Starting phenix.real_space_refine on Thu Aug 8 02:50:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/08_2024/8un1_42390.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/08_2024/8un1_42390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/08_2024/8un1_42390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/08_2024/8un1_42390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/08_2024/8un1_42390.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/08_2024/8un1_42390.cif" } resolution = 3.9 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= 0.002 sd= 0.020 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 14157 2.51 5 N 3632 2.21 5 O 4254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 190": "OE1" <-> "OE2" Residue "D GLU 197": "OE1" <-> "OE2" Residue "E GLU 29": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 190": "OE1" <-> "OE2" Residue "F GLU 197": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 45": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 75": "OE1" <-> "OE2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 29": "OE1" <-> "OE2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "I GLU 75": "OE1" <-> "OE2" Residue "I TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 190": "OE1" <-> "OE2" Residue "J GLU 197": "OE1" <-> "OE2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 75": "OE1" <-> "OE2" Residue "K TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L GLU 197": "OE1" <-> "OE2" Residue "M GLU 29": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M GLU 61": "OE1" <-> "OE2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 190": "OE1" <-> "OE2" Residue "N GLU 197": "OE1" <-> "OE2" Residue "O GLU 29": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O GLU 61": "OE1" <-> "OE2" Residue "O GLU 75": "OE1" <-> "OE2" Residue "O TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 29": "OE1" <-> "OE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q GLU 61": "OE1" <-> "OE2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "Q TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 190": "OE1" <-> "OE2" Residue "R GLU 197": "OE1" <-> "OE2" Residue "S GLU 29": "OE1" <-> "OE2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S GLU 61": "OE1" <-> "OE2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "S TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 190": "OE1" <-> "OE2" Residue "T GLU 197": "OE1" <-> "OE2" Residue "U GLU 29": "OE1" <-> "OE2" Residue "U GLU 45": "OE1" <-> "OE2" Residue "U GLU 61": "OE1" <-> "OE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "U TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 190": "OE1" <-> "OE2" Residue "V GLU 197": "OE1" <-> "OE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W GLU 45": "OE1" <-> "OE2" Residue "W GLU 61": "OE1" <-> "OE2" Residue "W GLU 75": "OE1" <-> "OE2" Residue "W TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 22091 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "B" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1399 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "D" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "F" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "G" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "I" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "J" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "K" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "L" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "M" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "N" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "O" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "Q" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "R" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "S" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "T" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "U" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Chain: "V" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1400 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 175} Chain: "W" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 791 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 91} Time building chain proxies: 12.06, per 1000 atoms: 0.55 Number of scatterers: 22091 At special positions: 0 Unit cell: (140.18, 129, 135.02, 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 4254 8.00 N 3632 7.00 C 14157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.09 Conformation dependent library (CDL) restraints added in 4.0 seconds 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5526 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 35 sheets defined 41.6% alpha, 20.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN A 40 " --> pdb=" O LYS A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY B 33 " --> pdb=" O SER B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 81 Processing helix chain 'B' and resid 100 through 107 removed outlier: 4.473A pdb=" N PHE B 104 " --> pdb=" O GLN B 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 106 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU B 199 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN C 40 " --> pdb=" O LYS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 90 Processing helix chain 'C' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY D 33 " --> pdb=" O SER D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 81 Processing helix chain 'D' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE D 104 " --> pdb=" O GLN D 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS D 106 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 143 Processing helix chain 'D' and resid 167 through 183 Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 196 through 200 removed outlier: 3.514A pdb=" N LEU D 199 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN E 40 " --> pdb=" O LYS E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 90 Processing helix chain 'E' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 44 removed outlier: 3.522A pdb=" N GLY F 33 " --> pdb=" O SER F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 81 Processing helix chain 'F' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE F 104 " --> pdb=" O GLN F 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS F 106 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU F 107 " --> pdb=" O PRO F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 143 Processing helix chain 'F' and resid 167 through 183 Processing helix chain 'F' and resid 184 through 186 No H-bonds generated for 'chain 'F' and resid 184 through 186' Processing helix chain 'F' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU F 199 " --> pdb=" O VAL F 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN G 40 " --> pdb=" O LYS G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 90 Processing helix chain 'G' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR G 117 " --> pdb=" O VAL G 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 40 removed outlier: 3.775A pdb=" N ASN I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 90 Processing helix chain 'I' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR I 117 " --> pdb=" O VAL I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY J 33 " --> pdb=" O SER J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 81 Processing helix chain 'J' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE J 104 " --> pdb=" O GLN J 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS J 106 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU J 107 " --> pdb=" O PRO J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 143 Processing helix chain 'J' and resid 167 through 183 Processing helix chain 'J' and resid 184 through 186 No H-bonds generated for 'chain 'J' and resid 184 through 186' Processing helix chain 'J' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU J 199 " --> pdb=" O VAL J 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 40 removed outlier: 3.775A pdb=" N ASN K 40 " --> pdb=" O LYS K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 90 Processing helix chain 'K' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR K 117 " --> pdb=" O VAL K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 44 removed outlier: 3.522A pdb=" N GLY L 33 " --> pdb=" O SER L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 81 Processing helix chain 'L' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE L 104 " --> pdb=" O GLN L 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS L 106 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU L 107 " --> pdb=" O PRO L 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 143 Processing helix chain 'L' and resid 167 through 183 Processing helix chain 'L' and resid 184 through 186 No H-bonds generated for 'chain 'L' and resid 184 through 186' Processing helix chain 'L' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU L 199 " --> pdb=" O VAL L 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN M 40 " --> pdb=" O LYS M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 90 Processing helix chain 'M' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR M 117 " --> pdb=" O VAL M 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 3.522A pdb=" N GLY N 33 " --> pdb=" O SER N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 81 Processing helix chain 'N' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE N 104 " --> pdb=" O GLN N 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS N 106 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU N 107 " --> pdb=" O PRO N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 143 Processing helix chain 'N' and resid 167 through 183 Processing helix chain 'N' and resid 184 through 186 No H-bonds generated for 'chain 'N' and resid 184 through 186' Processing helix chain 'N' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU N 199 " --> pdb=" O VAL N 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN O 40 " --> pdb=" O LYS O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 90 Processing helix chain 'O' and resid 106 through 117 removed outlier: 3.656A pdb=" N THR O 117 " --> pdb=" O VAL O 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN Q 40 " --> pdb=" O LYS Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 90 Processing helix chain 'Q' and resid 106 through 117 removed outlier: 3.657A pdb=" N THR Q 117 " --> pdb=" O VAL Q 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY R 33 " --> pdb=" O SER R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 81 Processing helix chain 'R' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE R 104 " --> pdb=" O GLN R 100 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS R 106 " --> pdb=" O LEU R 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU R 107 " --> pdb=" O PRO R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 143 Processing helix chain 'R' and resid 167 through 183 Processing helix chain 'R' and resid 184 through 186 No H-bonds generated for 'chain 'R' and resid 184 through 186' Processing helix chain 'R' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU R 199 " --> pdb=" O VAL R 196 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN S 40 " --> pdb=" O LYS S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 90 Processing helix chain 'S' and resid 106 through 117 removed outlier: 3.657A pdb=" N THR S 117 " --> pdb=" O VAL S 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 44 removed outlier: 3.522A pdb=" N GLY T 33 " --> pdb=" O SER T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 81 Processing helix chain 'T' and resid 100 through 107 removed outlier: 4.472A pdb=" N PHE T 104 " --> pdb=" O GLN T 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS T 106 " --> pdb=" O LEU T 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU T 107 " --> pdb=" O PRO T 103 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 143 Processing helix chain 'T' and resid 167 through 183 Processing helix chain 'T' and resid 184 through 186 No H-bonds generated for 'chain 'T' and resid 184 through 186' Processing helix chain 'T' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU T 199 " --> pdb=" O VAL T 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 40 removed outlier: 3.775A pdb=" N ASN U 40 " --> pdb=" O LYS U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 78 through 90 Processing helix chain 'U' and resid 106 through 117 removed outlier: 3.657A pdb=" N THR U 117 " --> pdb=" O VAL U 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 44 removed outlier: 3.521A pdb=" N GLY V 33 " --> pdb=" O SER V 29 " (cutoff:3.500A) Processing helix chain 'V' and resid 66 through 81 Processing helix chain 'V' and resid 100 through 107 removed outlier: 4.473A pdb=" N PHE V 104 " --> pdb=" O GLN V 100 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS V 106 " --> pdb=" O LEU V 102 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU V 107 " --> pdb=" O PRO V 103 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 143 Processing helix chain 'V' and resid 167 through 183 Processing helix chain 'V' and resid 184 through 186 No H-bonds generated for 'chain 'V' and resid 184 through 186' Processing helix chain 'V' and resid 196 through 200 removed outlier: 3.515A pdb=" N LEU V 199 " --> pdb=" O VAL V 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 26 through 40 removed outlier: 3.776A pdb=" N ASN W 40 " --> pdb=" O LYS W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 78 through 90 Processing helix chain 'W' and resid 106 through 117 removed outlier: 3.657A pdb=" N THR W 117 " --> pdb=" O VAL W 113 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 24 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 18 through 24 current: chain 'I' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 67 through 74 current: chain 'Q' and resid 67 through 74 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 58 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU B 48 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 25 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 63 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 65 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 21 " --> pdb=" O GLY B 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 90 " --> pdb=" O GLU B 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU B 147 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE B 165 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER B 149 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA B 160 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 123 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP B 188 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 18 through 24 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 18 through 24 current: chain 'C' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 67 through 74 current: chain 'M' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 67 through 74 current: chain 'W' and resid 67 through 74 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AA7, first strand: chain 'D' and resid 47 through 54 removed outlier: 5.290A pdb=" N LEU D 48 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU D 64 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 25 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 63 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY D 65 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA D 21 " --> pdb=" O GLY D 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP D 90 " --> pdb=" O GLU D 26 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU D 147 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE D 165 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER D 149 " --> pdb=" O THR D 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 160 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 123 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP D 188 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 18 through 24 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 24 current: chain 'E' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 67 through 74 current: chain 'O' and resid 67 through 74 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 67 through 74 current: chain 'S' and resid 67 through 74 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 57 through 58 Processing sheet with id=AB2, first strand: chain 'F' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU F 48 " --> pdb=" O LEU F 64 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU F 64 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU F 25 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU F 63 " --> pdb=" O GLY F 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY F 65 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F 21 " --> pdb=" O GLY F 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP F 90 " --> pdb=" O GLU F 26 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 146 through 152 removed outlier: 5.698A pdb=" N LEU F 147 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE F 165 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER F 149 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA F 160 " --> pdb=" O VAL F 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL F 123 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP F 188 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 104 through 105 removed outlier: 4.085A pdb=" N ASP K 104 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL G 99 " --> pdb=" O ASP K 104 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 74 " --> pdb=" O ALA G 18 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL G 67 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR G 73 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU G 45 " --> pdb=" O TYR G 73 " (cutoff:3.500A) removed outlier: 16.904A pdb=" N THR G 49 " --> pdb=" O LEU K 52 " (cutoff:3.500A) removed outlier: 13.583A pdb=" N LEU K 52 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N ALA G 51 " --> pdb=" O PRO K 50 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR G 53 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE K 48 " --> pdb=" O THR G 53 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE G 55 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA K 46 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU K 45 " --> pdb=" O TYR K 73 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR K 73 " --> pdb=" O GLU K 45 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL K 67 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR K 74 " --> pdb=" O ALA K 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP U 104 " --> pdb=" O VAL K 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 57 through 58 Processing sheet with id=AB6, first strand: chain 'I' and resid 57 through 58 Processing sheet with id=AB7, first strand: chain 'J' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU J 48 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU J 64 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU J 25 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU J 63 " --> pdb=" O GLY J 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY J 65 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA J 21 " --> pdb=" O GLY J 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP J 90 " --> pdb=" O GLU J 26 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU J 147 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE J 165 " --> pdb=" O LEU J 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER J 149 " --> pdb=" O THR J 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA J 160 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL J 123 " --> pdb=" O GLU J 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP J 188 " --> pdb=" O GLU J 125 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 57 through 58 Processing sheet with id=AC1, first strand: chain 'L' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU L 48 " --> pdb=" O LEU L 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU L 64 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU L 25 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU L 63 " --> pdb=" O GLY L 23 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY L 65 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA L 21 " --> pdb=" O GLY L 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP L 90 " --> pdb=" O GLU L 26 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU L 147 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE L 165 " --> pdb=" O LEU L 147 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER L 149 " --> pdb=" O THR L 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA L 160 " --> pdb=" O VAL L 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL L 123 " --> pdb=" O GLU L 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP L 188 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 57 through 58 Processing sheet with id=AC4, first strand: chain 'N' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU N 48 " --> pdb=" O LEU N 64 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU N 64 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU N 25 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU N 63 " --> pdb=" O GLY N 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY N 65 " --> pdb=" O ALA N 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA N 21 " --> pdb=" O GLY N 65 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP N 90 " --> pdb=" O GLU N 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 146 through 152 removed outlier: 5.698A pdb=" N LEU N 147 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE N 165 " --> pdb=" O LEU N 147 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER N 149 " --> pdb=" O THR N 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA N 160 " --> pdb=" O VAL N 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL N 123 " --> pdb=" O GLU N 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP N 188 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 57 through 58 Processing sheet with id=AC7, first strand: chain 'Q' and resid 57 through 58 Processing sheet with id=AC8, first strand: chain 'R' and resid 47 through 54 removed outlier: 5.289A pdb=" N LEU R 48 " --> pdb=" O LEU R 64 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU R 64 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU R 25 " --> pdb=" O ILE R 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU R 63 " --> pdb=" O GLY R 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY R 65 " --> pdb=" O ALA R 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA R 21 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP R 90 " --> pdb=" O GLU R 26 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU R 147 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE R 165 " --> pdb=" O LEU R 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER R 149 " --> pdb=" O THR R 163 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA R 160 " --> pdb=" O VAL R 126 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL R 123 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP R 188 " --> pdb=" O GLU R 125 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 57 through 58 Processing sheet with id=AD2, first strand: chain 'T' and resid 47 through 54 removed outlier: 5.290A pdb=" N LEU T 48 " --> pdb=" O LEU T 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU T 64 " --> pdb=" O LEU T 48 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU T 25 " --> pdb=" O ILE T 61 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU T 63 " --> pdb=" O GLY T 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY T 65 " --> pdb=" O ALA T 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA T 21 " --> pdb=" O GLY T 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP T 90 " --> pdb=" O GLU T 26 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU T 147 " --> pdb=" O ILE T 165 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE T 165 " --> pdb=" O LEU T 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER T 149 " --> pdb=" O THR T 163 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA T 160 " --> pdb=" O VAL T 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL T 123 " --> pdb=" O GLU T 190 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP T 188 " --> pdb=" O GLU T 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 45 through 52 removed outlier: 4.437A pdb=" N GLU U 45 " --> pdb=" O TYR U 73 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR U 73 " --> pdb=" O GLU U 45 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL U 67 " --> pdb=" O ALA U 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR U 74 " --> pdb=" O ALA U 18 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 57 through 58 Processing sheet with id=AD6, first strand: chain 'V' and resid 47 through 54 removed outlier: 5.290A pdb=" N LEU V 48 " --> pdb=" O LEU V 64 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU V 64 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU V 25 " --> pdb=" O ILE V 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU V 63 " --> pdb=" O GLY V 23 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY V 65 " --> pdb=" O ALA V 21 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA V 21 " --> pdb=" O GLY V 65 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP V 90 " --> pdb=" O GLU V 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 146 through 152 removed outlier: 5.699A pdb=" N LEU V 147 " --> pdb=" O ILE V 165 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE V 165 " --> pdb=" O LEU V 147 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER V 149 " --> pdb=" O THR V 163 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA V 160 " --> pdb=" O VAL V 126 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL V 123 " --> pdb=" O GLU V 190 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP V 188 " --> pdb=" O GLU V 125 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 57 through 58 1096 hydrogen bonds defined for protein. 3153 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: 6.57 Time building geometry restraints manager: 9.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.14: 12 1.14 - 1.31: 3909 1.31 - 1.48: 7860 1.48 - 1.65: 10564 1.65 - 1.82: 99 Bond restraints: 22444 Sorted by residual: bond pdb=" CG PRO U 25 " pdb=" CD PRO U 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 bond pdb=" CG PRO M 25 " pdb=" CD PRO M 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 bond pdb=" CG PRO A 25 " pdb=" CD PRO A 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 bond pdb=" CG PRO Q 25 " pdb=" CD PRO Q 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 bond pdb=" CG PRO I 25 " pdb=" CD PRO I 25 " ideal model delta sigma weight residual 1.503 0.974 0.529 3.40e-02 8.65e+02 2.42e+02 ... (remaining 22439 not shown) Histogram of bond angle deviations from ideal: 80.17 - 90.92: 24 90.92 - 101.67: 99 101.67 - 112.43: 12572 112.43 - 123.18: 16622 123.18 - 133.93: 1249 Bond angle restraints: 30566 Sorted by residual: angle pdb=" N PRO E 25 " pdb=" CD PRO E 25 " pdb=" CG PRO E 25 " ideal model delta sigma weight residual 103.20 80.17 23.03 1.50e+00 4.44e-01 2.36e+02 angle pdb=" N PRO S 25 " pdb=" CD PRO S 25 " pdb=" CG PRO S 25 " ideal model delta sigma weight residual 103.20 80.18 23.02 1.50e+00 4.44e-01 2.36e+02 angle pdb=" N PRO G 25 " pdb=" CD PRO G 25 " pdb=" CG PRO G 25 " ideal model delta sigma weight residual 103.20 80.18 23.02 1.50e+00 4.44e-01 2.36e+02 angle pdb=" N PRO O 25 " pdb=" CD PRO O 25 " pdb=" CG PRO O 25 " ideal model delta sigma weight residual 103.20 80.19 23.01 1.50e+00 4.44e-01 2.35e+02 angle pdb=" N PRO K 25 " pdb=" CD PRO K 25 " pdb=" CG PRO K 25 " ideal model delta sigma weight residual 103.20 80.19 23.01 1.50e+00 4.44e-01 2.35e+02 ... (remaining 30561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 11958 16.48 - 32.95: 1626 32.95 - 49.43: 414 49.43 - 65.91: 60 65.91 - 82.39: 33 Dihedral angle restraints: 14091 sinusoidal: 5607 harmonic: 8484 Sorted by residual: dihedral pdb=" CA LEU B 152 " pdb=" C LEU B 152 " pdb=" N ALA B 153 " pdb=" CA ALA B 153 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA LEU V 152 " pdb=" C LEU V 152 " pdb=" N ALA V 153 " pdb=" CA ALA V 153 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU T 152 " pdb=" C LEU T 152 " pdb=" N ALA T 153 " pdb=" CA ALA T 153 " ideal model delta harmonic sigma weight residual 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 14088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2765 0.053 - 0.105: 809 0.105 - 0.158: 132 0.158 - 0.211: 11 0.211 - 0.264: 36 Chirality restraints: 3753 Sorted by residual: chirality pdb=" CA PRO W 25 " pdb=" N PRO W 25 " pdb=" C PRO W 25 " pdb=" CB PRO W 25 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO O 25 " pdb=" N PRO O 25 " pdb=" C PRO O 25 " pdb=" CB PRO O 25 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA PRO S 25 " pdb=" N PRO S 25 " pdb=" C PRO S 25 " pdb=" CB PRO S 25 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3750 not shown) Planarity restraints: 3918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR U 24 " -0.085 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO U 25 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO U 25 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO U 25 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR Q 24 " 0.085 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO Q 25 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO Q 25 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO Q 25 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR W 24 " 0.085 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO W 25 " -0.198 5.00e-02 4.00e+02 pdb=" CA PRO W 25 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO W 25 " 0.059 5.00e-02 4.00e+02 ... (remaining 3915 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 417 2.65 - 3.21: 21451 3.21 - 3.77: 34998 3.77 - 4.34: 44033 4.34 - 4.90: 70701 Nonbonded interactions: 171600 Sorted by model distance: nonbonded pdb=" NH1 ARG J 176 " pdb=" OXT THR Q 117 " model vdw 2.085 3.120 nonbonded pdb=" OG SER V 85 " pdb=" OD1 ASN V 87 " model vdw 2.140 3.040 nonbonded pdb=" OG SER T 85 " pdb=" OD1 ASN T 87 " model vdw 2.140 3.040 nonbonded pdb=" OG SER R 85 " pdb=" OD1 ASN R 87 " model vdw 2.140 3.040 nonbonded pdb=" OG SER N 85 " pdb=" OD1 ASN N 87 " model vdw 2.141 3.040 ... (remaining 171595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'F' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'J' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'L' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'N' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'R' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'T' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) selection = (chain 'V' and (resid 16 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CZ or name NH1 or name NH2) \ ) or resid 33 through 203)) } 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: 0.700 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: 0.020 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 57.760 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.150 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.529 22444 Z= 0.894 Angle : 1.168 23.032 30566 Z= 0.672 Chirality : 0.054 0.264 3753 Planarity : 0.010 0.115 3918 Dihedral : 16.243 82.386 8565 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.47 % Allowed : 31.60 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.76 (0.16), residues: 2862 helix: 0.62 (0.15), residues: 1035 sheet: -1.03 (0.17), residues: 885 loop : -1.01 (0.21), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 112 HIS 0.004 0.001 HIS W 90 PHE 0.021 0.004 PHE G 115 TYR 0.030 0.003 TYR C 109 ARG 0.008 0.001 ARG L 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 992 time to evaluate : 2.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 GLU cc_start: 0.7076 (tt0) cc_final: 0.6620 (tm-30) REVERT: A 62 ILE cc_start: 0.7990 (mm) cc_final: 0.7582 (mm) REVERT: A 63 LYS cc_start: 0.7203 (mmtt) cc_final: 0.6860 (mmpt) REVERT: B 62 MET cc_start: 0.8307 (tpp) cc_final: 0.8058 (mmp) REVERT: B 199 LEU cc_start: 0.9199 (pp) cc_final: 0.8908 (tp) REVERT: C 102 PRO cc_start: 0.5747 (Cg_endo) cc_final: 0.5459 (Cg_endo) REVERT: D 75 ILE cc_start: 0.8811 (mm) cc_final: 0.8292 (mm) REVERT: D 150 MET cc_start: 0.7573 (ttp) cc_final: 0.7323 (pmm) REVERT: D 151 ARG cc_start: 0.6230 (mtm-85) cc_final: 0.5913 (mtp-110) REVERT: E 35 LYS cc_start: 0.9045 (tptp) cc_final: 0.8646 (mttt) REVERT: E 36 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7501 (tptp) REVERT: E 75 GLU cc_start: 0.8308 (pm20) cc_final: 0.7865 (pm20) REVERT: F 58 ARG cc_start: 0.7137 (mmp-170) cc_final: 0.6286 (mmm-85) REVERT: G 72 LEU cc_start: 0.8905 (mp) cc_final: 0.8652 (mp) REVERT: G 101 THR cc_start: 0.5163 (p) cc_final: 0.4609 (p) REVERT: I 42 LEU cc_start: 0.6813 (OUTLIER) cc_final: 0.6479 (tp) REVERT: I 92 ASP cc_start: 0.7800 (m-30) cc_final: 0.6732 (t0) REVERT: K 63 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8706 (mmtp) REVERT: L 103 PRO cc_start: 0.8287 (Cg_exo) cc_final: 0.8025 (Cg_endo) REVERT: L 115 LYS cc_start: 0.9144 (ttpp) cc_final: 0.8829 (mmmt) REVERT: M 17 MET cc_start: 0.3645 (ptm) cc_final: 0.2732 (ptm) REVERT: M 87 LYS cc_start: 0.8852 (tptt) cc_final: 0.8566 (tttm) REVERT: M 97 ILE cc_start: 0.8333 (pt) cc_final: 0.8098 (pt) REVERT: N 26 GLU cc_start: 0.5822 (tm-30) cc_final: 0.5356 (tp30) REVERT: N 61 ILE cc_start: 0.8171 (tt) cc_final: 0.7812 (mp) REVERT: N 68 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8039 (tp30) REVERT: O 116 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7300 (mm-30) REVERT: Q 19 ILE cc_start: 0.7772 (mm) cc_final: 0.7393 (mm) REVERT: R 58 ARG cc_start: 0.7682 (mmp-170) cc_final: 0.7219 (mmp-170) REVERT: T 24 ILE cc_start: 0.7981 (mp) cc_final: 0.7670 (mt) REVERT: T 148 THR cc_start: 0.8588 (p) cc_final: 0.8359 (p) REVERT: V 19 ARG cc_start: 0.7092 (mtm-85) cc_final: 0.6855 (mpp80) REVERT: V 96 GLU cc_start: 0.8199 (mm-30) cc_final: 0.6973 (pp20) REVERT: V 199 LEU cc_start: 0.7551 (pp) cc_final: 0.7107 (tp) REVERT: W 78 ASN cc_start: 0.8598 (t0) cc_final: 0.7925 (t0) outliers start: 11 outliers final: 3 residues processed: 996 average time/residue: 0.4057 time to fit residues: 591.0766 Evaluate side-chains 542 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 538 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain U residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 3.9990 chunk 213 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 144 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 134 optimal weight: 9.9990 chunk 164 optimal weight: 0.9990 chunk 256 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN E 59 ASN K 59 ASN O 59 ASN O 78 ASN ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN R 202 ASN S 59 ASN ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 59 ASN V 155 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22444 Z= 0.339 Angle : 0.887 9.835 30566 Z= 0.445 Chirality : 0.054 0.323 3753 Planarity : 0.007 0.077 3918 Dihedral : 6.078 58.818 3094 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 7.79 % Allowed : 25.72 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2862 helix: 0.72 (0.15), residues: 1023 sheet: -0.97 (0.17), residues: 888 loop : -0.69 (0.21), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP O 112 HIS 0.006 0.001 HIS F 155 PHE 0.025 0.004 PHE O 115 TYR 0.034 0.003 TYR G 109 ARG 0.011 0.001 ARG N 179 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 568 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.5381 (mm) cc_final: 0.4926 (mm) REVERT: B 24 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6471 (tp) REVERT: B 69 ASP cc_start: 0.7298 (OUTLIER) cc_final: 0.6872 (t0) REVERT: B 199 LEU cc_start: 0.9192 (pp) cc_final: 0.8850 (tp) REVERT: C 54 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8298 (ttpp) REVERT: C 55 ILE cc_start: 0.9234 (mm) cc_final: 0.8947 (tp) REVERT: D 24 ILE cc_start: 0.8928 (mp) cc_final: 0.8369 (tt) REVERT: D 52 GLU cc_start: 0.5291 (OUTLIER) cc_final: 0.4842 (pm20) REVERT: D 60 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8222 (tp) REVERT: D 90 ASP cc_start: 0.7647 (t0) cc_final: 0.7409 (t0) REVERT: E 76 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8166 (mm-30) REVERT: E 77 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7548 (tm-30) REVERT: F 69 ASP cc_start: 0.6425 (OUTLIER) cc_final: 0.6098 (t0) REVERT: G 23 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8558 (m) REVERT: G 75 GLU cc_start: 0.5959 (pm20) cc_final: 0.5577 (pm20) REVERT: I 21 GLU cc_start: 0.7708 (tp30) cc_final: 0.7186 (tp30) REVERT: I 42 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6873 (tp) REVERT: I 92 ASP cc_start: 0.7690 (m-30) cc_final: 0.6833 (t70) REVERT: J 24 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5276 (mp) REVERT: J 90 ASP cc_start: 0.7848 (t0) cc_final: 0.7644 (t0) REVERT: J 168 LYS cc_start: 0.8241 (mppt) cc_final: 0.8016 (mmmt) REVERT: K 77 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8380 (tp30) REVERT: L 69 ASP cc_start: 0.6827 (OUTLIER) cc_final: 0.6113 (t70) REVERT: M 33 ILE cc_start: 0.8925 (mt) cc_final: 0.8708 (mm) REVERT: Q 21 GLU cc_start: 0.5910 (tp30) cc_final: 0.5152 (mp0) REVERT: Q 98 ILE cc_start: 0.8335 (mp) cc_final: 0.8077 (mp) REVERT: R 58 ARG cc_start: 0.7857 (mmp-170) cc_final: 0.7310 (mmp80) REVERT: R 69 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7753 (t70) REVERT: S 40 ASN cc_start: 0.8112 (p0) cc_final: 0.7545 (p0) REVERT: S 42 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7528 (mt) REVERT: T 62 MET cc_start: 0.7586 (tpp) cc_final: 0.7002 (tpp) REVERT: T 69 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6374 (t0) REVERT: V 19 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7291 (mpt-90) REVERT: V 53 PRO cc_start: 0.5463 (Cg_endo) cc_final: 0.5144 (Cg_exo) REVERT: V 60 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6827 (tp) REVERT: V 199 LEU cc_start: 0.7732 (pp) cc_final: 0.7169 (tp) REVERT: W 78 ASN cc_start: 0.8789 (t0) cc_final: 0.7954 (t0) REVERT: W 86 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8615 (pt) outliers start: 183 outliers final: 89 residues processed: 691 average time/residue: 0.3402 time to fit residues: 356.5864 Evaluate side-chains 548 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 445 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 149 SER Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 22 THR Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 83 VAL Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 69 ASP Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 65 GLU Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 73 TYR Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain T residue 48 LEU Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 97 ILE Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 52 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 48 LEU Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 60 LEU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 92 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 174 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 chunk 256 optimal weight: 0.9990 chunk 277 optimal weight: 30.0000 chunk 228 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN L 155 HIS M 59 ASN O 78 ASN Q 59 ASN ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22444 Z= 0.309 Angle : 0.809 12.441 30566 Z= 0.406 Chirality : 0.052 0.278 3753 Planarity : 0.007 0.087 3918 Dihedral : 5.957 58.557 3094 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 8.09 % Allowed : 26.19 % Favored : 65.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.38 (0.16), residues: 2862 helix: 0.81 (0.16), residues: 1023 sheet: -0.82 (0.16), residues: 912 loop : -0.59 (0.22), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP Q 112 HIS 0.032 0.002 HIS V 155 PHE 0.033 0.004 PHE E 115 TYR 0.027 0.002 TYR A 109 ARG 0.006 0.001 ARG R 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 477 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 ILE cc_start: 0.5323 (mm) cc_final: 0.4827 (mm) REVERT: B 69 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6892 (t0) REVERT: B 74 MET cc_start: 0.8484 (mmm) cc_final: 0.8281 (mmm) REVERT: B 199 LEU cc_start: 0.9243 (pp) cc_final: 0.8893 (tp) REVERT: C 49 THR cc_start: 0.7882 (t) cc_final: 0.7565 (p) REVERT: C 54 LYS cc_start: 0.8917 (ttpp) cc_final: 0.8556 (ttpp) REVERT: D 24 ILE cc_start: 0.9132 (mp) cc_final: 0.8468 (tt) REVERT: D 68 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8167 (tp30) REVERT: D 90 ASP cc_start: 0.7772 (t0) cc_final: 0.7569 (t0) REVERT: E 76 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7877 (mm-30) REVERT: F 69 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6512 (t0) REVERT: F 90 ASP cc_start: 0.7731 (m-30) cc_final: 0.7327 (m-30) REVERT: J 24 ILE cc_start: 0.6231 (OUTLIER) cc_final: 0.6017 (tt) REVERT: J 62 MET cc_start: 0.6054 (tpp) cc_final: 0.5629 (tpp) REVERT: J 142 LEU cc_start: 0.6549 (tp) cc_final: 0.5371 (tp) REVERT: K 41 ARG cc_start: 0.8442 (mtp85) cc_final: 0.7914 (tpp-160) REVERT: M 33 ILE cc_start: 0.9047 (mt) cc_final: 0.8816 (mm) REVERT: M 52 LEU cc_start: 0.6400 (mm) cc_final: 0.6039 (mp) REVERT: O 28 GLU cc_start: 0.8095 (pm20) cc_final: 0.7771 (pm20) REVERT: Q 112 TRP cc_start: 0.7723 (t-100) cc_final: 0.7083 (t-100) REVERT: Q 116 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7468 (tp30) REVERT: R 58 ARG cc_start: 0.7790 (mmp-170) cc_final: 0.7363 (mmp80) REVERT: R 69 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7773 (t70) REVERT: S 21 GLU cc_start: 0.8687 (tp30) cc_final: 0.8175 (tp30) REVERT: S 42 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7805 (mt) REVERT: T 69 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6536 (t0) REVERT: T 165 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7049 (pt) REVERT: V 19 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7427 (mpp80) REVERT: V 53 PRO cc_start: 0.5665 (Cg_endo) cc_final: 0.5271 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6210 (mmp80) cc_final: 0.5450 (mtt180) REVERT: V 96 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7756 (pt0) REVERT: V 112 GLU cc_start: 0.7592 (mp0) cc_final: 0.7259 (pp20) REVERT: V 199 LEU cc_start: 0.7804 (pp) cc_final: 0.7270 (tp) REVERT: W 78 ASN cc_start: 0.8886 (t0) cc_final: 0.7987 (t0) REVERT: W 86 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (pt) outliers start: 190 outliers final: 112 residues processed: 598 average time/residue: 0.3182 time to fit residues: 290.1699 Evaluate side-chains 537 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 417 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 52 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 196 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 39 GLU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 17 MET Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 37 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain J residue 24 ILE Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 42 LEU Chi-restraints excluded: chain S residue 73 TYR Chi-restraints excluded: chain S residue 78 ASN Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 122 ILE Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 165 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain W residue 92 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 2.9990 chunk 192 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 172 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 134 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN G 78 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN ** Q 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22444 Z= 0.326 Angle : 0.808 11.218 30566 Z= 0.407 Chirality : 0.052 0.268 3753 Planarity : 0.007 0.065 3918 Dihedral : 6.000 55.228 3092 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 8.26 % Allowed : 26.83 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.41 (0.16), residues: 2862 helix: 0.70 (0.15), residues: 1023 sheet: -0.88 (0.17), residues: 900 loop : -0.46 (0.22), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 112 HIS 0.005 0.001 HIS K 90 PHE 0.021 0.004 PHE O 115 TYR 0.024 0.002 TYR G 85 ARG 0.012 0.001 ARG J 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 442 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 94 ILE cc_start: 0.5547 (mm) cc_final: 0.5031 (mm) REVERT: B 69 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7070 (t0) REVERT: B 74 MET cc_start: 0.8507 (mmm) cc_final: 0.8186 (mmt) REVERT: B 90 ASP cc_start: 0.7758 (t0) cc_final: 0.7506 (t0) REVERT: B 165 ILE cc_start: 0.7589 (pt) cc_final: 0.7285 (pt) REVERT: B 199 LEU cc_start: 0.9330 (pp) cc_final: 0.8885 (tp) REVERT: C 54 LYS cc_start: 0.9011 (ttpp) cc_final: 0.8741 (ttpp) REVERT: D 24 ILE cc_start: 0.9113 (mp) cc_final: 0.8534 (tt) REVERT: E 31 LYS cc_start: 0.8644 (mttt) cc_final: 0.8170 (mmmt) REVERT: F 69 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6981 (t0) REVERT: F 90 ASP cc_start: 0.7995 (m-30) cc_final: 0.7676 (m-30) REVERT: I 35 LYS cc_start: 0.9133 (tptp) cc_final: 0.8821 (tptp) REVERT: J 19 ARG cc_start: 0.8799 (mmt180) cc_final: 0.8297 (mpp80) REVERT: J 62 MET cc_start: 0.6058 (tpp) cc_final: 0.5567 (tpp) REVERT: K 17 MET cc_start: 0.4374 (mmm) cc_final: 0.1493 (pmm) REVERT: M 52 LEU cc_start: 0.6802 (mm) cc_final: 0.6523 (mp) REVERT: R 58 ARG cc_start: 0.7877 (mmp-170) cc_final: 0.7468 (mmp80) REVERT: R 69 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7855 (t70) REVERT: R 142 LEU cc_start: 0.6570 (tp) cc_final: 0.6353 (tp) REVERT: S 21 GLU cc_start: 0.8566 (tp30) cc_final: 0.8090 (tp30) REVERT: T 69 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6806 (t0) REVERT: V 19 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7405 (mpp80) REVERT: V 53 PRO cc_start: 0.5820 (Cg_endo) cc_final: 0.5428 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6512 (mmp80) cc_final: 0.5730 (ptp-170) REVERT: V 96 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8085 (pt0) REVERT: W 78 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8558 (t0) outliers start: 194 outliers final: 123 residues processed: 568 average time/residue: 0.3340 time to fit residues: 290.2438 Evaluate side-chains 523 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 395 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 178 ILE Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain O residue 23 THR Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 77 GLU Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 46 VAL Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN K 78 ASN ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 HIS R 202 ASN S 78 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.7263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22444 Z= 0.277 Angle : 0.765 11.852 30566 Z= 0.383 Chirality : 0.050 0.260 3753 Planarity : 0.006 0.061 3918 Dihedral : 5.775 55.834 3090 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 7.07 % Allowed : 28.58 % Favored : 64.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.16), residues: 2862 helix: 0.92 (0.16), residues: 1023 sheet: -0.73 (0.17), residues: 804 loop : -0.66 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 112 HIS 0.031 0.002 HIS V 155 PHE 0.022 0.003 PHE M 115 TYR 0.021 0.002 TYR E 109 ARG 0.010 0.001 ARG L 179 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 438 time to evaluate : 3.572 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 58 GLU cc_start: 0.7244 (tt0) cc_final: 0.6767 (tm-30) REVERT: B 69 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7036 (t0) REVERT: B 74 MET cc_start: 0.8562 (mmm) cc_final: 0.8252 (mmt) REVERT: B 199 LEU cc_start: 0.9348 (pp) cc_final: 0.8859 (tp) REVERT: C 54 LYS cc_start: 0.9067 (ttpp) cc_final: 0.8686 (ttpp) REVERT: D 24 ILE cc_start: 0.9138 (mp) cc_final: 0.8501 (tt) REVERT: D 68 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8032 (tp30) REVERT: E 31 LYS cc_start: 0.8596 (mttt) cc_final: 0.8154 (mmmt) REVERT: E 67 VAL cc_start: 0.7699 (m) cc_final: 0.7467 (m) REVERT: F 69 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7086 (t0) REVERT: F 90 ASP cc_start: 0.7951 (m-30) cc_final: 0.7610 (m-30) REVERT: G 77 GLU cc_start: 0.8342 (mp0) cc_final: 0.8074 (mp0) REVERT: I 35 LYS cc_start: 0.9127 (tptp) cc_final: 0.8840 (tptp) REVERT: J 19 ARG cc_start: 0.8846 (mmt180) cc_final: 0.8398 (pmt-80) REVERT: J 32 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8183 (ttm-80) REVERT: J 62 MET cc_start: 0.6033 (tpp) cc_final: 0.5536 (tpp) REVERT: K 41 ARG cc_start: 0.8374 (mtp85) cc_final: 0.8060 (mmm-85) REVERT: R 58 ARG cc_start: 0.7760 (mmp-170) cc_final: 0.7188 (mmp80) REVERT: R 69 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7852 (t70) REVERT: S 17 MET cc_start: 0.2604 (ptm) cc_final: 0.2229 (mpp) REVERT: S 21 GLU cc_start: 0.8622 (tp30) cc_final: 0.8118 (tp30) REVERT: S 40 ASN cc_start: 0.7809 (p0) cc_final: 0.7576 (p0) REVERT: T 18 GLU cc_start: 0.7817 (mm-30) cc_final: 0.6893 (mt-10) REVERT: T 69 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6922 (t0) REVERT: U 104 ASP cc_start: 0.8639 (m-30) cc_final: 0.8415 (m-30) REVERT: V 19 ARG cc_start: 0.8129 (mtm-85) cc_final: 0.7503 (mpp80) REVERT: V 53 PRO cc_start: 0.6019 (Cg_endo) cc_final: 0.5605 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6589 (mmp80) cc_final: 0.5731 (ptp-170) REVERT: V 96 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8130 (pt0) REVERT: V 155 HIS cc_start: 0.4549 (OUTLIER) cc_final: 0.4100 (m90) REVERT: W 69 ARG cc_start: 0.8238 (ttm-80) cc_final: 0.8032 (ttm-80) REVERT: W 78 ASN cc_start: 0.9062 (OUTLIER) cc_final: 0.8380 (t0) outliers start: 166 outliers final: 113 residues processed: 548 average time/residue: 0.3310 time to fit residues: 279.1842 Evaluate side-chains 509 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 390 time to evaluate : 2.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 46 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 69 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 33 ILE Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 272 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.7705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22444 Z= 0.278 Angle : 0.764 11.615 30566 Z= 0.381 Chirality : 0.050 0.325 3753 Planarity : 0.006 0.056 3918 Dihedral : 5.756 59.374 3090 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.73 % Allowed : 29.73 % Favored : 63.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.16), residues: 2862 helix: 0.98 (0.16), residues: 1023 sheet: -0.64 (0.18), residues: 792 loop : -0.81 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 112 HIS 0.015 0.001 HIS V 155 PHE 0.022 0.003 PHE M 115 TYR 0.023 0.002 TYR G 109 ARG 0.012 0.001 ARG L 179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 431 time to evaluate : 2.611 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 58 GLU cc_start: 0.7319 (tt0) cc_final: 0.6823 (tm-30) REVERT: A 116 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8375 (mm-30) REVERT: B 74 MET cc_start: 0.8558 (mmm) cc_final: 0.8279 (mmt) REVERT: C 54 LYS cc_start: 0.9096 (ttpp) cc_final: 0.8680 (ttpp) REVERT: D 24 ILE cc_start: 0.9156 (mp) cc_final: 0.8502 (tt) REVERT: D 68 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8405 (tp30) REVERT: E 31 LYS cc_start: 0.8584 (mttt) cc_final: 0.8279 (mmmt) REVERT: F 90 ASP cc_start: 0.7996 (m-30) cc_final: 0.7653 (m-30) REVERT: F 159 ARG cc_start: 0.7976 (tpp80) cc_final: 0.7556 (tpp80) REVERT: I 35 LYS cc_start: 0.9162 (tptp) cc_final: 0.8882 (tptp) REVERT: I 85 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6283 (m-80) REVERT: J 19 ARG cc_start: 0.8970 (mmt180) cc_final: 0.8437 (pmt-80) REVERT: J 58 ARG cc_start: 0.6939 (mmp-170) cc_final: 0.6581 (mmp80) REVERT: J 62 MET cc_start: 0.6033 (tpp) cc_final: 0.5466 (tpp) REVERT: K 17 MET cc_start: 0.3730 (tpp) cc_final: 0.0402 (pmm) REVERT: K 41 ARG cc_start: 0.8368 (mtp85) cc_final: 0.7937 (tpp-160) REVERT: N 137 ASP cc_start: 0.7849 (t0) cc_final: 0.7583 (t0) REVERT: Q 116 GLU cc_start: 0.7931 (tp30) cc_final: 0.7625 (tp30) REVERT: R 58 ARG cc_start: 0.7821 (mmp-170) cc_final: 0.7263 (mmp80) REVERT: R 69 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7915 (t70) REVERT: S 17 MET cc_start: 0.2930 (OUTLIER) cc_final: 0.2618 (mpp) REVERT: S 40 ASN cc_start: 0.7921 (p0) cc_final: 0.7707 (p0) REVERT: T 18 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7025 (mt-10) REVERT: T 69 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6903 (t0) REVERT: U 104 ASP cc_start: 0.8669 (m-30) cc_final: 0.8451 (m-30) REVERT: V 19 ARG cc_start: 0.8180 (mtm-85) cc_final: 0.7590 (mpp80) REVERT: V 53 PRO cc_start: 0.6079 (Cg_endo) cc_final: 0.5681 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6641 (mmp80) cc_final: 0.5902 (ptp-170) REVERT: V 96 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8109 (pt0) REVERT: V 155 HIS cc_start: 0.4664 (OUTLIER) cc_final: 0.3627 (m90) REVERT: W 78 ASN cc_start: 0.9026 (OUTLIER) cc_final: 0.8198 (t0) outliers start: 158 outliers final: 125 residues processed: 527 average time/residue: 0.3513 time to fit residues: 286.1055 Evaluate side-chains 526 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 395 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 112 TRP Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 69 ASP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 33 ILE Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 199 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 229 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 chunk 271 optimal weight: 20.0000 chunk 170 optimal weight: 4.9990 chunk 165 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS W 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.8255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 22444 Z= 0.324 Angle : 0.803 13.410 30566 Z= 0.403 Chirality : 0.051 0.280 3753 Planarity : 0.006 0.059 3918 Dihedral : 5.798 56.213 3088 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 7.84 % Allowed : 29.39 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.48 (0.16), residues: 2862 helix: 0.78 (0.15), residues: 1035 sheet: -0.82 (0.17), residues: 804 loop : -0.86 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 112 HIS 0.036 0.002 HIS V 155 PHE 0.028 0.003 PHE M 115 TYR 0.028 0.002 TYR G 109 ARG 0.012 0.001 ARG L 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 409 time to evaluate : 2.633 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 58 GLU cc_start: 0.7421 (tt0) cc_final: 0.6870 (tm-30) REVERT: B 69 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7206 (t0) REVERT: B 74 MET cc_start: 0.8635 (mmm) cc_final: 0.8340 (mmt) REVERT: C 54 LYS cc_start: 0.9110 (ttpp) cc_final: 0.8719 (ttpp) REVERT: D 24 ILE cc_start: 0.9188 (mp) cc_final: 0.8582 (tt) REVERT: D 68 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8231 (tp30) REVERT: D 112 GLU cc_start: 0.3335 (pm20) cc_final: 0.2968 (pm20) REVERT: E 31 LYS cc_start: 0.8580 (mttt) cc_final: 0.8239 (mmmt) REVERT: F 90 ASP cc_start: 0.8020 (m-30) cc_final: 0.7628 (m-30) REVERT: F 159 ARG cc_start: 0.8030 (tpp80) cc_final: 0.7806 (tpp80) REVERT: I 35 LYS cc_start: 0.9235 (tptp) cc_final: 0.9017 (tptp) REVERT: J 19 ARG cc_start: 0.9105 (mmt180) cc_final: 0.8440 (ppt170) REVERT: J 32 ARG cc_start: 0.8733 (mtt-85) cc_final: 0.8252 (ttm-80) REVERT: J 35 LYS cc_start: 0.9349 (tppt) cc_final: 0.9107 (tppt) REVERT: J 58 ARG cc_start: 0.7012 (mmp-170) cc_final: 0.6681 (mmp80) REVERT: J 62 MET cc_start: 0.5993 (OUTLIER) cc_final: 0.5287 (tpp) REVERT: K 17 MET cc_start: 0.4026 (tpp) cc_final: 0.0879 (pmm) REVERT: K 37 LEU cc_start: 0.8832 (tp) cc_final: 0.8512 (mm) REVERT: K 41 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7945 (ptm-80) REVERT: M 116 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8087 (tp30) REVERT: N 74 MET cc_start: 0.9374 (mmt) cc_final: 0.9051 (mmt) REVERT: Q 116 GLU cc_start: 0.7992 (tp30) cc_final: 0.7728 (tp30) REVERT: R 42 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8757 (mmmt) REVERT: R 58 ARG cc_start: 0.7903 (mmp-170) cc_final: 0.7328 (mmp80) REVERT: R 72 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8355 (pttp) REVERT: S 40 ASN cc_start: 0.7816 (p0) cc_final: 0.7533 (p0) REVERT: S 42 LEU cc_start: 0.8532 (mt) cc_final: 0.8231 (mt) REVERT: T 18 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7309 (mt-10) REVERT: T 69 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.7012 (t0) REVERT: V 19 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.7751 (mpp80) REVERT: V 53 PRO cc_start: 0.6321 (Cg_endo) cc_final: 0.5926 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6837 (mmp80) cc_final: 0.6072 (ptp-170) REVERT: V 62 MET cc_start: 0.8579 (ttm) cc_final: 0.8272 (ttp) REVERT: V 96 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7726 (pm20) REVERT: V 155 HIS cc_start: 0.4574 (OUTLIER) cc_final: 0.3600 (m90) REVERT: W 78 ASN cc_start: 0.9017 (OUTLIER) cc_final: 0.8304 (t0) outliers start: 184 outliers final: 132 residues processed: 533 average time/residue: 0.3275 time to fit residues: 267.9702 Evaluate side-chains 525 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 388 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 69 ASP Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 202 ASN Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 29 SER Chi-restraints excluded: chain J residue 62 MET Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain N residue 189 LEU Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 112 TRP Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain T residue 196 VAL Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 26 GLU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 122 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain V residue 202 ASN Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 33 ILE Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.8539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22444 Z= 0.280 Angle : 0.776 10.968 30566 Z= 0.386 Chirality : 0.050 0.349 3753 Planarity : 0.006 0.058 3918 Dihedral : 5.703 57.886 3088 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 6.86 % Allowed : 31.05 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.40 (0.16), residues: 2862 helix: 0.96 (0.16), residues: 1035 sheet: -0.74 (0.18), residues: 792 loop : -0.99 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 112 HIS 0.027 0.002 HIS V 155 PHE 0.040 0.004 PHE U 115 TYR 0.026 0.002 TYR G 109 ARG 0.012 0.001 ARG L 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 426 time to evaluate : 2.650 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 41 ARG cc_start: 0.7504 (mmm160) cc_final: 0.7059 (mmm-85) REVERT: B 74 MET cc_start: 0.8620 (mmm) cc_final: 0.8348 (mmt) REVERT: C 54 LYS cc_start: 0.9152 (ttpp) cc_final: 0.8782 (ttpp) REVERT: D 24 ILE cc_start: 0.9232 (mp) cc_final: 0.8607 (tt) REVERT: D 68 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8237 (tp30) REVERT: E 31 LYS cc_start: 0.8580 (mttt) cc_final: 0.8265 (mmmt) REVERT: F 90 ASP cc_start: 0.8001 (m-30) cc_final: 0.7642 (m-30) REVERT: F 159 ARG cc_start: 0.8026 (tpp80) cc_final: 0.7806 (tpp80) REVERT: G 17 MET cc_start: 0.4529 (tpt) cc_final: 0.4304 (tpt) REVERT: I 35 LYS cc_start: 0.9174 (tptp) cc_final: 0.8888 (tptp) REVERT: I 85 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6302 (m-80) REVERT: J 19 ARG cc_start: 0.9129 (mmt180) cc_final: 0.8468 (ppt170) REVERT: J 32 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.8180 (ttm-80) REVERT: J 58 ARG cc_start: 0.7044 (mmp-170) cc_final: 0.6722 (mmp80) REVERT: J 62 MET cc_start: 0.6003 (tpp) cc_final: 0.5353 (tpp) REVERT: J 137 ASP cc_start: 0.8496 (t0) cc_final: 0.8235 (t0) REVERT: K 17 MET cc_start: 0.3980 (tpp) cc_final: 0.1145 (pmm) REVERT: K 41 ARG cc_start: 0.8364 (mtp85) cc_final: 0.7924 (ptm-80) REVERT: L 74 MET cc_start: 0.9193 (mmp) cc_final: 0.8988 (mmt) REVERT: N 74 MET cc_start: 0.9367 (mmt) cc_final: 0.9046 (mmt) REVERT: N 79 ASP cc_start: 0.9272 (t0) cc_final: 0.8962 (t0) REVERT: Q 116 GLU cc_start: 0.7965 (tp30) cc_final: 0.7749 (tp30) REVERT: R 58 ARG cc_start: 0.7980 (mmp-170) cc_final: 0.7481 (mmp80) REVERT: R 72 LYS cc_start: 0.8670 (ptmt) cc_final: 0.8333 (pttp) REVERT: S 17 MET cc_start: 0.2538 (tpp) cc_final: 0.2101 (mmm) REVERT: S 40 ASN cc_start: 0.7808 (p0) cc_final: 0.7495 (p0) REVERT: S 42 LEU cc_start: 0.8592 (mt) cc_final: 0.8263 (mt) REVERT: T 18 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7424 (mt-10) REVERT: T 69 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7055 (t0) REVERT: V 19 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7712 (mpp80) REVERT: V 53 PRO cc_start: 0.6524 (Cg_endo) cc_final: 0.6141 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6879 (mmp80) cc_final: 0.6111 (ptp-170) REVERT: V 62 MET cc_start: 0.8611 (ttm) cc_final: 0.8387 (ttm) REVERT: V 96 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7738 (pm20) REVERT: V 155 HIS cc_start: 0.4904 (OUTLIER) cc_final: 0.3842 (m90) REVERT: W 78 ASN cc_start: 0.9032 (OUTLIER) cc_final: 0.8753 (m-40) outliers start: 161 outliers final: 126 residues processed: 533 average time/residue: 0.3248 time to fit residues: 265.7443 Evaluate side-chains 527 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 397 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 66 GLU Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain M residue 86 ILE Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 78 LEU Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain O residue 113 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 43 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 122 ILE Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 98 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 137 ASP Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 20 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 48 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 97 ILE Chi-restraints excluded: chain V residue 129 VAL Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 186 LEU Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 33 ILE Chi-restraints excluded: chain W residue 37 LEU Chi-restraints excluded: chain W residue 78 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 237 optimal weight: 0.8980 chunk 253 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 198 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 239 optimal weight: 0.7980 chunk 252 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN L 155 HIS ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS V 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.8600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22444 Z= 0.219 Angle : 0.759 11.507 30566 Z= 0.372 Chirality : 0.049 0.336 3753 Planarity : 0.006 0.054 3918 Dihedral : 5.414 58.530 3088 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 4.73 % Allowed : 33.39 % Favored : 61.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.20 (0.16), residues: 2862 helix: 1.21 (0.16), residues: 1035 sheet: -0.64 (0.18), residues: 792 loop : -0.98 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 112 HIS 0.021 0.001 HIS V 155 PHE 0.039 0.003 PHE U 115 TYR 0.022 0.001 TYR G 109 ARG 0.014 0.001 ARG L 179 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 443 time to evaluate : 2.508 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ARG B 32 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 58 ARG cc_start: 0.8081 (mmp80) cc_final: 0.7502 (mmm-85) REVERT: B 116 ASP cc_start: 0.8081 (t0) cc_final: 0.7519 (p0) REVERT: C 54 LYS cc_start: 0.9156 (ttpp) cc_final: 0.8732 (ttpp) REVERT: D 24 ILE cc_start: 0.9123 (mp) cc_final: 0.8513 (tt) REVERT: D 112 GLU cc_start: 0.3498 (pm20) cc_final: 0.3264 (pm20) REVERT: D 115 LYS cc_start: 0.8412 (tmtt) cc_final: 0.7791 (mmtt) REVERT: E 31 LYS cc_start: 0.8552 (mttt) cc_final: 0.8275 (mmmt) REVERT: F 19 ARG cc_start: 0.7883 (mmt180) cc_final: 0.7598 (mmt180) REVERT: F 90 ASP cc_start: 0.7886 (m-30) cc_final: 0.7530 (m-30) REVERT: I 35 LYS cc_start: 0.9156 (tptp) cc_final: 0.8903 (tptp) REVERT: I 85 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: J 19 ARG cc_start: 0.9122 (mmt180) cc_final: 0.8487 (ppt170) REVERT: J 58 ARG cc_start: 0.7012 (mmp-170) cc_final: 0.6692 (mmp80) REVERT: J 62 MET cc_start: 0.5990 (tpp) cc_final: 0.5358 (tpp) REVERT: J 63 LEU cc_start: 0.8216 (pt) cc_final: 0.7941 (pp) REVERT: K 17 MET cc_start: 0.3802 (tpp) cc_final: 0.1624 (pmm) REVERT: K 41 ARG cc_start: 0.8302 (mtp85) cc_final: 0.7923 (ptm-80) REVERT: L 58 ARG cc_start: 0.7160 (ptm160) cc_final: 0.6891 (ptp-170) REVERT: L 74 MET cc_start: 0.9197 (mmp) cc_final: 0.8925 (mmt) REVERT: M 116 GLU cc_start: 0.8504 (tp30) cc_final: 0.7857 (tp30) REVERT: N 74 MET cc_start: 0.9358 (mmt) cc_final: 0.9048 (mmt) REVERT: N 79 ASP cc_start: 0.9226 (t0) cc_final: 0.8915 (t0) REVERT: O 109 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.5179 (t80) REVERT: R 72 LYS cc_start: 0.8638 (ptmt) cc_final: 0.8249 (pttp) REVERT: S 17 MET cc_start: 0.2912 (tpp) cc_final: 0.2334 (mmm) REVERT: S 40 ASN cc_start: 0.7682 (p0) cc_final: 0.7328 (p0) REVERT: S 42 LEU cc_start: 0.8622 (mt) cc_final: 0.8351 (mt) REVERT: T 18 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7478 (mt-10) REVERT: T 69 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6949 (t0) REVERT: V 19 ARG cc_start: 0.8234 (mtm-85) cc_final: 0.7463 (mpp80) REVERT: V 53 PRO cc_start: 0.6419 (Cg_endo) cc_final: 0.6025 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6857 (mmp80) cc_final: 0.6065 (ptp-170) REVERT: V 62 MET cc_start: 0.8630 (ttm) cc_final: 0.8420 (ttm) REVERT: V 68 GLU cc_start: 0.9266 (OUTLIER) cc_final: 0.8982 (mm-30) REVERT: V 155 HIS cc_start: 0.4410 (OUTLIER) cc_final: 0.3507 (m90) REVERT: V 159 ARG cc_start: 0.7577 (tpp80) cc_final: 0.7277 (tpp80) outliers start: 111 outliers final: 83 residues processed: 520 average time/residue: 0.3238 time to fit residues: 260.0417 Evaluate side-chains 495 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 407 time to evaluate : 2.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 123 VAL Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 33 ILE Chi-restraints excluded: chain W residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 4.9990 chunk 267 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 280 optimal weight: 5.9990 chunk 258 optimal weight: 8.9990 chunk 223 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 137 optimal weight: 0.6980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.8778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22444 Z= 0.242 Angle : 0.779 11.373 30566 Z= 0.381 Chirality : 0.050 0.391 3753 Planarity : 0.006 0.072 3918 Dihedral : 5.388 58.738 3088 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 4.51 % Allowed : 34.16 % Favored : 61.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.16), residues: 2862 helix: 1.19 (0.16), residues: 1035 sheet: -0.62 (0.18), residues: 792 loop : -0.99 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 112 HIS 0.010 0.001 HIS V 155 PHE 0.029 0.003 PHE O 115 TYR 0.020 0.001 TYR G 109 ARG 0.014 0.001 ARG L 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5724 Ramachandran restraints generated. 2862 Oldfield, 0 Emsley, 2862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 414 time to evaluate : 2.724 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: B 62 MET cc_start: 0.8585 (tpp) cc_final: 0.8223 (mmm) REVERT: C 54 LYS cc_start: 0.9202 (ttpp) cc_final: 0.8836 (ttpp) REVERT: D 24 ILE cc_start: 0.9070 (mp) cc_final: 0.8509 (tt) REVERT: D 112 GLU cc_start: 0.3650 (pm20) cc_final: 0.3380 (pm20) REVERT: D 115 LYS cc_start: 0.8481 (tmtt) cc_final: 0.7830 (mmtt) REVERT: E 31 LYS cc_start: 0.8625 (mttt) cc_final: 0.8339 (mmmt) REVERT: F 19 ARG cc_start: 0.8057 (mmt180) cc_final: 0.7529 (mtt-85) REVERT: F 90 ASP cc_start: 0.7884 (m-30) cc_final: 0.7518 (m-30) REVERT: I 85 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6193 (m-80) REVERT: J 19 ARG cc_start: 0.9144 (mmt180) cc_final: 0.8437 (ppt170) REVERT: J 32 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.7613 (ttm170) REVERT: J 62 MET cc_start: 0.5908 (tpp) cc_final: 0.5226 (tpp) REVERT: J 63 LEU cc_start: 0.8236 (pt) cc_final: 0.7988 (pp) REVERT: J 102 LEU cc_start: 0.8506 (mp) cc_final: 0.7715 (tt) REVERT: K 17 MET cc_start: 0.4164 (tpp) cc_final: 0.1480 (pmm) REVERT: K 41 ARG cc_start: 0.8298 (mtp85) cc_final: 0.7963 (ptm-80) REVERT: L 74 MET cc_start: 0.9234 (mmp) cc_final: 0.8974 (mmt) REVERT: M 36 LYS cc_start: 0.8873 (mmtm) cc_final: 0.8168 (tptp) REVERT: N 74 MET cc_start: 0.9357 (mmt) cc_final: 0.9014 (mmt) REVERT: N 79 ASP cc_start: 0.9216 (t0) cc_final: 0.8927 (t0) REVERT: O 109 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.5363 (t80) REVERT: S 17 MET cc_start: 0.2914 (tpp) cc_final: 0.1019 (mtp) REVERT: S 40 ASN cc_start: 0.7741 (p0) cc_final: 0.7375 (p0) REVERT: S 42 LEU cc_start: 0.8677 (mt) cc_final: 0.8386 (mt) REVERT: T 18 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7516 (mt-10) REVERT: T 69 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6967 (t0) REVERT: V 27 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.7140 (mm) REVERT: V 53 PRO cc_start: 0.6602 (Cg_endo) cc_final: 0.6240 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6939 (mmp80) cc_final: 0.6112 (ptp-170) REVERT: V 62 MET cc_start: 0.8657 (ttm) cc_final: 0.8427 (ttm) REVERT: V 68 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8971 (mm-30) REVERT: V 74 MET cc_start: 0.9344 (mmm) cc_final: 0.9099 (mmp) REVERT: V 155 HIS cc_start: 0.4243 (OUTLIER) cc_final: 0.3303 (m90) REVERT: V 159 ARG cc_start: 0.7588 (tpp80) cc_final: 0.7362 (tpp80) outliers start: 106 outliers final: 91 residues processed: 488 average time/residue: 0.3228 time to fit residues: 244.5737 Evaluate side-chains 498 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 401 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 24 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain C residue 17 MET Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 144 ASN Chi-restraints excluded: chain F residue 189 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 125 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain N residue 46 VAL Chi-restraints excluded: chain N residue 122 ILE Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain N residue 178 ILE Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain Q residue 23 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 39 GLU Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain R residue 137 ASP Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain S residue 48 ILE Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 69 ASP Chi-restraints excluded: chain T residue 78 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 127 SER Chi-restraints excluded: chain T residue 142 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 27 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 54 VAL Chi-restraints excluded: chain V residue 68 GLU Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 142 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 156 ILE Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 31 LYS Chi-restraints excluded: chain W residue 33 ILE Chi-restraints excluded: chain W residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 9.9990 chunk 238 optimal weight: 0.2980 chunk 68 optimal weight: 8.9990 chunk 206 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 230 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 20.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.120795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.098346 restraints weight = 80395.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.101124 restraints weight = 53449.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.103199 restraints weight = 39715.882| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.8907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22444 Z= 0.233 Angle : 0.777 11.364 30566 Z= 0.379 Chirality : 0.050 0.362 3753 Planarity : 0.006 0.068 3918 Dihedral : 5.317 59.757 3088 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.60 % Allowed : 33.99 % Favored : 61.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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 (0.16), residues: 2862 helix: 1.19 (0.16), residues: 1035 sheet: -0.62 (0.18), residues: 792 loop : -0.99 (0.20), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 112 HIS 0.030 0.002 HIS V 155 PHE 0.020 0.003 PHE O 115 TYR 0.022 0.001 TYR G 109 ARG 0.015 0.001 ARG L 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5631.20 seconds wall clock time: 106 minutes 11.14 seconds (6371.14 seconds total)