 0.8939 (mttm) cc_final: 0.8628 (mmtp) REVERT: F 69 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: G 185 LYS cc_start: 0.8977 (mttm) cc_final: 0.8579 (mmtp) REVERT: H 58 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7664 (mtp180) REVERT: I 52 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7007 (pm20) REVERT: I 90 ASP cc_start: 0.8708 (t0) cc_final: 0.8442 (t0) REVERT: I 185 LYS cc_start: 0.8919 (mttm) cc_final: 0.8376 (mptt) REVERT: K 184 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7473 (pp20) REVERT: K 185 LYS cc_start: 0.8945 (mttm) cc_final: 0.8658 (mmtm) REVERT: L 69 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: L 87 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7230 (mp0) REVERT: M 90 ASP cc_start: 0.8856 (t0) cc_final: 0.8236 (t70) REVERT: N 18 ARG cc_start: 0.7838 (mtt90) cc_final: 0.7430 (mtt-85) REVERT: N 85 ASP cc_start: 0.8253 (t70) cc_final: 0.8016 (t70) REVERT: O 150 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8330 (tpt) REVERT: O 184 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7762 (pt0) REVERT: O 185 LYS cc_start: 0.8973 (mttm) cc_final: 0.8619 (mmtp) REVERT: P 58 ARG cc_start: 0.8035 (mtp-110) cc_final: 0.7826 (mtp180) REVERT: Q 47 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8042 (tt0) REVERT: Q 52 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7834 (pt0) REVERT: R 58 ARG cc_start: 0.7664 (mtp-110) cc_final: 0.7432 (tpp-160) REVERT: S 79 GLU cc_start: 0.6384 (mt-10) cc_final: 0.6145 (mt-10) REVERT: S 184 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: S 185 LYS cc_start: 0.8831 (mttm) cc_final: 0.8542 (mmtm) REVERT: T 74 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7310 (p0) REVERT: T 87 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7290 (mp0) REVERT: U 184 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7330 (pp20) REVERT: U 185 LYS cc_start: 0.8908 (mttm) cc_final: 0.8642 (mmtm) REVERT: V 35 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7910 (ttp80) REVERT: V 69 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: X 58 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7561 (mtp180) outliers start: 36 outliers final: 10 residues processed: 299 average time/residue: 1.8902 time to fit residues: 633.2063 Evaluate side-chains 299 residues out of total 2664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 273 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 74 ASP Chi-restraints excluded: chain B residue 76 ILE Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain D residue 69 GLU Chi-restraints excluded: chain F residue 69 GLU Chi-restraints excluded: chain G residue 29 SER Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 52 GLU Chi-restraints excluded: chain K residue 184 GLU Chi-restraints excluded: chain L residue 69 GLU Chi-restraints excluded: chain O residue 29 SER Chi-restraints excluded: chain O residue 150 MET Chi-restraints excluded: chain O residue 184 GLU Chi-restraints excluded: chain Q residue 29 SER Chi-restraints excluded: chain Q residue 47 GLU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain S residue 150 MET Chi-restraints excluded: chain S residue 184 GLU Chi-restraints excluded: chain T residue 74 ASP Chi-restraints excluded: chain U residue 184 GLU Chi-restraints excluded: chain V residue 69 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 8.9990 chunk 283 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.156102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123123 restraints weight = 27835.771| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.14 r_work: 0.3269 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 27036 Z= 0.174 Angle : 0.500 5.250 36792 Z= 0.247 Chirality : 0.043 0.127 4404 Planarity : 0.004 0.036 4788 Dihedral : 4.011 56.564 3840 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.31 % Allowed : 27.33 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.64 (0.15), residues: 3444 helix: 1.31 (0.14), residues: 1404 sheet: 0.77 (0.17), residues: 972 loop : -1.06 (0.18), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 67 HIS 0.002 0.001 HIS U 91 PHE 0.011 0.001 PHE G 162 TYR 0.011 0.001 TYR I 161 ARG 0.005 0.000 ARG L 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10087.80 seconds wall clock time: 175 minutes 41.93 seconds (10541.93 seconds total)