Starting phenix.real_space_refine on Wed Jul 24 12:27:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/07_2024/8ukm_42355.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/07_2024/8ukm_42355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/07_2024/8ukm_42355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/07_2024/8ukm_42355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/07_2024/8ukm_42355.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ukm_42355/07_2024/8ukm_42355.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 17004 2.51 5 N 4464 2.21 5 O 4668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 38": "OD1" <-> "OD2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ASP 188": "OD1" <-> "OD2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "C ASP 38": "OD1" <-> "OD2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 97": "OE1" <-> "OE2" Residue "E ASP 38": "OD1" <-> "OD2" Residue "E ASP 118": "OD1" <-> "OD2" Residue "E ASP 137": "OD1" <-> "OD2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E ASP 188": "OD1" <-> "OD2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "G ASP 38": "OD1" <-> "OD2" Residue "G ASP 118": "OD1" <-> "OD2" Residue "G ASP 137": "OD1" <-> "OD2" Residue "G ASP 184": "OD1" <-> "OD2" Residue "G ASP 188": "OD1" <-> "OD2" Residue "H PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "I ASP 38": "OD1" <-> "OD2" Residue "I ASP 118": "OD1" <-> "OD2" Residue "I ASP 137": "OD1" <-> "OD2" Residue "I ASP 184": "OD1" <-> "OD2" Residue "I ASP 188": "OD1" <-> "OD2" Residue "J PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 97": "OE1" <-> "OE2" Residue "K ASP 38": "OD1" <-> "OD2" Residue "K ASP 118": "OD1" <-> "OD2" Residue "K ASP 137": "OD1" <-> "OD2" Residue "K ASP 184": "OD1" <-> "OD2" Residue "K ASP 188": "OD1" <-> "OD2" Residue "L PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 97": "OE1" <-> "OE2" Residue "M ASP 38": "OD1" <-> "OD2" Residue "M ASP 118": "OD1" <-> "OD2" Residue "M ASP 137": "OD1" <-> "OD2" Residue "M ASP 184": "OD1" <-> "OD2" Residue "M ASP 188": "OD1" <-> "OD2" Residue "N PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 97": "OE1" <-> "OE2" Residue "O ASP 38": "OD1" <-> "OD2" Residue "O ASP 118": "OD1" <-> "OD2" Residue "O ASP 137": "OD1" <-> "OD2" Residue "O ASP 184": "OD1" <-> "OD2" Residue "O ASP 188": "OD1" <-> "OD2" Residue "P PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 97": "OE1" <-> "OE2" Residue "Q ASP 38": "OD1" <-> "OD2" Residue "Q ASP 118": "OD1" <-> "OD2" Residue "Q ASP 137": "OD1" <-> "OD2" Residue "Q ASP 184": "OD1" <-> "OD2" Residue "Q ASP 188": "OD1" <-> "OD2" Residue "R PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "S ASP 38": "OD1" <-> "OD2" Residue "S ASP 118": "OD1" <-> "OD2" Residue "S ASP 137": "OD1" <-> "OD2" Residue "S ASP 184": "OD1" <-> "OD2" Residue "S ASP 188": "OD1" <-> "OD2" Residue "T PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 97": "OE1" <-> "OE2" Residue "U ASP 38": "OD1" <-> "OD2" Residue "U ASP 118": "OD1" <-> "OD2" Residue "U ASP 137": "OD1" <-> "OD2" Residue "U ASP 184": "OD1" <-> "OD2" Residue "U ASP 188": "OD1" <-> "OD2" Residue "V PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 97": "OE1" <-> "OE2" Residue "W ASP 38": "OD1" <-> "OD2" Residue "W ASP 118": "OD1" <-> "OD2" Residue "W ASP 137": "OD1" <-> "OD2" Residue "W ASP 184": "OD1" <-> "OD2" Residue "W ASP 188": "OD1" <-> "OD2" Residue "X PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 97": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 26184 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "B" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "C" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "D" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "E" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "F" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "G" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "H" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "I" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "J" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "K" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "M" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "N" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "O" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "P" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "Q" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "R" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "S" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "T" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "U" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "V" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain: "W" Number of atoms: 1375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1375 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 168} Chain: "X" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 807 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Time building chain proxies: 13.98, per 1000 atoms: 0.53 Number of scatterers: 26184 At special positions: 0 Unit cell: (144.1, 141.9, 137.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 4668 8.00 N 4464 7.00 C 17004 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.45 Conformation dependent library (CDL) restraints added in 5.1 seconds 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6648 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 48 sheets defined 43.5% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 167 through 183 Processing helix chain 'B' and resid 13 through 33 Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 73 through 93 Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 100 through 107 removed outlier: 3.682A pdb=" N PHE C 104 " --> pdb=" O ALA C 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU C 107 " --> pdb=" O PRO C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 143 Processing helix chain 'C' and resid 167 through 183 Processing helix chain 'D' and resid 13 through 33 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 47 through 50 Processing helix chain 'D' and resid 73 through 93 Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'E' and resid 29 through 44 Processing helix chain 'E' and resid 66 through 82 Processing helix chain 'E' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU E 107 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 143 Processing helix chain 'E' and resid 167 through 183 Processing helix chain 'F' and resid 13 through 33 Processing helix chain 'F' and resid 35 through 39 Processing helix chain 'F' and resid 47 through 50 Processing helix chain 'F' and resid 73 through 93 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 66 through 82 Processing helix chain 'G' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU G 107 " --> pdb=" O PRO G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 143 Processing helix chain 'G' and resid 167 through 183 Processing helix chain 'H' and resid 13 through 33 Processing helix chain 'H' and resid 35 through 39 Processing helix chain 'H' and resid 47 through 50 Processing helix chain 'H' and resid 73 through 93 Processing helix chain 'H' and resid 95 through 97 No H-bonds generated for 'chain 'H' and resid 95 through 97' Processing helix chain 'I' and resid 29 through 44 Processing helix chain 'I' and resid 66 through 82 Processing helix chain 'I' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE I 104 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU I 107 " --> pdb=" O PRO I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 128 through 143 Processing helix chain 'I' and resid 167 through 183 Processing helix chain 'J' and resid 13 through 33 Processing helix chain 'J' and resid 35 through 39 Processing helix chain 'J' and resid 47 through 50 Processing helix chain 'J' and resid 73 through 93 Processing helix chain 'J' and resid 95 through 97 No H-bonds generated for 'chain 'J' and resid 95 through 97' Processing helix chain 'K' and resid 29 through 44 Processing helix chain 'K' and resid 66 through 82 Processing helix chain 'K' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU K 107 " --> pdb=" O PRO K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 143 Processing helix chain 'K' and resid 167 through 183 Processing helix chain 'L' and resid 13 through 33 Processing helix chain 'L' and resid 35 through 39 Processing helix chain 'L' and resid 47 through 50 Processing helix chain 'L' and resid 73 through 93 Processing helix chain 'L' and resid 95 through 97 No H-bonds generated for 'chain 'L' and resid 95 through 97' Processing helix chain 'M' and resid 29 through 44 Processing helix chain 'M' and resid 66 through 82 Processing helix chain 'M' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE M 104 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU M 107 " --> pdb=" O PRO M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 143 Processing helix chain 'M' and resid 167 through 183 Processing helix chain 'N' and resid 13 through 33 Processing helix chain 'N' and resid 35 through 39 Processing helix chain 'N' and resid 47 through 50 Processing helix chain 'N' and resid 73 through 93 Processing helix chain 'N' and resid 95 through 97 No H-bonds generated for 'chain 'N' and resid 95 through 97' Processing helix chain 'O' and resid 29 through 44 Processing helix chain 'O' and resid 66 through 82 Processing helix chain 'O' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE O 104 " --> pdb=" O ALA O 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU O 107 " --> pdb=" O PRO O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 128 through 143 Processing helix chain 'O' and resid 167 through 183 Processing helix chain 'P' and resid 13 through 33 Processing helix chain 'P' and resid 35 through 39 Processing helix chain 'P' and resid 47 through 50 Processing helix chain 'P' and resid 73 through 93 Processing helix chain 'P' and resid 95 through 97 No H-bonds generated for 'chain 'P' and resid 95 through 97' Processing helix chain 'Q' and resid 29 through 44 Processing helix chain 'Q' and resid 66 through 82 Processing helix chain 'Q' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE Q 104 " --> pdb=" O ALA Q 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU Q 107 " --> pdb=" O PRO Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 143 Processing helix chain 'Q' and resid 167 through 183 Processing helix chain 'R' and resid 13 through 33 Processing helix chain 'R' and resid 35 through 39 Processing helix chain 'R' and resid 47 through 50 Processing helix chain 'R' and resid 73 through 93 Processing helix chain 'R' and resid 95 through 97 No H-bonds generated for 'chain 'R' and resid 95 through 97' Processing helix chain 'S' and resid 29 through 44 Processing helix chain 'S' and resid 66 through 82 Processing helix chain 'S' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE S 104 " --> pdb=" O ALA S 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU S 107 " --> pdb=" O PRO S 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 128 through 143 Processing helix chain 'S' and resid 167 through 183 Processing helix chain 'T' and resid 13 through 33 Processing helix chain 'T' and resid 35 through 39 Processing helix chain 'T' and resid 47 through 50 Processing helix chain 'T' and resid 73 through 93 Processing helix chain 'T' and resid 95 through 97 No H-bonds generated for 'chain 'T' and resid 95 through 97' Processing helix chain 'U' and resid 29 through 44 Processing helix chain 'U' and resid 66 through 82 Processing helix chain 'U' and resid 100 through 107 removed outlier: 3.683A pdb=" N PHE U 104 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU U 107 " --> pdb=" O PRO U 103 " (cutoff:3.500A) Processing helix chain 'U' and resid 128 through 143 Processing helix chain 'U' and resid 167 through 183 Processing helix chain 'V' and resid 13 through 33 Processing helix chain 'V' and resid 35 through 39 Processing helix chain 'V' and resid 47 through 50 Processing helix chain 'V' and resid 73 through 93 Processing helix chain 'V' and resid 95 through 97 No H-bonds generated for 'chain 'V' and resid 95 through 97' Processing helix chain 'W' and resid 29 through 44 Processing helix chain 'W' and resid 66 through 82 Processing helix chain 'W' and resid 100 through 107 removed outlier: 3.682A pdb=" N PHE W 104 " --> pdb=" O ALA W 100 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU W 107 " --> pdb=" O PRO W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 128 through 143 Processing helix chain 'W' and resid 167 through 183 Processing helix chain 'X' and resid 13 through 33 Processing helix chain 'X' and resid 35 through 39 Processing helix chain 'X' and resid 47 through 50 Processing helix chain 'X' and resid 73 through 93 Processing helix chain 'X' and resid 95 through 97 No H-bonds generated for 'chain 'X' and resid 95 through 97' Processing sheet with id=1, first strand: chain 'A' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU A 48 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR A 64 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 50 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP A 90 " --> pdb=" O GLU A 26 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU A 147 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL A 165 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 149 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA A 160 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 126 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE A 162 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 124 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 121 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE A 191 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE A 123 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE A 189 " --> pdb=" O PHE A 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU A 125 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU B 4 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR B 44 " --> pdb=" O LEU B 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL B 6 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR B 46 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 8 " --> pdb=" O TYR B 46 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=5, first strand: chain 'C' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU C 48 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR C 64 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 50 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP C 90 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU C 147 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 165 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 149 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA C 160 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL C 126 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE C 162 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 124 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU C 121 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE C 191 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE C 123 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE C 189 " --> pdb=" O PHE C 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU C 125 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU D 4 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR D 44 " --> pdb=" O LEU D 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL D 6 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR D 46 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL D 8 " --> pdb=" O TYR D 46 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=9, first strand: chain 'E' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU E 48 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR E 64 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS E 50 " --> pdb=" O MET E 62 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP E 90 " --> pdb=" O GLU E 26 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU E 147 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL E 165 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG E 149 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA E 160 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL E 126 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE E 162 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL E 124 " --> pdb=" O PHE E 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU E 121 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE E 191 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE E 123 " --> pdb=" O ILE E 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE E 189 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU E 125 " --> pdb=" O LEU E 187 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU F 4 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR F 44 " --> pdb=" O LEU F 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL F 6 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR F 46 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL F 8 " --> pdb=" O TYR F 46 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=13, first strand: chain 'G' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU G 48 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR G 64 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS G 50 " --> pdb=" O MET G 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP G 90 " --> pdb=" O GLU G 26 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU G 147 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL G 165 " --> pdb=" O LEU G 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG G 149 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA G 160 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL G 126 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE G 162 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL G 124 " --> pdb=" O PHE G 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU G 121 " --> pdb=" O ILE G 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE G 191 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE G 123 " --> pdb=" O ILE G 189 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE G 189 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU G 125 " --> pdb=" O LEU G 187 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU H 4 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR H 44 " --> pdb=" O LEU H 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL H 6 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR H 46 " --> pdb=" O VAL H 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL H 8 " --> pdb=" O TYR H 46 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=17, first strand: chain 'I' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU I 48 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR I 64 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS I 50 " --> pdb=" O MET I 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP I 90 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'I' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU I 147 " --> pdb=" O VAL I 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL I 165 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG I 149 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA I 160 " --> pdb=" O VAL I 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL I 126 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE I 162 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL I 124 " --> pdb=" O PHE I 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU I 121 " --> pdb=" O ILE I 191 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE I 191 " --> pdb=" O LEU I 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE I 123 " --> pdb=" O ILE I 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE I 189 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU I 125 " --> pdb=" O LEU I 187 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'J' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU J 4 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR J 44 " --> pdb=" O LEU J 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL J 6 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR J 46 " --> pdb=" O VAL J 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL J 8 " --> pdb=" O TYR J 46 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=21, first strand: chain 'K' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU K 48 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR K 64 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS K 50 " --> pdb=" O MET K 62 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASP K 90 " --> pdb=" O GLU K 26 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'K' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU K 147 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL K 165 " --> pdb=" O LEU K 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG K 149 " --> pdb=" O ALA K 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA K 160 " --> pdb=" O VAL K 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL K 126 " --> pdb=" O ALA K 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE K 162 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL K 124 " --> pdb=" O PHE K 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU K 121 " --> pdb=" O ILE K 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE K 191 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE K 123 " --> pdb=" O ILE K 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE K 189 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU K 125 " --> pdb=" O LEU K 187 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'L' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU L 4 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR L 44 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL L 6 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR L 46 " --> pdb=" O VAL L 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL L 8 " --> pdb=" O TYR L 46 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'L' and resid 52 through 53 Processing sheet with id=25, first strand: chain 'M' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU M 48 " --> pdb=" O THR M 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR M 64 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 50 " --> pdb=" O MET M 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP M 90 " --> pdb=" O GLU M 26 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'M' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU M 147 " --> pdb=" O VAL M 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL M 165 " --> pdb=" O LEU M 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG M 149 " --> pdb=" O ALA M 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA M 160 " --> pdb=" O VAL M 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL M 126 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE M 162 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL M 124 " --> pdb=" O PHE M 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 121 " --> pdb=" O ILE M 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE M 191 " --> pdb=" O LEU M 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE M 123 " --> pdb=" O ILE M 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE M 189 " --> pdb=" O PHE M 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU M 125 " --> pdb=" O LEU M 187 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'N' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU N 4 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR N 44 " --> pdb=" O LEU N 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL N 6 " --> pdb=" O THR N 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR N 46 " --> pdb=" O VAL N 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL N 8 " --> pdb=" O TYR N 46 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'N' and resid 52 through 53 Processing sheet with id=29, first strand: chain 'O' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU O 48 " --> pdb=" O THR O 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR O 64 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS O 50 " --> pdb=" O MET O 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP O 90 " --> pdb=" O GLU O 26 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'O' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU O 147 " --> pdb=" O VAL O 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL O 165 " --> pdb=" O LEU O 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG O 149 " --> pdb=" O ALA O 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA O 160 " --> pdb=" O VAL O 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL O 126 " --> pdb=" O ALA O 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE O 162 " --> pdb=" O VAL O 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL O 124 " --> pdb=" O PHE O 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU O 121 " --> pdb=" O ILE O 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE O 191 " --> pdb=" O LEU O 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE O 123 " --> pdb=" O ILE O 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE O 189 " --> pdb=" O PHE O 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU O 125 " --> pdb=" O LEU O 187 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'P' and resid 42 through 46 removed outlier: 5.526A pdb=" N LEU P 4 " --> pdb=" O ILE P 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR P 44 " --> pdb=" O LEU P 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL P 6 " --> pdb=" O THR P 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR P 46 " --> pdb=" O VAL P 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL P 8 " --> pdb=" O TYR P 46 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'P' and resid 52 through 53 Processing sheet with id=33, first strand: chain 'Q' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU Q 48 " --> pdb=" O THR Q 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR Q 64 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS Q 50 " --> pdb=" O MET Q 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP Q 90 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'Q' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU Q 147 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL Q 165 " --> pdb=" O LEU Q 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG Q 149 " --> pdb=" O ALA Q 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA Q 160 " --> pdb=" O VAL Q 126 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL Q 126 " --> pdb=" O ALA Q 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE Q 162 " --> pdb=" O VAL Q 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL Q 124 " --> pdb=" O PHE Q 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU Q 121 " --> pdb=" O ILE Q 191 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE Q 191 " --> pdb=" O LEU Q 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE Q 123 " --> pdb=" O ILE Q 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE Q 189 " --> pdb=" O PHE Q 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU Q 125 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'R' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU R 4 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR R 44 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL R 6 " --> pdb=" O THR R 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR R 46 " --> pdb=" O VAL R 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL R 8 " --> pdb=" O TYR R 46 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'R' and resid 52 through 53 Processing sheet with id=37, first strand: chain 'S' and resid 47 through 54 removed outlier: 5.638A pdb=" N LEU S 48 " --> pdb=" O THR S 64 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR S 64 " --> pdb=" O LEU S 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS S 50 " --> pdb=" O MET S 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP S 90 " --> pdb=" O GLU S 26 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'S' and resid 146 through 152 removed outlier: 6.383A pdb=" N LEU S 147 " --> pdb=" O VAL S 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL S 165 " --> pdb=" O LEU S 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG S 149 " --> pdb=" O ALA S 163 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA S 160 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL S 126 " --> pdb=" O ALA S 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE S 162 " --> pdb=" O VAL S 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL S 124 " --> pdb=" O PHE S 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU S 121 " --> pdb=" O ILE S 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE S 191 " --> pdb=" O LEU S 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE S 123 " --> pdb=" O ILE S 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE S 189 " --> pdb=" O PHE S 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU S 125 " --> pdb=" O LEU S 187 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'T' and resid 42 through 46 removed outlier: 5.525A pdb=" N LEU T 4 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR T 44 " --> pdb=" O LEU T 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL T 6 " --> pdb=" O THR T 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR T 46 " --> pdb=" O VAL T 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL T 8 " --> pdb=" O TYR T 46 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'T' and resid 52 through 53 Processing sheet with id=41, first strand: chain 'U' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU U 48 " --> pdb=" O THR U 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR U 64 " --> pdb=" O LEU U 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS U 50 " --> pdb=" O MET U 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP U 90 " --> pdb=" O GLU U 26 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'U' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU U 147 " --> pdb=" O VAL U 165 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL U 165 " --> pdb=" O LEU U 147 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG U 149 " --> pdb=" O ALA U 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA U 160 " --> pdb=" O VAL U 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL U 126 " --> pdb=" O ALA U 160 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE U 162 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL U 124 " --> pdb=" O PHE U 162 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU U 121 " --> pdb=" O ILE U 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE U 191 " --> pdb=" O LEU U 121 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE U 123 " --> pdb=" O ILE U 189 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE U 189 " --> pdb=" O PHE U 123 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU U 125 " --> pdb=" O LEU U 187 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'V' and resid 42 through 46 removed outlier: 5.524A pdb=" N LEU V 4 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR V 44 " --> pdb=" O LEU V 4 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL V 6 " --> pdb=" O THR V 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR V 46 " --> pdb=" O VAL V 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL V 8 " --> pdb=" O TYR V 46 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'V' and resid 52 through 53 Processing sheet with id=45, first strand: chain 'W' and resid 47 through 54 removed outlier: 5.637A pdb=" N LEU W 48 " --> pdb=" O THR W 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR W 64 " --> pdb=" O LEU W 48 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS W 50 " --> pdb=" O MET W 62 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP W 90 " --> pdb=" O GLU W 26 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'W' and resid 146 through 152 removed outlier: 6.382A pdb=" N LEU W 147 " --> pdb=" O VAL W 165 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N VAL W 165 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ARG W 149 " --> pdb=" O ALA W 163 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA W 160 " --> pdb=" O VAL W 126 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL W 126 " --> pdb=" O ALA W 160 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE W 162 " --> pdb=" O VAL W 124 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL W 124 " --> pdb=" O PHE W 162 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU W 121 " --> pdb=" O ILE W 191 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE W 191 " --> pdb=" O LEU W 121 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE W 123 " --> pdb=" O ILE W 189 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE W 189 " --> pdb=" O PHE W 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLU W 125 " --> pdb=" O LEU W 187 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'X' and resid 42 through 46 removed outlier: 5.526A pdb=" N LEU X 4 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N THR X 44 " --> pdb=" O LEU X 4 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N VAL X 6 " --> pdb=" O THR X 44 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N TYR X 46 " --> pdb=" O VAL X 6 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL X 8 " --> pdb=" O TYR X 46 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'X' and resid 52 through 53 1512 hydrogen bonds defined for protein. 4284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.03 Time building geometry restraints manager: 12.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8669 1.34 - 1.46: 4132 1.46 - 1.58: 13755 1.58 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 26640 Sorted by residual: bond pdb=" N VAL V 62 " pdb=" CA VAL V 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.27e+00 bond pdb=" N VAL L 62 " pdb=" CA VAL L 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.15e+00 bond pdb=" N VAL N 62 " pdb=" CA VAL N 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.09e+00 bond pdb=" N VAL F 62 " pdb=" CA VAL F 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.05e+00 bond pdb=" N VAL X 62 " pdb=" CA VAL X 62 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.04e+00 ... (remaining 26635 not shown) Histogram of bond angle deviations from ideal: 100.63 - 106.83: 1260 106.83 - 113.02: 14992 113.02 - 119.21: 7001 119.21 - 125.40: 12843 125.40 - 131.59: 324 Bond angle restraints: 36420 Sorted by residual: angle pdb=" N GLY M 201 " pdb=" CA GLY M 201 " pdb=" C GLY M 201 " ideal model delta sigma weight residual 115.08 110.47 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N GLY K 201 " pdb=" CA GLY K 201 " pdb=" C GLY K 201 " ideal model delta sigma weight residual 115.08 110.47 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N GLY Q 201 " pdb=" CA GLY Q 201 " pdb=" C GLY Q 201 " ideal model delta sigma weight residual 115.08 110.49 4.59 1.19e+00 7.06e-01 1.49e+01 angle pdb=" N GLY I 201 " pdb=" CA GLY I 201 " pdb=" C GLY I 201 " ideal model delta sigma weight residual 115.08 110.49 4.59 1.19e+00 7.06e-01 1.49e+01 angle pdb=" N GLY C 201 " pdb=" CA GLY C 201 " pdb=" C GLY C 201 " ideal model delta sigma weight residual 115.08 110.50 4.58 1.19e+00 7.06e-01 1.48e+01 ... (remaining 36415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 15080 17.47 - 34.93: 1276 34.93 - 52.40: 168 52.40 - 69.87: 36 69.87 - 87.34: 12 Dihedral angle restraints: 16572 sinusoidal: 6348 harmonic: 10224 Sorted by residual: dihedral pdb=" CA LEU O 152 " pdb=" C LEU O 152 " pdb=" N SER O 153 " pdb=" CA SER O 153 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA LEU G 152 " pdb=" C LEU G 152 " pdb=" N SER G 153 " pdb=" CA SER G 153 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA LEU C 152 " pdb=" C LEU C 152 " pdb=" N SER C 153 " pdb=" CA SER C 153 " ideal model delta harmonic sigma weight residual 180.00 157.33 22.67 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 16569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3100 0.042 - 0.083: 932 0.083 - 0.125: 448 0.125 - 0.166: 72 0.166 - 0.208: 20 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CA ILE P 64 " pdb=" N ILE P 64 " pdb=" C ILE P 64 " pdb=" CB ILE P 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE J 64 " pdb=" N ILE J 64 " pdb=" C ILE J 64 " pdb=" CB ILE J 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 4569 not shown) Planarity restraints: 4680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 19 " 0.179 9.50e-02 1.11e+02 8.05e-02 4.18e+00 pdb=" NE ARG G 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG G 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG G 19 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 19 " 0.179 9.50e-02 1.11e+02 8.04e-02 4.17e+00 pdb=" NE ARG A 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 19 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 19 " 0.179 9.50e-02 1.11e+02 8.05e-02 4.17e+00 pdb=" NE ARG Q 19 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG Q 19 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 19 " 0.009 2.00e-02 2.50e+03 ... (remaining 4677 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3740 2.76 - 3.29: 27993 3.29 - 3.83: 44337 3.83 - 4.36: 48519 4.36 - 4.90: 82777 Nonbonded interactions: 207366 Sorted by model distance: nonbonded pdb=" O GLU J 97 " pdb=" NH1 ARG J 100 " model vdw 2.220 2.520 nonbonded pdb=" O GLU R 97 " pdb=" NH1 ARG R 100 " model vdw 2.220 2.520 nonbonded pdb=" O GLU F 97 " pdb=" NH1 ARG F 100 " model vdw 2.220 2.520 nonbonded pdb=" O GLU T 97 " pdb=" NH1 ARG T 100 " model vdw 2.220 2.520 nonbonded pdb=" O GLU H 97 " pdb=" NH1 ARG H 100 " model vdw 2.220 2.520 ... (remaining 207361 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.180 Set scattering table: 0.270 Process input model: 71.240 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.180 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 26640 Z= 0.261 Angle : 0.752 6.988 36420 Z= 0.394 Chirality : 0.050 0.208 4572 Planarity : 0.007 0.081 4680 Dihedral : 13.153 87.335 9924 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3480 helix: 1.21 (0.13), residues: 1308 sheet: -1.51 (0.15), residues: 876 loop : 0.44 (0.21), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS U 196 PHE 0.013 0.002 PHE K 162 TYR 0.009 0.002 TYR I 30 ARG 0.008 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 2.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 TYR cc_start: 0.8819 (m-10) cc_final: 0.8590 (m-10) REVERT: B 17 LYS cc_start: 0.9096 (pttm) cc_final: 0.8799 (pttm) REVERT: B 90 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8329 (tm-30) REVERT: C 75 LYS cc_start: 0.9336 (pttm) cc_final: 0.9115 (ptmm) REVERT: C 150 MET cc_start: 0.8584 (tmm) cc_final: 0.8324 (tmm) REVERT: D 90 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8413 (tm-30) REVERT: E 75 LYS cc_start: 0.9303 (pttm) cc_final: 0.9040 (ptmm) REVERT: H 90 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8276 (tm-30) REVERT: I 150 MET cc_start: 0.8576 (tmm) cc_final: 0.8283 (tmm) REVERT: J 90 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8265 (tm-30) REVERT: L 7 TYR cc_start: 0.8913 (m-10) cc_final: 0.8710 (m-10) REVERT: L 90 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8404 (tm-30) REVERT: M 75 LYS cc_start: 0.9363 (pttm) cc_final: 0.9133 (ptmm) REVERT: M 150 MET cc_start: 0.8491 (tmm) cc_final: 0.8217 (tmm) REVERT: N 90 GLU cc_start: 0.8724 (tm-30) cc_final: 0.8399 (tm-30) REVERT: O 75 LYS cc_start: 0.9366 (pttm) cc_final: 0.9141 (ptmm) REVERT: P 90 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8379 (tm-30) REVERT: Q 75 LYS cc_start: 0.9265 (pttm) cc_final: 0.9041 (ptmm) REVERT: Q 150 MET cc_start: 0.8464 (tmm) cc_final: 0.8005 (tmm) REVERT: R 7 TYR cc_start: 0.9016 (m-10) cc_final: 0.8766 (m-10) REVERT: R 90 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8178 (tm-30) REVERT: T 12 TYR cc_start: 0.8788 (m-10) cc_final: 0.8534 (m-10) REVERT: T 17 LYS cc_start: 0.9073 (pttm) cc_final: 0.8776 (pttm) REVERT: T 90 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8361 (tm-30) REVERT: U 75 LYS cc_start: 0.9305 (pttm) cc_final: 0.9072 (ptmm) REVERT: U 150 MET cc_start: 0.8473 (tmm) cc_final: 0.8254 (tmm) REVERT: V 90 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8382 (tm-30) REVERT: W 75 LYS cc_start: 0.9403 (pttm) cc_final: 0.9149 (ptmm) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.3690 time to fit residues: 293.6432 Evaluate side-chains 416 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 8.9990 chunk 254 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 86 optimal weight: 0.0020 chunk 171 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 263 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 20.0000 chunk 305 optimal weight: 8.9990 overall best weight: 5.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 38 ASN B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 ASN H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 ASN J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 ASN L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 ASN N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 ASN P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 38 ASN R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 ASN T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 38 ASN V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 38 ASN X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 26640 Z= 0.311 Angle : 0.677 8.127 36420 Z= 0.346 Chirality : 0.047 0.184 4572 Planarity : 0.007 0.046 4680 Dihedral : 4.809 25.386 3780 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.78 % Allowed : 9.07 % Favored : 90.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.14), residues: 3480 helix: 1.29 (0.13), residues: 1260 sheet: -1.44 (0.15), residues: 864 loop : 0.05 (0.19), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS M 98 PHE 0.015 0.002 PHE E 162 TYR 0.009 0.001 TYR F 46 ARG 0.006 0.001 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 475 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8900 (tmmt) cc_final: 0.8646 (mmtt) REVERT: A 150 MET cc_start: 0.8670 (tmm) cc_final: 0.7870 (tmm) REVERT: B 17 LYS cc_start: 0.9038 (pttm) cc_final: 0.8730 (pttm) REVERT: B 90 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8333 (tm-30) REVERT: B 97 GLU cc_start: 0.8987 (mp0) cc_final: 0.8778 (mp0) REVERT: C 42 LYS cc_start: 0.9039 (tmmt) cc_final: 0.8685 (mmmm) REVERT: C 75 LYS cc_start: 0.9374 (pttm) cc_final: 0.9121 (ptmm) REVERT: C 150 MET cc_start: 0.8781 (tmm) cc_final: 0.8497 (tmm) REVERT: D 90 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8397 (tm-30) REVERT: D 97 GLU cc_start: 0.8947 (mp0) cc_final: 0.8706 (mp0) REVERT: E 75 LYS cc_start: 0.9276 (pttm) cc_final: 0.9020 (ptmm) REVERT: F 53 LEU cc_start: 0.8913 (tp) cc_final: 0.8532 (tp) REVERT: G 75 LYS cc_start: 0.9336 (pttm) cc_final: 0.9058 (pttp) REVERT: H 90 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8238 (tm-30) REVERT: I 150 MET cc_start: 0.8739 (tmm) cc_final: 0.8214 (tmm) REVERT: J 90 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8245 (tm-30) REVERT: J 95 ASP cc_start: 0.8767 (p0) cc_final: 0.8495 (p0) REVERT: J 97 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8916 (mp0) REVERT: K 75 LYS cc_start: 0.9295 (pttm) cc_final: 0.9047 (pttt) REVERT: K 150 MET cc_start: 0.8654 (tmm) cc_final: 0.8391 (tmm) REVERT: L 53 LEU cc_start: 0.8902 (tp) cc_final: 0.8634 (tp) REVERT: M 75 LYS cc_start: 0.9303 (pttm) cc_final: 0.9052 (ptmm) REVERT: M 150 MET cc_start: 0.8728 (tmm) cc_final: 0.8209 (tmm) REVERT: N 53 LEU cc_start: 0.8922 (tp) cc_final: 0.8696 (tp) REVERT: N 68 LEU cc_start: 0.8635 (tp) cc_final: 0.8419 (tp) REVERT: N 90 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8358 (tm-30) REVERT: O 75 LYS cc_start: 0.9398 (pttm) cc_final: 0.9146 (ptmm) REVERT: P 38 ASN cc_start: 0.6663 (OUTLIER) cc_final: 0.6301 (m110) REVERT: P 53 LEU cc_start: 0.8881 (tp) cc_final: 0.8484 (tp) REVERT: P 90 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8397 (tm-30) REVERT: Q 75 LYS cc_start: 0.9328 (pttm) cc_final: 0.8970 (pttp) REVERT: Q 150 MET cc_start: 0.8588 (tmm) cc_final: 0.7929 (tmm) REVERT: R 7 TYR cc_start: 0.9096 (m-10) cc_final: 0.8882 (m-10) REVERT: R 17 LYS cc_start: 0.8968 (pttm) cc_final: 0.8749 (pttm) REVERT: R 90 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8329 (tm-30) REVERT: S 150 MET cc_start: 0.8679 (tmm) cc_final: 0.8070 (tmm) REVERT: T 17 LYS cc_start: 0.9111 (pttm) cc_final: 0.8778 (pttm) REVERT: T 38 ASN cc_start: 0.6513 (OUTLIER) cc_final: 0.6276 (t0) REVERT: T 90 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8430 (tm-30) REVERT: U 75 LYS cc_start: 0.9300 (pttm) cc_final: 0.9055 (ptmm) REVERT: U 150 MET cc_start: 0.8683 (tmm) cc_final: 0.8391 (tmm) REVERT: V 53 LEU cc_start: 0.9004 (tp) cc_final: 0.8754 (tp) REVERT: V 95 ASP cc_start: 0.8758 (p0) cc_final: 0.8416 (p0) REVERT: V 97 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8994 (mp0) REVERT: W 75 LYS cc_start: 0.9367 (pttm) cc_final: 0.9075 (ptmm) REVERT: X 53 LEU cc_start: 0.8959 (tp) cc_final: 0.8646 (tp) REVERT: X 95 ASP cc_start: 0.8887 (p0) cc_final: 0.8623 (p0) outliers start: 21 outliers final: 1 residues processed: 491 average time/residue: 0.3773 time to fit residues: 286.2320 Evaluate side-chains 400 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 397 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 84 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 chunk 330 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 303 optimal weight: 9.9990 chunk 104 optimal weight: 5.9990 chunk 245 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** H 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** J 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 GLN ** L 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** P 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** R 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** T 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 GLN ** V 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** X 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26640 Z= 0.206 Angle : 0.630 7.146 36420 Z= 0.312 Chirality : 0.047 0.193 4572 Planarity : 0.006 0.039 4680 Dihedral : 4.669 24.093 3780 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.14), residues: 3480 helix: 1.44 (0.13), residues: 1248 sheet: -1.30 (0.15), residues: 864 loop : 0.10 (0.19), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 196 PHE 0.012 0.002 PHE E 162 TYR 0.010 0.001 TYR P 12 ARG 0.005 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 497 time to evaluate : 3.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8950 (tmmt) cc_final: 0.8693 (mmmm) REVERT: B 17 LYS cc_start: 0.9031 (pttm) cc_final: 0.8707 (pttm) REVERT: B 90 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 97 GLU cc_start: 0.8976 (mp0) cc_final: 0.8758 (mp0) REVERT: C 42 LYS cc_start: 0.8991 (tmmt) cc_final: 0.8685 (mmmm) REVERT: C 75 LYS cc_start: 0.9368 (pttm) cc_final: 0.9130 (ptmm) REVERT: C 150 MET cc_start: 0.8803 (tmm) cc_final: 0.8444 (tmm) REVERT: D 53 LEU cc_start: 0.8896 (tp) cc_final: 0.8678 (tp) REVERT: D 90 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8424 (tm-30) REVERT: D 97 GLU cc_start: 0.8938 (mp0) cc_final: 0.8686 (mp0) REVERT: E 75 LYS cc_start: 0.9284 (pttm) cc_final: 0.8964 (ptmm) REVERT: F 97 GLU cc_start: 0.8972 (mp0) cc_final: 0.8770 (mp0) REVERT: G 75 LYS cc_start: 0.9345 (pttm) cc_final: 0.9050 (pttp) REVERT: H 53 LEU cc_start: 0.8889 (tp) cc_final: 0.8599 (tp) REVERT: H 90 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8275 (tm-30) REVERT: I 42 LYS cc_start: 0.8977 (tmmt) cc_final: 0.8768 (mmmm) REVERT: I 75 LYS cc_start: 0.9478 (ptmm) cc_final: 0.9071 (pttt) REVERT: I 150 MET cc_start: 0.8768 (tmm) cc_final: 0.8143 (tmm) REVERT: J 53 LEU cc_start: 0.8831 (tp) cc_final: 0.8492 (tp) REVERT: J 68 LEU cc_start: 0.8506 (tp) cc_final: 0.8271 (tp) REVERT: J 90 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8208 (tm-30) REVERT: K 150 MET cc_start: 0.8688 (tmm) cc_final: 0.8335 (tmm) REVERT: K 188 ASP cc_start: 0.8143 (t70) cc_final: 0.7933 (t0) REVERT: L 12 TYR cc_start: 0.8647 (m-10) cc_final: 0.8409 (m-10) REVERT: N 90 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8317 (tm-30) REVERT: O 75 LYS cc_start: 0.9343 (pttm) cc_final: 0.9030 (pttp) REVERT: O 150 MET cc_start: 0.8680 (tmm) cc_final: 0.8255 (tmm) REVERT: P 90 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8430 (tm-30) REVERT: P 95 ASP cc_start: 0.8883 (p0) cc_final: 0.8629 (p0) REVERT: Q 42 LYS cc_start: 0.8939 (mmmm) cc_final: 0.8417 (mmmm) REVERT: Q 75 LYS cc_start: 0.9308 (pttm) cc_final: 0.9025 (pttp) REVERT: Q 150 MET cc_start: 0.8666 (tmm) cc_final: 0.8286 (tmm) REVERT: R 7 TYR cc_start: 0.9049 (m-10) cc_final: 0.8837 (m-10) REVERT: R 17 LYS cc_start: 0.8916 (pttm) cc_final: 0.8701 (pttm) REVERT: R 53 LEU cc_start: 0.8816 (tp) cc_final: 0.8503 (tp) REVERT: R 90 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8272 (tm-30) REVERT: S 42 LYS cc_start: 0.8822 (mmmm) cc_final: 0.8240 (mmmm) REVERT: T 12 TYR cc_start: 0.8667 (m-10) cc_final: 0.8465 (m-10) REVERT: T 17 LYS cc_start: 0.9047 (pttm) cc_final: 0.8795 (pttm) REVERT: T 90 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8238 (tm-30) REVERT: U 75 LYS cc_start: 0.9321 (pttm) cc_final: 0.9024 (pttp) REVERT: U 150 MET cc_start: 0.8730 (tmm) cc_final: 0.8426 (tmm) REVERT: V 90 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8344 (tm-30) REVERT: V 95 ASP cc_start: 0.8756 (p0) cc_final: 0.8459 (p0) REVERT: V 97 GLU cc_start: 0.9279 (mm-30) cc_final: 0.9007 (mp0) REVERT: W 75 LYS cc_start: 0.9373 (pttm) cc_final: 0.9070 (pttp) REVERT: X 97 GLU cc_start: 0.8931 (mp0) cc_final: 0.8729 (mp0) outliers start: 2 outliers final: 0 residues processed: 499 average time/residue: 0.3834 time to fit residues: 294.8864 Evaluate side-chains 407 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.2980 chunk 229 optimal weight: 10.0000 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 306 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26640 Z= 0.265 Angle : 0.644 7.908 36420 Z= 0.320 Chirality : 0.047 0.179 4572 Planarity : 0.006 0.040 4680 Dihedral : 4.720 25.243 3780 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.11 % Allowed : 7.04 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3480 helix: 1.63 (0.13), residues: 1320 sheet: -1.31 (0.15), residues: 864 loop : 0.28 (0.20), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.002 HIS C 196 PHE 0.014 0.002 PHE E 162 TYR 0.007 0.001 TYR P 7 ARG 0.003 0.000 ARG Q 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 494 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9057 (pttm) cc_final: 0.8732 (pttm) REVERT: B 53 LEU cc_start: 0.8927 (tp) cc_final: 0.8534 (tp) REVERT: B 90 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8346 (tm-30) REVERT: B 97 GLU cc_start: 0.8954 (mp0) cc_final: 0.8718 (mp0) REVERT: C 75 LYS cc_start: 0.9404 (pttm) cc_final: 0.9158 (ptmm) REVERT: C 150 MET cc_start: 0.8873 (tmm) cc_final: 0.8470 (tmm) REVERT: D 90 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8399 (tm-30) REVERT: D 97 GLU cc_start: 0.8955 (mp0) cc_final: 0.8708 (mp0) REVERT: E 75 LYS cc_start: 0.9335 (pttm) cc_final: 0.9023 (ptmm) REVERT: F 97 GLU cc_start: 0.8978 (mp0) cc_final: 0.8774 (mp0) REVERT: G 75 LYS cc_start: 0.9389 (pttm) cc_final: 0.9168 (pttt) REVERT: G 150 MET cc_start: 0.9060 (tmm) cc_final: 0.8060 (tmm) REVERT: H 90 GLU cc_start: 0.8676 (tm-30) cc_final: 0.8267 (tm-30) REVERT: I 75 LYS cc_start: 0.9486 (ptmm) cc_final: 0.9141 (pttt) REVERT: I 150 MET cc_start: 0.8832 (tmm) cc_final: 0.8134 (tmm) REVERT: J 90 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8100 (tm-30) REVERT: J 97 GLU cc_start: 0.8890 (mp0) cc_final: 0.8687 (mp0) REVERT: K 75 LYS cc_start: 0.9281 (pttp) cc_final: 0.9065 (pttt) REVERT: K 150 MET cc_start: 0.8805 (tmm) cc_final: 0.8355 (tmm) REVERT: M 75 LYS cc_start: 0.9266 (pttm) cc_final: 0.8964 (ptmm) REVERT: M 150 MET cc_start: 0.8878 (tmm) cc_final: 0.7804 (tmm) REVERT: N 90 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8293 (tm-30) REVERT: O 75 LYS cc_start: 0.9398 (pttm) cc_final: 0.9189 (pttt) REVERT: O 150 MET cc_start: 0.8882 (tmm) cc_final: 0.8206 (tmm) REVERT: P 68 LEU cc_start: 0.8454 (tp) cc_final: 0.8243 (tp) REVERT: P 90 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8409 (tm-30) REVERT: Q 150 MET cc_start: 0.8741 (tmm) cc_final: 0.8306 (tmm) REVERT: R 7 TYR cc_start: 0.9086 (m-10) cc_final: 0.8800 (m-10) REVERT: R 17 LYS cc_start: 0.8943 (pttm) cc_final: 0.8728 (pttm) REVERT: R 90 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8199 (tm-30) REVERT: S 75 LYS cc_start: 0.9433 (pttp) cc_final: 0.9187 (pttt) REVERT: S 150 MET cc_start: 0.8556 (tmm) cc_final: 0.8163 (tmm) REVERT: T 17 LYS cc_start: 0.9102 (pttm) cc_final: 0.8818 (pttm) REVERT: T 90 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8280 (tm-30) REVERT: U 75 LYS cc_start: 0.9368 (pttm) cc_final: 0.9149 (pttt) REVERT: U 150 MET cc_start: 0.8819 (tmm) cc_final: 0.8491 (tmm) REVERT: V 90 GLU cc_start: 0.8662 (tm-30) cc_final: 0.8370 (tm-30) REVERT: V 95 ASP cc_start: 0.8762 (p0) cc_final: 0.8469 (p0) REVERT: V 97 GLU cc_start: 0.9293 (mm-30) cc_final: 0.9008 (mp0) REVERT: W 75 LYS cc_start: 0.9398 (pttm) cc_final: 0.9139 (pttt) REVERT: X 97 GLU cc_start: 0.8948 (mp0) cc_final: 0.8745 (mp0) outliers start: 3 outliers final: 0 residues processed: 497 average time/residue: 0.3768 time to fit residues: 290.7903 Evaluate side-chains 415 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 chunk 4 optimal weight: 20.0000 chunk 241 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 277 optimal weight: 4.9990 chunk 224 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 0.2980 chunk 291 optimal weight: 10.0000 chunk 81 optimal weight: 0.4980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN D 76 GLN F 76 GLN H 76 GLN H 98 ASN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN L 76 GLN N 76 GLN ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN T 76 GLN X 76 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 26640 Z= 0.207 Angle : 0.640 8.119 36420 Z= 0.313 Chirality : 0.049 0.188 4572 Planarity : 0.006 0.043 4680 Dihedral : 4.620 24.280 3780 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.15), residues: 3480 helix: 1.64 (0.13), residues: 1320 sheet: -1.29 (0.16), residues: 864 loop : 0.38 (0.20), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 196 PHE 0.013 0.002 PHE E 162 TYR 0.013 0.001 TYR B 46 ARG 0.003 0.000 ARG C 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8729 (tmm) cc_final: 0.7848 (tmm) REVERT: B 17 LYS cc_start: 0.9062 (pttm) cc_final: 0.8775 (pttm) REVERT: B 90 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8296 (tm-30) REVERT: B 97 GLU cc_start: 0.8971 (mp0) cc_final: 0.8749 (mp0) REVERT: C 75 LYS cc_start: 0.9410 (pttm) cc_final: 0.9152 (ptmm) REVERT: C 150 MET cc_start: 0.8877 (tmm) cc_final: 0.8407 (tmm) REVERT: D 90 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8375 (tm-30) REVERT: D 97 GLU cc_start: 0.8962 (mp0) cc_final: 0.8716 (mp0) REVERT: E 75 LYS cc_start: 0.9348 (pttm) cc_final: 0.9026 (ptmm) REVERT: E 150 MET cc_start: 0.8871 (tmm) cc_final: 0.7958 (tmm) REVERT: F 97 GLU cc_start: 0.8920 (mp0) cc_final: 0.8706 (mp0) REVERT: H 90 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8225 (tm-30) REVERT: I 75 LYS cc_start: 0.9469 (ptmm) cc_final: 0.9083 (pttt) REVERT: I 150 MET cc_start: 0.8816 (tmm) cc_final: 0.8094 (tmm) REVERT: J 90 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8071 (tm-30) REVERT: J 97 GLU cc_start: 0.8860 (mp0) cc_final: 0.8631 (mp0) REVERT: K 75 LYS cc_start: 0.9299 (pttp) cc_final: 0.9099 (pttt) REVERT: K 150 MET cc_start: 0.8759 (tmm) cc_final: 0.8300 (tmm) REVERT: M 75 LYS cc_start: 0.9266 (pttm) cc_final: 0.9006 (ptmm) REVERT: M 150 MET cc_start: 0.8886 (tmm) cc_final: 0.7819 (tmm) REVERT: N 90 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8165 (tm-30) REVERT: O 75 LYS cc_start: 0.9397 (pttm) cc_final: 0.8990 (pttp) REVERT: O 150 MET cc_start: 0.8884 (tmm) cc_final: 0.8163 (tmm) REVERT: P 68 LEU cc_start: 0.8380 (tp) cc_final: 0.8170 (tp) REVERT: P 90 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8450 (tm-30) REVERT: Q 75 LYS cc_start: 0.9293 (pttt) cc_final: 0.8959 (pttp) REVERT: Q 150 MET cc_start: 0.8732 (tmm) cc_final: 0.8247 (tmm) REVERT: R 7 TYR cc_start: 0.9044 (m-10) cc_final: 0.8770 (m-10) REVERT: R 90 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8178 (tm-30) REVERT: S 75 LYS cc_start: 0.9436 (pttp) cc_final: 0.9196 (pttt) REVERT: S 150 MET cc_start: 0.8566 (tmm) cc_final: 0.8091 (tmm) REVERT: T 17 LYS cc_start: 0.9106 (pttm) cc_final: 0.8841 (pttm) REVERT: T 53 LEU cc_start: 0.8922 (tp) cc_final: 0.8600 (tp) REVERT: T 90 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8355 (tm-30) REVERT: U 75 LYS cc_start: 0.9378 (pttm) cc_final: 0.9058 (ptmm) REVERT: U 150 MET cc_start: 0.8837 (tmm) cc_final: 0.8484 (tmm) REVERT: V 90 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8317 (tm-30) REVERT: V 95 ASP cc_start: 0.8766 (p0) cc_final: 0.8506 (p0) REVERT: V 97 GLU cc_start: 0.9285 (mm-30) cc_final: 0.9020 (mp0) REVERT: W 75 LYS cc_start: 0.9402 (pttm) cc_final: 0.9039 (ptmm) REVERT: W 150 MET cc_start: 0.9012 (tmm) cc_final: 0.7856 (tmm) REVERT: X 97 GLU cc_start: 0.8982 (mp0) cc_final: 0.8764 (mp0) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.3732 time to fit residues: 293.5909 Evaluate side-chains 419 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 2.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 7.9990 chunk 292 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 190 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 325 optimal weight: 10.0000 chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 107 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26640 Z= 0.286 Angle : 0.671 9.137 36420 Z= 0.331 Chirality : 0.049 0.187 4572 Planarity : 0.006 0.041 4680 Dihedral : 4.747 25.896 3780 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3480 helix: 1.62 (0.13), residues: 1320 sheet: -1.37 (0.16), residues: 864 loop : 0.37 (0.20), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 196 PHE 0.012 0.002 PHE W 162 TYR 0.011 0.002 TYR X 46 ARG 0.003 0.001 ARG V 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8470 (tmm) cc_final: 0.8078 (tmm) REVERT: B 17 LYS cc_start: 0.9055 (pttm) cc_final: 0.8739 (pttm) REVERT: B 90 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 97 GLU cc_start: 0.8998 (mp0) cc_final: 0.8790 (mp0) REVERT: C 75 LYS cc_start: 0.9431 (pttm) cc_final: 0.9171 (ptmm) REVERT: C 150 MET cc_start: 0.8900 (tmm) cc_final: 0.8391 (tmm) REVERT: D 90 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8350 (tm-30) REVERT: E 75 LYS cc_start: 0.9374 (pttm) cc_final: 0.9065 (ptmm) REVERT: E 150 MET cc_start: 0.8530 (tmm) cc_final: 0.8037 (tmm) REVERT: F 97 GLU cc_start: 0.8989 (mp0) cc_final: 0.8764 (mp0) REVERT: G 75 LYS cc_start: 0.9483 (pttp) cc_final: 0.9182 (pttt) REVERT: H 90 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8190 (tm-30) REVERT: I 75 LYS cc_start: 0.9503 (ptmm) cc_final: 0.9119 (pttt) REVERT: I 150 MET cc_start: 0.8919 (tmm) cc_final: 0.8134 (tmm) REVERT: J 90 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8026 (tm-30) REVERT: J 97 GLU cc_start: 0.8849 (mp0) cc_final: 0.8617 (mp0) REVERT: K 75 LYS cc_start: 0.9373 (pttp) cc_final: 0.9134 (pttt) REVERT: K 150 MET cc_start: 0.8844 (tmm) cc_final: 0.8370 (tmm) REVERT: M 75 LYS cc_start: 0.9311 (pttm) cc_final: 0.8998 (ptmm) REVERT: M 150 MET cc_start: 0.8867 (tmm) cc_final: 0.8007 (tmm) REVERT: N 90 GLU cc_start: 0.8565 (tm-30) cc_final: 0.8101 (tm-30) REVERT: O 75 LYS cc_start: 0.9410 (pttm) cc_final: 0.9092 (ptmm) REVERT: O 150 MET cc_start: 0.8988 (tmm) cc_final: 0.8167 (tmm) REVERT: P 90 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8419 (tm-30) REVERT: Q 42 LYS cc_start: 0.8992 (tmmt) cc_final: 0.8784 (mmmt) REVERT: Q 75 LYS cc_start: 0.9351 (pttt) cc_final: 0.9101 (pttp) REVERT: Q 150 MET cc_start: 0.8852 (tmm) cc_final: 0.8326 (tmm) REVERT: R 7 TYR cc_start: 0.9056 (m-10) cc_final: 0.8736 (m-10) REVERT: R 90 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8220 (tm-30) REVERT: S 75 LYS cc_start: 0.9450 (pttp) cc_final: 0.9207 (pttt) REVERT: S 150 MET cc_start: 0.8680 (tmm) cc_final: 0.8000 (tmm) REVERT: T 17 LYS cc_start: 0.9122 (pttm) cc_final: 0.8844 (pttm) REVERT: T 90 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8339 (tm-30) REVERT: U 75 LYS cc_start: 0.9338 (pttm) cc_final: 0.8970 (ptmm) REVERT: U 150 MET cc_start: 0.8874 (tmm) cc_final: 0.8396 (tmm) REVERT: V 90 GLU cc_start: 0.8593 (tm-30) cc_final: 0.8317 (tm-30) REVERT: V 95 ASP cc_start: 0.8775 (p0) cc_final: 0.8493 (p0) REVERT: V 97 GLU cc_start: 0.9286 (mm-30) cc_final: 0.9026 (mp0) REVERT: W 75 LYS cc_start: 0.9433 (pttm) cc_final: 0.9067 (ptmm) REVERT: W 150 MET cc_start: 0.8991 (tmm) cc_final: 0.7962 (tmm) REVERT: X 97 GLU cc_start: 0.8925 (mp0) cc_final: 0.8691 (mp0) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.3776 time to fit residues: 287.7136 Evaluate side-chains 407 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 185 optimal weight: 0.1980 chunk 237 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 273 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 323 optimal weight: 9.9990 chunk 202 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 149 optimal weight: 40.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 76 GLN F 76 GLN ** G 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 26640 Z= 0.207 Angle : 0.672 7.626 36420 Z= 0.327 Chirality : 0.050 0.188 4572 Planarity : 0.006 0.044 4680 Dihedral : 4.691 25.406 3780 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 17.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.15), residues: 3480 helix: 1.65 (0.13), residues: 1320 sheet: -1.39 (0.16), residues: 864 loop : 0.41 (0.20), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.001 HIS M 196 PHE 0.015 0.002 PHE K 162 TYR 0.016 0.002 TYR W 30 ARG 0.003 0.000 ARG F 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 509 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9044 (pttm) cc_final: 0.8750 (pttm) REVERT: B 90 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 97 GLU cc_start: 0.8995 (mp0) cc_final: 0.8774 (mp0) REVERT: C 75 LYS cc_start: 0.9414 (pttm) cc_final: 0.9149 (ptmm) REVERT: C 150 MET cc_start: 0.8855 (tmm) cc_final: 0.8337 (tmm) REVERT: D 90 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8374 (tm-30) REVERT: D 97 GLU cc_start: 0.9054 (mp0) cc_final: 0.8836 (mp0) REVERT: E 75 LYS cc_start: 0.9368 (pttm) cc_final: 0.9051 (ptmm) REVERT: F 97 GLU cc_start: 0.8975 (mp0) cc_final: 0.8746 (mp0) REVERT: G 75 LYS cc_start: 0.9472 (pttp) cc_final: 0.9160 (pttt) REVERT: H 90 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8176 (tm-30) REVERT: I 75 LYS cc_start: 0.9502 (ptmm) cc_final: 0.9110 (pttt) REVERT: I 150 MET cc_start: 0.8860 (tmm) cc_final: 0.8021 (tmm) REVERT: J 90 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8021 (tm-30) REVERT: J 97 GLU cc_start: 0.8835 (mp0) cc_final: 0.8599 (mp0) REVERT: K 75 LYS cc_start: 0.9376 (pttp) cc_final: 0.9136 (pttt) REVERT: K 123 PHE cc_start: 0.7855 (t80) cc_final: 0.7614 (m-80) REVERT: K 150 MET cc_start: 0.8821 (tmm) cc_final: 0.8328 (tmm) REVERT: K 188 ASP cc_start: 0.8739 (p0) cc_final: 0.8462 (p0) REVERT: L 90 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8348 (tm-30) REVERT: M 75 LYS cc_start: 0.9306 (pttm) cc_final: 0.8980 (ptmm) REVERT: N 68 LEU cc_start: 0.8646 (tp) cc_final: 0.8434 (tp) REVERT: N 90 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8067 (tm-30) REVERT: O 75 LYS cc_start: 0.9415 (pttm) cc_final: 0.9107 (ptmm) REVERT: O 150 MET cc_start: 0.8932 (tmm) cc_final: 0.8156 (tmm) REVERT: P 90 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8438 (tm-30) REVERT: Q 75 LYS cc_start: 0.9359 (pttt) cc_final: 0.9006 (pttp) REVERT: Q 150 MET cc_start: 0.8813 (tmm) cc_final: 0.8284 (tmm) REVERT: R 7 TYR cc_start: 0.9023 (m-10) cc_final: 0.8716 (m-10) REVERT: R 90 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8179 (tm-30) REVERT: S 75 LYS cc_start: 0.9451 (pttp) cc_final: 0.9224 (pttt) REVERT: S 150 MET cc_start: 0.8677 (tmm) cc_final: 0.7956 (tmm) REVERT: T 17 LYS cc_start: 0.9110 (pttm) cc_final: 0.8852 (pttm) REVERT: T 90 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8325 (tm-30) REVERT: U 75 LYS cc_start: 0.9366 (pttm) cc_final: 0.9043 (ptmm) REVERT: U 150 MET cc_start: 0.8870 (tmm) cc_final: 0.8384 (tmm) REVERT: V 90 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8261 (tm-30) REVERT: V 97 GLU cc_start: 0.9262 (mm-30) cc_final: 0.9045 (mp0) REVERT: W 75 LYS cc_start: 0.9439 (pttm) cc_final: 0.9060 (ptmm) REVERT: X 68 LEU cc_start: 0.8738 (tp) cc_final: 0.8485 (tt) REVERT: X 97 GLU cc_start: 0.8924 (mp0) cc_final: 0.8694 (mp0) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.3750 time to fit residues: 296.7230 Evaluate side-chains 425 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 97 optimal weight: 0.2980 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 205 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 chunk 254 optimal weight: 8.9990 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN ** C 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 GLN ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN ** O 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** Q 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 26640 Z= 0.309 Angle : 0.700 9.241 36420 Z= 0.349 Chirality : 0.050 0.183 4572 Planarity : 0.007 0.041 4680 Dihedral : 4.822 26.154 3780 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 20.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.15), residues: 3480 helix: 1.51 (0.13), residues: 1332 sheet: -1.52 (0.16), residues: 864 loop : 0.22 (0.20), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS M 196 PHE 0.015 0.002 PHE A 162 TYR 0.010 0.002 TYR W 30 ARG 0.007 0.001 ARG O 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 486 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 LYS cc_start: 0.9073 (pttm) cc_final: 0.8795 (pttm) REVERT: B 90 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 75 LYS cc_start: 0.9424 (pttm) cc_final: 0.9149 (ptmm) REVERT: C 150 MET cc_start: 0.8924 (tmm) cc_final: 0.8326 (tmm) REVERT: D 90 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8339 (tm-30) REVERT: D 97 GLU cc_start: 0.9059 (mp0) cc_final: 0.8854 (mp0) REVERT: E 75 LYS cc_start: 0.9390 (pttm) cc_final: 0.9071 (ptmm) REVERT: E 150 MET cc_start: 0.8494 (tmm) cc_final: 0.8050 (tmm) REVERT: F 97 GLU cc_start: 0.8997 (mp0) cc_final: 0.8738 (mp0) REVERT: G 75 LYS cc_start: 0.9476 (pttp) cc_final: 0.9164 (pttt) REVERT: H 90 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8046 (tm-30) REVERT: I 75 LYS cc_start: 0.9511 (ptmm) cc_final: 0.9125 (pttt) REVERT: I 150 MET cc_start: 0.8874 (tmm) cc_final: 0.7964 (tmm) REVERT: J 90 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8008 (tm-30) REVERT: J 97 GLU cc_start: 0.8843 (mp0) cc_final: 0.8608 (mp0) REVERT: K 75 LYS cc_start: 0.9378 (pttp) cc_final: 0.9140 (pttt) REVERT: K 150 MET cc_start: 0.8876 (tmm) cc_final: 0.8353 (tmm) REVERT: K 188 ASP cc_start: 0.8776 (p0) cc_final: 0.8437 (p0) REVERT: L 90 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8357 (tm-30) REVERT: N 90 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8101 (tm-30) REVERT: O 75 LYS cc_start: 0.9427 (pttm) cc_final: 0.9107 (ptmm) REVERT: P 90 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8414 (tm-30) REVERT: Q 150 MET cc_start: 0.8863 (tmm) cc_final: 0.8305 (tmm) REVERT: R 7 TYR cc_start: 0.9041 (m-10) cc_final: 0.8749 (m-10) REVERT: R 90 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8214 (tm-30) REVERT: S 75 LYS cc_start: 0.9463 (pttp) cc_final: 0.9190 (pttt) REVERT: S 150 MET cc_start: 0.8736 (tmm) cc_final: 0.7968 (tmm) REVERT: T 17 LYS cc_start: 0.9109 (pttm) cc_final: 0.8735 (pttm) REVERT: T 90 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8317 (tm-30) REVERT: U 75 LYS cc_start: 0.9358 (pttm) cc_final: 0.9024 (ptmm) REVERT: U 150 MET cc_start: 0.8915 (tmm) cc_final: 0.8335 (tmm) REVERT: V 90 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8292 (tm-30) REVERT: V 97 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9040 (mp0) REVERT: W 75 LYS cc_start: 0.9452 (pttm) cc_final: 0.9086 (ptmm) REVERT: X 97 GLU cc_start: 0.8940 (mp0) cc_final: 0.8710 (mp0) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.3669 time to fit residues: 280.6221 Evaluate side-chains 405 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 5.9990 chunk 310 optimal weight: 0.5980 chunk 283 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 181 optimal weight: 0.0170 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 300 optimal weight: 9.9990 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN D 76 GLN F 76 GLN F 98 ASN ** G 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 GLN ** I 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 GLN N 76 GLN P 76 GLN R 76 GLN T 76 GLN ** W 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26640 Z= 0.191 Angle : 0.707 7.645 36420 Z= 0.339 Chirality : 0.051 0.200 4572 Planarity : 0.006 0.045 4680 Dihedral : 4.696 24.580 3780 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.14), residues: 3480 helix: 1.52 (0.13), residues: 1332 sheet: -1.42 (0.15), residues: 876 loop : 0.31 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 196 PHE 0.015 0.002 PHE O 162 TYR 0.012 0.001 TYR U 30 ARG 0.005 0.000 ARG I 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8847 (tmm) cc_final: 0.8222 (tmm) REVERT: B 17 LYS cc_start: 0.9053 (pttm) cc_final: 0.8799 (pttm) REVERT: B 90 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8284 (tm-30) REVERT: B 97 GLU cc_start: 0.9052 (mp0) cc_final: 0.8769 (mp0) REVERT: C 75 LYS cc_start: 0.9399 (pttm) cc_final: 0.9143 (ptmm) REVERT: C 150 MET cc_start: 0.8890 (tmm) cc_final: 0.8313 (tmm) REVERT: D 90 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8279 (tm-30) REVERT: D 97 GLU cc_start: 0.9076 (mp0) cc_final: 0.8856 (mp0) REVERT: E 75 LYS cc_start: 0.9375 (pttm) cc_final: 0.9033 (ptmm) REVERT: F 97 GLU cc_start: 0.8930 (mp0) cc_final: 0.8631 (mp0) REVERT: G 75 LYS cc_start: 0.9454 (pttp) cc_final: 0.9120 (pttt) REVERT: H 90 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8030 (tm-30) REVERT: I 75 LYS cc_start: 0.9484 (ptmm) cc_final: 0.9111 (pttt) REVERT: I 150 MET cc_start: 0.8843 (tmm) cc_final: 0.7927 (tmm) REVERT: J 90 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8082 (tm-30) REVERT: J 97 GLU cc_start: 0.8848 (mp0) cc_final: 0.8578 (mp0) REVERT: K 75 LYS cc_start: 0.9355 (pttp) cc_final: 0.9107 (pttt) REVERT: K 150 MET cc_start: 0.8775 (tmm) cc_final: 0.8267 (tmm) REVERT: K 188 ASP cc_start: 0.8644 (p0) cc_final: 0.8383 (p0) REVERT: L 90 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8244 (tm-30) REVERT: M 75 LYS cc_start: 0.9234 (pttm) cc_final: 0.8920 (ptmm) REVERT: N 90 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8068 (tm-30) REVERT: O 75 LYS cc_start: 0.9369 (pttm) cc_final: 0.9039 (ptmm) REVERT: O 150 MET cc_start: 0.9005 (tmm) cc_final: 0.7766 (tmm) REVERT: O 188 ASP cc_start: 0.8759 (p0) cc_final: 0.8418 (p0) REVERT: P 90 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8446 (tm-30) REVERT: Q 75 LYS cc_start: 0.9279 (pttt) cc_final: 0.8970 (ptmm) REVERT: Q 150 MET cc_start: 0.8766 (tmm) cc_final: 0.8201 (tmm) REVERT: R 7 TYR cc_start: 0.9007 (m-10) cc_final: 0.8671 (m-10) REVERT: R 90 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8236 (tm-30) REVERT: S 75 LYS cc_start: 0.9461 (pttp) cc_final: 0.9213 (pttt) REVERT: S 150 MET cc_start: 0.8692 (tmm) cc_final: 0.7903 (tmm) REVERT: T 17 LYS cc_start: 0.9085 (pttm) cc_final: 0.8828 (pttm) REVERT: T 90 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8262 (tm-30) REVERT: U 75 LYS cc_start: 0.9374 (pttm) cc_final: 0.9061 (ptmm) REVERT: U 150 MET cc_start: 0.8863 (tmm) cc_final: 0.8365 (tmm) REVERT: V 90 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8266 (tm-30) REVERT: V 97 GLU cc_start: 0.9275 (mm-30) cc_final: 0.9050 (mp0) REVERT: W 75 LYS cc_start: 0.9445 (pttm) cc_final: 0.9060 (ptmm) REVERT: X 97 GLU cc_start: 0.8950 (mp0) cc_final: 0.8709 (mp0) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.3597 time to fit residues: 298.8371 Evaluate side-chains 424 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 334 optimal weight: 6.9990 chunk 308 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 GLN B 98 ASN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN F 76 GLN J 76 GLN ** K 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 GLN P 76 GLN ** Q 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26640 Z= 0.282 Angle : 0.715 9.218 36420 Z= 0.353 Chirality : 0.051 0.190 4572 Planarity : 0.006 0.042 4680 Dihedral : 4.727 25.623 3780 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3480 helix: 1.53 (0.13), residues: 1332 sheet: -1.48 (0.16), residues: 876 loop : 0.20 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS K 196 PHE 0.015 0.002 PHE E 162 TYR 0.011 0.002 TYR D 46 ARG 0.005 0.001 ARG K 194 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6960 Ramachandran restraints generated. 3480 Oldfield, 0 Emsley, 3480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 496 time to evaluate : 2.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8867 (tmm) cc_final: 0.8258 (tmm) REVERT: B 17 LYS cc_start: 0.9046 (pttm) cc_final: 0.8753 (pttm) REVERT: B 90 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8268 (tm-30) REVERT: B 97 GLU cc_start: 0.8956 (mp0) cc_final: 0.8652 (mp0) REVERT: C 75 LYS cc_start: 0.9401 (pttm) cc_final: 0.9127 (ptmm) REVERT: C 150 MET cc_start: 0.8913 (tmm) cc_final: 0.8299 (tmm) REVERT: D 90 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8241 (tm-30) REVERT: D 97 GLU cc_start: 0.8989 (mp0) cc_final: 0.8744 (mp0) REVERT: E 75 LYS cc_start: 0.9397 (pttm) cc_final: 0.9074 (ptmm) REVERT: E 150 MET cc_start: 0.8832 (tmm) cc_final: 0.8026 (tmm) REVERT: F 46 TYR cc_start: 0.8331 (p90) cc_final: 0.8122 (p90) REVERT: F 97 GLU cc_start: 0.8962 (mp0) cc_final: 0.8690 (mp0) REVERT: G 75 LYS cc_start: 0.9474 (pttp) cc_final: 0.9235 (pttp) REVERT: H 90 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8020 (tm-30) REVERT: I 75 LYS cc_start: 0.9510 (ptmm) cc_final: 0.9139 (pttt) REVERT: I 150 MET cc_start: 0.8838 (tmm) cc_final: 0.7936 (tmm) REVERT: J 90 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7986 (tm-30) REVERT: J 97 GLU cc_start: 0.8860 (mp0) cc_final: 0.8606 (mp0) REVERT: K 75 LYS cc_start: 0.9382 (pttp) cc_final: 0.9140 (pttt) REVERT: K 150 MET cc_start: 0.8864 (tmm) cc_final: 0.8356 (tmm) REVERT: K 188 ASP cc_start: 0.8752 (p0) cc_final: 0.8430 (p0) REVERT: L 90 GLU cc_start: 0.8540 (tm-30) cc_final: 0.8257 (tm-30) REVERT: M 75 LYS cc_start: 0.9262 (pttm) cc_final: 0.8949 (ptmm) REVERT: N 90 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8097 (tm-30) REVERT: O 75 LYS cc_start: 0.9427 (pttm) cc_final: 0.9103 (ptmm) REVERT: O 150 MET cc_start: 0.9057 (tmm) cc_final: 0.7877 (tmm) REVERT: O 188 ASP cc_start: 0.8810 (p0) cc_final: 0.8461 (p0) REVERT: P 90 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8406 (tm-30) REVERT: Q 75 LYS cc_start: 0.9308 (pttt) cc_final: 0.8995 (ptmm) REVERT: Q 150 MET cc_start: 0.8813 (tmm) cc_final: 0.8244 (tmm) REVERT: Q 188 ASP cc_start: 0.8420 (t0) cc_final: 0.8185 (p0) REVERT: R 7 TYR cc_start: 0.9057 (m-10) cc_final: 0.8766 (m-10) REVERT: R 90 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8212 (tm-30) REVERT: S 75 LYS cc_start: 0.9470 (pttp) cc_final: 0.9190 (pttt) REVERT: S 150 MET cc_start: 0.8743 (tmm) cc_final: 0.7955 (tmm) REVERT: T 17 LYS cc_start: 0.9112 (pttm) cc_final: 0.8863 (pttm) REVERT: T 90 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8272 (tm-30) REVERT: U 75 LYS cc_start: 0.9359 (pttm) cc_final: 0.9022 (ptmm) REVERT: U 150 MET cc_start: 0.8896 (tmm) cc_final: 0.8328 (tmm) REVERT: V 90 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8239 (tm-30) REVERT: V 97 GLU cc_start: 0.9312 (mm-30) cc_final: 0.9055 (mp0) REVERT: W 75 LYS cc_start: 0.9451 (pttm) cc_final: 0.9078 (ptmm) REVERT: X 97 GLU cc_start: 0.8948 (mp0) cc_final: 0.8728 (mp0) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.3654 time to fit residues: 285.4542 Evaluate side-chains 404 residues out of total 2700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 6.9990 chunk 283 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 245 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 266 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 274 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 49 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 GLN D 76 GLN ** E 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN H 76 GLN J 76 GLN N 76 GLN ** O 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 GLN ** Q 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 GLN ** S 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 GLN X 76 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.074085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059597 restraints weight = 118597.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.061203 restraints weight = 84376.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062430 restraints weight = 65177.588| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 26640 Z= 0.197 Angle : 0.700 8.130 36420 Z= 0.339 Chirality : 0.051 0.201 4572 Planarity : 0.006 0.044 4680 Dihedral : 4.596 24.936 3780 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.15), residues: 3480 helix: 1.54 (0.13), residues: 1332 sheet: -1.46 (0.16), residues: 876 loop : 0.28 (0.20), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 196 PHE 0.013 0.002 PHE M 162 TYR 0.012 0.001 TYR O 30 ARG 0.009 0.000 ARG O 194 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5461.94 seconds wall clock time: 98 minutes 13.00 seconds (5893.00 seconds total)