Starting phenix.real_space_refine on Thu Apr 11 08:58:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/04_2024/8un1_42390.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/04_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_42390/04_2024/8un1_42390.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/04_2024/8un1_42390.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/04_2024/8un1_42390.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8un1_42390/04_2024/8un1_42390.pdb" } 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-5288/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: 11.61, per 1000 atoms: 0.53 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: 8.58 Conformation dependent library (CDL) restraints added in 4.2 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: 2.30 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: 6.68 Time building geometry restraints manager: 9.35 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 2.520 nonbonded pdb=" OG SER V 85 " pdb=" OD1 ASN V 87 " model vdw 2.140 2.440 nonbonded pdb=" OG SER T 85 " pdb=" OD1 ASN T 87 " model vdw 2.140 2.440 nonbonded pdb=" OG SER R 85 " pdb=" OD1 ASN R 87 " model vdw 2.140 2.440 nonbonded pdb=" OG SER N 85 " pdb=" OD1 ASN N 87 " model vdw 2.141 2.440 ... (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 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: 0.880 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: 0.010 Extract box with map and model: 4.240 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 56.610 Find NCS groups from input model: 1.660 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: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.740 ------------------------------------------------------------------------------- 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 : 2.472 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: 0.4036 time to fit residues: 581.2924 Evaluate side-chains 542 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 538 time to evaluate : 2.473 ------------------------------------------------------------------------------- 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: 5.9990 chunk 73 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 221 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 256 optimal weight: 30.0000 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 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 78 ASN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN R 202 ASN ** S 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS ** W 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 22444 Z= 0.366 Angle : 0.902 9.962 30566 Z= 0.456 Chirality : 0.054 0.324 3753 Planarity : 0.007 0.081 3918 Dihedral : 6.000 59.837 3094 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 8.48 % Allowed : 26.28 % Favored : 65.25 % 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: -0.51 (0.16), residues: 2862 helix: 0.61 (0.15), residues: 1023 sheet: -0.96 (0.17), residues: 909 loop : -0.46 (0.22), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP O 112 HIS 0.007 0.002 HIS F 98 PHE 0.024 0.004 PHE O 115 TYR 0.036 0.003 TYR Q 109 ARG 0.010 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 758 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 559 time to evaluate : 2.613 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: A 58 GLU cc_start: 0.7277 (tt0) cc_final: 0.6769 (tm-30) REVERT: A 94 ILE cc_start: 0.5497 (mm) cc_final: 0.4984 (mm) REVERT: B 69 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6897 (t0) REVERT: B 199 LEU cc_start: 0.9199 (pp) cc_final: 0.8825 (tp) REVERT: C 55 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8930 (tp) REVERT: D 24 ILE cc_start: 0.9012 (mp) cc_final: 0.8173 (tt) REVERT: D 68 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8149 (tp30) REVERT: D 90 ASP cc_start: 0.7592 (t0) cc_final: 0.7026 (t0) REVERT: D 188 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7357 (p0) REVERT: E 41 ARG cc_start: 0.7827 (tpt-90) cc_final: 0.7572 (tpt-90) REVERT: F 69 ASP cc_start: 0.6617 (OUTLIER) cc_final: 0.6186 (t0) REVERT: G 75 GLU cc_start: 0.6004 (pm20) cc_final: 0.5507 (pm20) REVERT: I 21 GLU cc_start: 0.7860 (tp30) cc_final: 0.7331 (tp30) REVERT: I 42 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6903 (tp) REVERT: I 92 ASP cc_start: 0.7845 (m-30) cc_final: 0.6813 (t70) REVERT: J 24 ILE cc_start: 0.5869 (OUTLIER) cc_final: 0.5581 (tt) REVERT: J 62 MET cc_start: 0.5998 (tpp) cc_final: 0.5406 (tpp) REVERT: J 168 LYS cc_start: 0.8417 (mppt) cc_final: 0.8143 (mmmt) REVERT: K 41 ARG cc_start: 0.8199 (mtp85) cc_final: 0.7773 (ptm-80) REVERT: K 77 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8403 (tp30) REVERT: K 78 ASN cc_start: 0.8168 (m-40) cc_final: 0.7953 (m-40) REVERT: M 33 ILE cc_start: 0.8963 (mt) cc_final: 0.8753 (mm) REVERT: R 58 ARG cc_start: 0.7823 (mmp-170) cc_final: 0.7373 (mmp80) REVERT: R 69 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7795 (t70) REVERT: S 40 ASN cc_start: 0.8144 (p0) cc_final: 0.7594 (p0) REVERT: S 42 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7538 (mt) REVERT: T 62 MET cc_start: 0.7647 (tpp) cc_final: 0.7104 (tpp) REVERT: T 69 ASP cc_start: 0.6848 (OUTLIER) cc_final: 0.6418 (t0) REVERT: V 19 ARG cc_start: 0.7959 (mtm-85) cc_final: 0.7384 (mpt-90) REVERT: V 53 PRO cc_start: 0.5547 (Cg_endo) cc_final: 0.5190 (Cg_exo) REVERT: V 60 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7236 (tp) REVERT: V 96 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7966 (pt0) REVERT: V 199 LEU cc_start: 0.7802 (pp) cc_final: 0.7214 (tp) REVERT: W 33 ILE cc_start: 0.7763 (mm) cc_final: 0.7490 (mm) REVERT: W 78 ASN cc_start: 0.8854 (t0) cc_final: 0.8395 (t0) outliers start: 199 outliers final: 106 residues processed: 691 average time/residue: 0.3527 time to fit residues: 368.5205 Evaluate side-chains 563 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 447 time to evaluate : 2.614 ------------------------------------------------------------------------------- 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 92 ASP 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 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 24 THR Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 100 ILE 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 122 ILE Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 188 ASP 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 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 87 ASN 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 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 33 ILE 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 170 ASP Chi-restraints excluded: chain J residue 196 VAL 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 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 M residue 99 VAL 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 20 ILE Chi-restraints excluded: chain O residue 99 VAL Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 55 ILE 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 72 LYS Chi-restraints excluded: chain R residue 80 VAL Chi-restraints excluded: chain R residue 89 ILE Chi-restraints excluded: chain R residue 161 SER 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 71 THR 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 127 SER 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 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 122 ILE Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 155 HIS Chi-restraints excluded: chain V residue 196 VAL Chi-restraints excluded: chain W residue 23 THR Chi-restraints excluded: chain W residue 71 THR 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: 4.9990 chunk 79 optimal weight: 7.9990 chunk 213 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 277 optimal weight: 7.9990 chunk 228 optimal weight: 9.9990 chunk 254 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 205 optimal weight: 8.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 HIS ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN ** S 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22444 Z= 0.237 Angle : 0.763 11.461 30566 Z= 0.378 Chirality : 0.050 0.333 3753 Planarity : 0.006 0.057 3918 Dihedral : 5.582 56.773 3094 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 6.73 % Allowed : 27.81 % Favored : 65.46 % 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: -0.14 (0.16), residues: 2862 helix: 0.95 (0.16), residues: 1023 sheet: -0.71 (0.17), residues: 900 loop : -0.36 (0.22), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 112 HIS 0.026 0.002 HIS V 155 PHE 0.029 0.003 PHE E 115 TYR 0.024 0.002 TYR I 109 ARG 0.005 0.001 ARG L 179 *********************** 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 644 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 486 time to evaluate : 2.341 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: A 94 ILE cc_start: 0.5242 (mm) cc_final: 0.4707 (mm) REVERT: B 24 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6628 (mt) REVERT: B 69 ASP cc_start: 0.7287 (OUTLIER) cc_final: 0.6853 (t0) REVERT: B 74 MET cc_start: 0.8531 (mmm) cc_final: 0.8147 (mmt) REVERT: B 199 LEU cc_start: 0.9203 (pp) cc_final: 0.8868 (tp) REVERT: C 49 THR cc_start: 0.7876 (t) cc_final: 0.7590 (p) REVERT: D 24 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8304 (tt) REVERT: D 26 GLU cc_start: 0.6646 (mp0) cc_final: 0.6349 (mp0) REVERT: D 68 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8216 (tp30) REVERT: D 90 ASP cc_start: 0.7438 (t0) cc_final: 0.6877 (t0) REVERT: D 188 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6671 (p0) REVERT: E 31 LYS cc_start: 0.8628 (mttt) cc_final: 0.8069 (mmmt) REVERT: E 76 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8093 (mm-30) REVERT: E 78 ASN cc_start: 0.8087 (m-40) cc_final: 0.7856 (m-40) REVERT: E 81 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8324 (tppt) REVERT: F 69 ASP cc_start: 0.6664 (OUTLIER) cc_final: 0.6233 (t70) REVERT: G 47 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7843 (mt) REVERT: G 75 GLU cc_start: 0.5966 (pm20) cc_final: 0.5667 (pm20) REVERT: J 24 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5994 (tt) REVERT: J 62 MET cc_start: 0.5944 (tpp) cc_final: 0.5431 (tpp) REVERT: K 41 ARG cc_start: 0.8222 (mtp85) cc_final: 0.7870 (ptm-80) REVERT: L 58 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6820 (mtp180) REVERT: M 29 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8677 (tm-30) REVERT: M 33 ILE cc_start: 0.9045 (mt) cc_final: 0.8264 (mm) REVERT: N 93 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.6150 (pt) REVERT: O 28 GLU cc_start: 0.8235 (pm20) cc_final: 0.7904 (pm20) REVERT: R 58 ARG cc_start: 0.7786 (mmp-170) cc_final: 0.7343 (mmp80) REVERT: R 69 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7708 (t70) REVERT: R 90 ASP cc_start: 0.8274 (t0) cc_final: 0.8033 (t0) REVERT: R 140 LEU cc_start: 0.8060 (tp) cc_final: 0.7819 (tp) REVERT: S 21 GLU cc_start: 0.8617 (tp30) cc_final: 0.8095 (tp30) REVERT: T 69 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6573 (t0) REVERT: U 115 PHE cc_start: 0.5414 (t80) cc_final: 0.5202 (t80) REVERT: V 19 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7426 (mpp80) REVERT: V 53 PRO cc_start: 0.5626 (Cg_endo) cc_final: 0.5258 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6112 (mmp80) cc_final: 0.5304 (mtt180) REVERT: V 96 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7420 (pm20) REVERT: V 199 LEU cc_start: 0.7733 (pp) cc_final: 0.7210 (tp) REVERT: W 78 ASN cc_start: 0.8965 (t0) cc_final: 0.8408 (t0) outliers start: 158 outliers final: 89 residues processed: 588 average time/residue: 0.3537 time to fit residues: 314.5671 Evaluate side-chains 531 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 430 time to evaluate : 2.587 ------------------------------------------------------------------------------- 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 92 ASP 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 196 VAL Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 52 GLU 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 140 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 188 ASP 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 81 LYS 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 69 ASP Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 87 ASN 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 47 ILE Chi-restraints excluded: chain G residue 70 VAL 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 33 ILE Chi-restraints excluded: chain I residue 40 ASN 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 33 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 187 LEU 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 93 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 26 THR Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 68 THR 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 189 LEU Chi-restraints excluded: chain R residue 196 VAL Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 71 THR Chi-restraints excluded: chain S residue 73 TYR 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 122 ILE 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 52 LEU Chi-restraints excluded: chain V residue 38 ASP Chi-restraints excluded: chain V residue 61 ILE Chi-restraints excluded: chain V residue 93 LEU Chi-restraints excluded: chain V residue 129 VAL 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 37 LEU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 117 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 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: 3.9990 chunk 272 optimal weight: 30.0000 chunk 134 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 202 ASN S 78 ASN ** S 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 ASN ** 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: 0.7279 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22444 Z= 0.318 Angle : 0.803 10.822 30566 Z= 0.407 Chirality : 0.052 0.317 3753 Planarity : 0.007 0.064 3918 Dihedral : 5.604 51.409 3090 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 8.01 % Allowed : 26.83 % Favored : 65.16 % 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: -0.30 (0.16), residues: 2862 helix: 0.80 (0.16), residues: 1023 sheet: -0.81 (0.17), residues: 900 loop : -0.42 (0.22), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 112 HIS 0.016 0.002 HIS V 155 PHE 0.023 0.003 PHE O 115 TYR 0.031 0.002 TYR I 109 ARG 0.012 0.001 ARG L 179 *********************** 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 641 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 453 time to evaluate : 2.661 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7044 (t0) REVERT: B 74 MET cc_start: 0.8538 (mmm) cc_final: 0.8160 (mmt) REVERT: B 199 LEU cc_start: 0.9301 (pp) cc_final: 0.8863 (tp) REVERT: D 24 ILE cc_start: 0.9194 (mp) cc_final: 0.8453 (tt) REVERT: D 52 GLU cc_start: 0.5025 (OUTLIER) cc_final: 0.4789 (pm20) REVERT: D 69 ASP cc_start: 0.7590 (m-30) cc_final: 0.7351 (m-30) REVERT: E 31 LYS cc_start: 0.8613 (mttt) cc_final: 0.8145 (mmmt) REVERT: E 81 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8373 (tppt) REVERT: F 69 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.6869 (t0) REVERT: F 74 MET cc_start: 0.8901 (mmt) cc_final: 0.8636 (mmp) REVERT: F 90 ASP cc_start: 0.7686 (m-30) cc_final: 0.7408 (m-30) REVERT: F 159 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7104 (tpp-160) REVERT: I 35 LYS cc_start: 0.9161 (tptp) cc_final: 0.8912 (tptp) REVERT: I 85 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.6379 (m-80) REVERT: J 19 ARG cc_start: 0.8868 (mmt180) cc_final: 0.8543 (mpt-90) REVERT: J 62 MET cc_start: 0.6140 (tpp) cc_final: 0.5605 (tpp) REVERT: J 142 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7301 (mm) REVERT: K 41 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7875 (ptm-80) REVERT: K 102 PRO cc_start: 0.6673 (Cg_endo) cc_final: 0.6287 (Cg_exo) REVERT: M 33 ILE cc_start: 0.9073 (mt) cc_final: 0.8803 (mm) REVERT: M 41 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7508 (tpp80) REVERT: M 87 LYS cc_start: 0.9024 (tppt) cc_final: 0.8682 (tttm) REVERT: N 159 ARG cc_start: 0.6063 (mmm160) cc_final: 0.5770 (mmm160) REVERT: O 28 GLU cc_start: 0.8361 (pm20) cc_final: 0.7828 (pm20) REVERT: R 58 ARG cc_start: 0.7830 (mmp-170) cc_final: 0.7432 (mmp80) REVERT: R 69 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7859 (t70) REVERT: R 90 ASP cc_start: 0.8512 (t0) cc_final: 0.8235 (t0) REVERT: R 142 LEU cc_start: 0.6607 (tp) cc_final: 0.6400 (tp) REVERT: S 40 ASN cc_start: 0.7866 (p0) cc_final: 0.7623 (p0) REVERT: T 69 ASP cc_start: 0.7229 (OUTLIER) cc_final: 0.6777 (t0) REVERT: V 19 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7653 (mpp80) REVERT: V 53 PRO cc_start: 0.6025 (Cg_endo) cc_final: 0.5634 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6516 (mmp80) cc_final: 0.6280 (mmp80) REVERT: V 96 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7837 (pm20) REVERT: V 155 HIS cc_start: 0.4559 (OUTLIER) cc_final: 0.3852 (m90) outliers start: 188 outliers final: 116 residues processed: 581 average time/residue: 0.3583 time to fit residues: 315.5239 Evaluate side-chains 532 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 406 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP 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 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 24 THR Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain C residue 99 VAL 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 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 23 THR 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 81 LYS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 109 TYR Chi-restraints excluded: chain F residue 29 SER 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 87 ASN 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 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 142 LEU Chi-restraints excluded: chain J residue 156 ILE Chi-restraints excluded: chain J residue 170 ASP Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain K residue 33 ILE 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 102 LEU Chi-restraints excluded: chain L residue 129 VAL 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 20 ILE Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 41 ARG Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 52 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 178 ILE Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 71 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 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 16 ASP 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 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 71 THR 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 127 SER 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 47 ILE Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 71 THR Chi-restraints excluded: chain U residue 100 ILE Chi-restraints excluded: chain V residue 38 ASP 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 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 37 LEU Chi-restraints excluded: chain W residue 84 THR Chi-restraints excluded: chain W residue 92 ASP Chi-restraints excluded: chain W residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 9.9990 chunk 154 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 202 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 232 optimal weight: 0.1980 chunk 188 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 59 ASN ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** 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** ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS W 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22444 Z= 0.268 Angle : 0.740 11.404 30566 Z= 0.372 Chirality : 0.050 0.273 3753 Planarity : 0.006 0.058 3918 Dihedral : 5.450 51.865 3090 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 7.67 % Allowed : 27.85 % Favored : 64.48 % 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: -0.14 (0.16), residues: 2862 helix: 0.98 (0.16), residues: 1023 sheet: -0.61 (0.18), residues: 843 loop : -0.56 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 112 HIS 0.024 0.002 HIS V 155 PHE 0.032 0.003 PHE E 115 TYR 0.021 0.002 TYR U 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 630 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 450 time to evaluate : 2.609 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: symmetry clash revert: symmetry clash REVERT: B 69 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7021 (t0) REVERT: B 74 MET cc_start: 0.8612 (mmm) cc_final: 0.8186 (mmt) REVERT: B 199 LEU cc_start: 0.9337 (pp) cc_final: 0.8906 (tp) REVERT: D 24 ILE cc_start: 0.9215 (mp) cc_final: 0.8489 (tt) REVERT: D 68 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8123 (tp30) REVERT: D 69 ASP cc_start: 0.7816 (m-30) cc_final: 0.7561 (m-30) REVERT: E 31 LYS cc_start: 0.8567 (mttt) cc_final: 0.8133 (mmmt) REVERT: F 69 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.7005 (t0) REVERT: F 74 MET cc_start: 0.8821 (mmt) cc_final: 0.8609 (mmp) REVERT: F 90 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: I 35 LYS cc_start: 0.9162 (tptp) cc_final: 0.8961 (tptp) REVERT: I 85 TYR cc_start: 0.7378 (OUTLIER) cc_final: 0.6444 (m-80) REVERT: J 19 ARG cc_start: 0.8933 (mmt180) cc_final: 0.8447 (pmt-80) REVERT: J 62 MET cc_start: 0.6176 (tpp) cc_final: 0.5565 (tpp) REVERT: J 170 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.4025 (t0) REVERT: K 17 MET cc_start: 0.3913 (tpp) cc_final: 0.0449 (pmm) REVERT: K 41 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7993 (ptm-80) REVERT: K 42 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8409 (mm) REVERT: K 45 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7795 (mt-10) REVERT: M 52 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6240 (mp) REVERT: N 137 ASP cc_start: 0.7920 (t0) cc_final: 0.7359 (t0) REVERT: N 159 ARG cc_start: 0.6426 (mmm160) cc_final: 0.6082 (mmm160) REVERT: O 17 MET cc_start: 0.4325 (mmt) cc_final: 0.3916 (mmt) REVERT: O 28 GLU cc_start: 0.8469 (pm20) cc_final: 0.7913 (pm20) REVERT: R 58 ARG cc_start: 0.7874 (mmp-170) cc_final: 0.7439 (mmp80) REVERT: R 69 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7870 (t70) REVERT: S 21 GLU cc_start: 0.8622 (tp30) cc_final: 0.8093 (tp30) REVERT: S 40 ASN cc_start: 0.7820 (p0) cc_final: 0.7600 (p0) REVERT: T 69 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6843 (t0) REVERT: U 54 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8722 (mmmt) REVERT: V 19 ARG cc_start: 0.8278 (mtm-85) cc_final: 0.7675 (mpp80) REVERT: V 53 PRO cc_start: 0.6071 (Cg_endo) cc_final: 0.5698 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6565 (mmp80) cc_final: 0.5674 (ptp90) REVERT: V 62 MET cc_start: 0.8337 (ttm) cc_final: 0.8110 (ttm) REVERT: V 96 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7817 (pm20) REVERT: V 155 HIS cc_start: 0.4454 (OUTLIER) cc_final: 0.4162 (m90) outliers start: 180 outliers final: 114 residues processed: 573 average time/residue: 0.3540 time to fit residues: 308.2521 Evaluate side-chains 543 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 419 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE 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 196 VAL Chi-restraints excluded: chain B residue 202 ASN 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 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 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 69 ASP Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 90 ASP 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 47 ILE 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 49 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain I residue 97 ILE 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 170 ASP Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 42 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain L residue 63 LEU Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 129 VAL 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 L residue 190 GLU 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 52 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 189 LEU Chi-restraints excluded: chain N residue 196 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 103 THR 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 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 16 ASP 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 156 ILE Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain S residue 98 ILE 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 T residue 196 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 62 ILE Chi-restraints excluded: chain U residue 71 THR 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 122 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 37 LEU Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 99 VAL Chi-restraints excluded: chain W residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 2.9990 chunk 245 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 272 optimal weight: 40.0000 chunk 226 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 ASN ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 100 GLN ** R 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** U 59 ASN ** 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: 0.7309 moved from start: 0.7743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22444 Z= 0.267 Angle : 0.740 11.227 30566 Z= 0.371 Chirality : 0.049 0.255 3753 Planarity : 0.006 0.056 3918 Dihedral : 5.431 56.824 3090 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 7.16 % Allowed : 29.26 % Favored : 63.59 % 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: -0.05 (0.16), residues: 2862 helix: 1.10 (0.16), residues: 1011 sheet: -0.58 (0.18), residues: 843 loop : -0.54 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 112 HIS 0.028 0.002 HIS V 155 PHE 0.028 0.003 PHE E 115 TYR 0.023 0.002 TYR G 109 ARG 0.010 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 603 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 435 time to evaluate : 2.710 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 41 ARG cc_start: 0.7303 (mmm160) cc_final: 0.6701 (mmm160) REVERT: A 94 ILE cc_start: 0.5574 (OUTLIER) cc_final: 0.4916 (pt) REVERT: B 74 MET cc_start: 0.8611 (mmm) cc_final: 0.8221 (mmt) REVERT: B 199 LEU cc_start: 0.9379 (pp) cc_final: 0.8880 (tp) REVERT: C 49 THR cc_start: 0.8060 (t) cc_final: 0.7736 (p) REVERT: D 24 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8590 (tt) REVERT: D 68 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8179 (tp30) REVERT: D 69 ASP cc_start: 0.8033 (m-30) cc_final: 0.7734 (m-30) REVERT: E 31 LYS cc_start: 0.8592 (mttt) cc_final: 0.8243 (mmmt) REVERT: E 115 PHE cc_start: 0.6958 (t80) cc_final: 0.6491 (t80) REVERT: F 90 ASP cc_start: 0.7883 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: I 35 LYS cc_start: 0.9201 (tptp) cc_final: 0.8926 (tptp) REVERT: I 85 TYR cc_start: 0.7468 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: J 19 ARG cc_start: 0.9026 (mmt180) cc_final: 0.8440 (pmt-80) REVERT: J 62 MET cc_start: 0.6180 (tpp) cc_final: 0.5486 (tpp) REVERT: J 142 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7563 (mm) REVERT: J 170 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.4163 (t70) REVERT: K 17 MET cc_start: 0.3932 (tpp) cc_final: 0.0275 (pmm) REVERT: K 41 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8034 (ptm-80) REVERT: M 52 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6488 (mp) REVERT: N 137 ASP cc_start: 0.7940 (t0) cc_final: 0.7468 (t0) REVERT: N 150 MET cc_start: 0.8609 (pmm) cc_final: 0.8326 (pmm) REVERT: N 159 ARG cc_start: 0.6782 (mmm160) cc_final: 0.6537 (mmp80) REVERT: O 17 MET cc_start: 0.4225 (mmt) cc_final: 0.3689 (mmt) REVERT: O 92 ASP cc_start: 0.7729 (m-30) cc_final: 0.7271 (t70) REVERT: R 58 ARG cc_start: 0.7949 (mmp-170) cc_final: 0.7385 (mmp80) REVERT: R 62 MET cc_start: 0.7346 (mpp) cc_final: 0.6917 (mpp) REVERT: R 69 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7922 (t70) REVERT: S 17 MET cc_start: 0.3133 (OUTLIER) cc_final: 0.2039 (mmp) REVERT: S 40 ASN cc_start: 0.7866 (p0) cc_final: 0.7665 (p0) REVERT: T 18 GLU cc_start: 0.7906 (mm-30) cc_final: 0.6988 (mt-10) REVERT: T 69 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6923 (t0) REVERT: U 54 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8647 (mmmm) REVERT: V 19 ARG cc_start: 0.8353 (mtm-85) cc_final: 0.7749 (mpp80) REVERT: V 53 PRO cc_start: 0.6342 (Cg_endo) cc_final: 0.5959 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6747 (mmp80) cc_final: 0.5888 (ptp-170) REVERT: V 96 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7872 (pm20) outliers start: 168 outliers final: 120 residues processed: 543 average time/residue: 0.3551 time to fit residues: 294.3939 Evaluate side-chains 534 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 404 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 98 ILE 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 196 VAL Chi-restraints excluded: chain B residue 202 ASN 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 97 ILE Chi-restraints excluded: chain D residue 24 ILE 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 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 170 ASP 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 29 SER Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 90 ASP 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 33 ILE Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain J residue 79 ASP Chi-restraints excluded: chain J residue 87 ASN 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 142 LEU 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 46 VAL Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 190 GLU 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 48 ILE Chi-restraints excluded: chain M residue 52 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 122 ILE 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 22 THR 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 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 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 142 LEU Chi-restraints excluded: chain R residue 148 THR Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 22 THR 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 42 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 49 THR 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 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 37 LEU Chi-restraints excluded: chain W residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 0.5980 chunk 30 optimal weight: 8.9990 chunk 155 optimal weight: 8.9990 chunk 199 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 229 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 165 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 HIS R 202 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** ** U 59 ASN ** 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: 0.7277 moved from start: 0.7960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22444 Z= 0.223 Angle : 0.721 11.727 30566 Z= 0.356 Chirality : 0.048 0.210 3753 Planarity : 0.006 0.053 3918 Dihedral : 5.276 57.155 3090 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.88 % Allowed : 30.58 % 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: 0.08 (0.16), residues: 2862 helix: 1.28 (0.16), residues: 1011 sheet: -0.44 (0.18), residues: 807 loop : -0.62 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 112 HIS 0.004 0.001 HIS F 155 PHE 0.025 0.003 PHE M 115 TYR 0.021 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 582 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 444 time to evaluate : 2.666 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6028 (mp0) REVERT: A 94 ILE cc_start: 0.5530 (OUTLIER) cc_final: 0.4891 (pt) REVERT: B 199 LEU cc_start: 0.9392 (pp) cc_final: 0.8965 (tp) REVERT: D 24 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8557 (tt) REVERT: D 69 ASP cc_start: 0.8004 (m-30) cc_final: 0.7691 (m-30) REVERT: E 31 LYS cc_start: 0.8566 (mttt) cc_final: 0.8327 (mmmt) REVERT: E 115 PHE cc_start: 0.6988 (t80) cc_final: 0.6527 (t80) REVERT: F 90 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: F 159 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7504 (tpp80) REVERT: G 77 GLU cc_start: 0.8447 (mp0) cc_final: 0.7835 (pp20) REVERT: I 35 LYS cc_start: 0.9219 (tptp) cc_final: 0.8946 (tptp) REVERT: I 85 TYR cc_start: 0.7377 (OUTLIER) cc_final: 0.6295 (m-80) REVERT: J 19 ARG cc_start: 0.9054 (mmt180) cc_final: 0.8505 (pmt-80) REVERT: J 62 MET cc_start: 0.6156 (tpp) cc_final: 0.5409 (tpp) REVERT: J 90 ASP cc_start: 0.7807 (t0) cc_final: 0.7594 (t0) REVERT: J 142 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7642 (mm) REVERT: J 170 ASP cc_start: 0.6241 (OUTLIER) cc_final: 0.4207 (t0) REVERT: K 17 MET cc_start: 0.3864 (tpp) cc_final: 0.0743 (pmm) REVERT: K 37 LEU cc_start: 0.8991 (tp) cc_final: 0.8590 (mm) REVERT: K 41 ARG cc_start: 0.8318 (mtp85) cc_final: 0.8078 (ptm-80) REVERT: M 52 LEU cc_start: 0.7482 (tp) cc_final: 0.6727 (mp) REVERT: N 74 MET cc_start: 0.9359 (mmt) cc_final: 0.9031 (mmt) REVERT: N 137 ASP cc_start: 0.7904 (t0) cc_final: 0.7453 (t0) REVERT: N 150 MET cc_start: 0.8624 (pmm) cc_final: 0.8381 (pmm) REVERT: O 92 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7254 (t70) REVERT: R 38 ASP cc_start: 0.8078 (t0) cc_final: 0.7789 (t0) REVERT: R 42 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8740 (mmmt) REVERT: R 72 LYS cc_start: 0.8635 (ptmt) cc_final: 0.8381 (pttp) REVERT: S 40 ASN cc_start: 0.7840 (p0) cc_final: 0.7625 (p0) REVERT: T 18 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7006 (mt-10) REVERT: T 69 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6938 (t0) REVERT: U 54 LYS cc_start: 0.9099 (mmmm) cc_final: 0.8831 (mmmt) REVERT: V 19 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.7700 (mpp80) REVERT: V 53 PRO cc_start: 0.6423 (Cg_endo) cc_final: 0.6035 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6784 (mmp80) cc_final: 0.6028 (ptp-170) REVERT: V 62 MET cc_start: 0.8627 (ttm) cc_final: 0.8382 (ttp) REVERT: W 17 MET cc_start: 0.3606 (mtt) cc_final: 0.2690 (ttt) REVERT: W 78 ASN cc_start: 0.8810 (t0) cc_final: 0.8479 (t0) outliers start: 138 outliers final: 106 residues processed: 534 average time/residue: 0.3436 time to fit residues: 279.8421 Evaluate side-chains 526 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 412 time to evaluate : 2.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 98 ILE 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 191 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 202 ASN 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 97 ILE Chi-restraints excluded: chain D residue 24 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 144 ASN Chi-restraints excluded: chain D residue 170 ASP 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 29 SER Chi-restraints excluded: chain F residue 46 VAL 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 87 ASN Chi-restraints excluded: chain F residue 90 ASP 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 48 ILE 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 128 THR Chi-restraints excluded: chain J residue 142 LEU 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 L residue 58 ARG Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 190 GLU 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 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 N residue 189 LEU Chi-restraints excluded: chain O residue 22 THR 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 49 THR Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 99 VAL 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 R residue 161 SER Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 52 LEU 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 142 LEU Chi-restraints excluded: chain T residue 196 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 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 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 71 THR Chi-restraints excluded: chain W residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 172 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 HIS ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 155 HIS R 202 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** ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.8407 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= 0.287 Angle : 0.749 9.764 30566 Z= 0.377 Chirality : 0.049 0.247 3753 Planarity : 0.006 0.065 3918 Dihedral : 5.426 57.848 3090 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 20.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.64 % Allowed : 30.79 % Favored : 62.56 % 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: -0.13 (0.16), residues: 2862 helix: 1.04 (0.16), residues: 1023 sheet: -0.62 (0.18), residues: 837 loop : -0.61 (0.21), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 112 HIS 0.005 0.001 HIS Q 90 PHE 0.043 0.003 PHE M 115 TYR 0.022 0.002 TYR G 109 ARG 0.013 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 575 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 419 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6565 (mp0) REVERT: A 116 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8181 (mm-30) REVERT: B 199 LEU cc_start: 0.9419 (pp) cc_final: 0.8942 (tp) REVERT: C 75 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7722 (pm20) REVERT: D 24 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8504 (tt) REVERT: D 68 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8273 (tp30) REVERT: D 69 ASP cc_start: 0.8216 (m-30) cc_final: 0.7912 (m-30) REVERT: E 31 LYS cc_start: 0.8582 (mttt) cc_final: 0.8356 (mmmt) REVERT: E 115 PHE cc_start: 0.7132 (t80) cc_final: 0.6725 (t80) REVERT: F 90 ASP cc_start: 0.7959 (m-30) cc_final: 0.7509 (m-30) REVERT: G 77 GLU cc_start: 0.8589 (mp0) cc_final: 0.7951 (pp20) REVERT: I 35 LYS cc_start: 0.9245 (tptp) cc_final: 0.8990 (tptp) REVERT: I 85 TYR cc_start: 0.7569 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: J 19 ARG cc_start: 0.9146 (mmt180) cc_final: 0.8478 (ppt170) REVERT: J 58 ARG cc_start: 0.7148 (mmp-170) cc_final: 0.6911 (mmp80) REVERT: J 62 MET cc_start: 0.6111 (tpp) cc_final: 0.5279 (tpp) REVERT: J 63 LEU cc_start: 0.8392 (pt) cc_final: 0.8139 (pp) REVERT: J 142 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7517 (mm) REVERT: J 170 ASP cc_start: 0.6434 (OUTLIER) cc_final: 0.4209 (t70) REVERT: K 17 MET cc_start: 0.4086 (tpp) cc_final: 0.0606 (pmm) REVERT: K 37 LEU cc_start: 0.9010 (tp) cc_final: 0.8614 (mm) REVERT: M 52 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.6832 (mp) REVERT: N 74 MET cc_start: 0.9361 (mmt) cc_final: 0.9082 (mmt) REVERT: N 79 ASP cc_start: 0.9262 (t0) cc_final: 0.8965 (t0) REVERT: N 137 ASP cc_start: 0.7969 (t0) cc_final: 0.7560 (t0) REVERT: N 150 MET cc_start: 0.8617 (pmm) cc_final: 0.8310 (pmm) REVERT: O 92 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7464 (t70) REVERT: R 42 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8786 (mmmt) REVERT: R 72 LYS cc_start: 0.8642 (ptmt) cc_final: 0.8285 (pttp) REVERT: R 170 ASP cc_start: 0.7385 (OUTLIER) cc_final: 0.7152 (p0) REVERT: S 17 MET cc_start: 0.2993 (OUTLIER) cc_final: 0.2276 (mmp) REVERT: S 40 ASN cc_start: 0.7833 (p0) cc_final: 0.7585 (p0) REVERT: T 18 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7178 (mt-10) REVERT: T 69 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7019 (t0) REVERT: U 21 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8215 (tm-30) REVERT: U 54 LYS cc_start: 0.9122 (mmmm) cc_final: 0.8794 (mmmt) REVERT: V 53 PRO cc_start: 0.6642 (Cg_endo) cc_final: 0.6272 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6927 (mmp80) cc_final: 0.6193 (ptp-170) REVERT: V 62 MET cc_start: 0.8719 (ttm) cc_final: 0.8514 (ttm) REVERT: W 47 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7532 (mm) outliers start: 156 outliers final: 122 residues processed: 522 average time/residue: 0.3415 time to fit residues: 274.0468 Evaluate side-chains 532 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 399 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 MET Chi-restraints excluded: chain A residue 92 ASP 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 61 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 137 ASP Chi-restraints excluded: chain B residue 170 ASP 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 71 THR Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 24 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 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain D residue 170 ASP 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 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 29 SER 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 87 ASN 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 106 ASN Chi-restraints excluded: chain G residue 109 TYR Chi-restraints excluded: chain I residue 23 THR Chi-restraints excluded: chain I residue 40 ASN Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 85 TYR Chi-restraints excluded: chain J residue 87 ASN 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 142 LEU 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 L residue 58 ARG Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 187 LEU Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain M residue 17 MET 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 M residue 52 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 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 22 THR Chi-restraints excluded: chain O residue 71 THR 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 99 VAL Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain R residue 80 VAL 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 R residue 161 SER Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 22 THR Chi-restraints excluded: chain S residue 52 LEU 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 142 LEU 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 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 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 47 ILE Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 99 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 8.9990 chunk 260 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 253 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 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 ** T 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.8526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22444 Z= 0.221 Angle : 0.731 9.941 30566 Z= 0.361 Chirality : 0.048 0.289 3753 Planarity : 0.006 0.061 3918 Dihedral : 5.271 57.986 3090 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.45 % Allowed : 32.11 % Favored : 62.44 % 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: -0.00 (0.16), residues: 2862 helix: 1.20 (0.16), residues: 1023 sheet: -0.48 (0.18), residues: 825 loop : -0.68 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 112 HIS 0.005 0.001 HIS U 90 PHE 0.033 0.003 PHE U 115 TYR 0.020 0.001 TYR G 109 ARG 0.015 0.001 ARG T 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 559 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 431 time to evaluate : 2.583 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 116 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 58 ARG cc_start: 0.8170 (mmp80) cc_final: 0.7867 (mmm160) REVERT: D 24 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8476 (tt) REVERT: D 69 ASP cc_start: 0.8148 (m-30) cc_final: 0.7864 (m-30) REVERT: D 112 GLU cc_start: 0.3297 (pm20) cc_final: 0.3037 (pm20) REVERT: D 115 LYS cc_start: 0.8422 (tmtt) cc_final: 0.7803 (mmtt) REVERT: E 31 LYS cc_start: 0.8687 (mttt) cc_final: 0.8321 (mmmt) REVERT: E 115 PHE cc_start: 0.7226 (t80) cc_final: 0.6899 (t80) REVERT: F 90 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: G 77 GLU cc_start: 0.8263 (mp0) cc_final: 0.7838 (pp20) REVERT: I 35 LYS cc_start: 0.9227 (tptp) cc_final: 0.8955 (tptp) REVERT: I 85 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: J 19 ARG cc_start: 0.9165 (mmt180) cc_final: 0.8497 (ppt170) REVERT: J 35 LYS cc_start: 0.9131 (tppt) cc_final: 0.8906 (tptt) REVERT: J 58 ARG cc_start: 0.7074 (mmp-170) cc_final: 0.6820 (mmp80) REVERT: J 62 MET cc_start: 0.6094 (tpp) cc_final: 0.5264 (tpp) REVERT: J 63 LEU cc_start: 0.8310 (pt) cc_final: 0.8075 (pp) REVERT: J 142 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7599 (mm) REVERT: J 170 ASP cc_start: 0.6417 (OUTLIER) cc_final: 0.4228 (t70) REVERT: K 17 MET cc_start: 0.3982 (tpp) cc_final: 0.0900 (pmm) REVERT: K 37 LEU cc_start: 0.9005 (tp) cc_final: 0.8666 (mm) REVERT: L 26 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6722 (mt-10) REVERT: L 74 MET cc_start: 0.8954 (mmt) cc_final: 0.8719 (mmp) REVERT: M 52 LEU cc_start: 0.7615 (tp) cc_final: 0.6906 (mp) REVERT: N 74 MET cc_start: 0.9354 (mmt) cc_final: 0.9056 (mmt) REVERT: N 79 ASP cc_start: 0.9224 (t0) cc_final: 0.8929 (t0) REVERT: N 137 ASP cc_start: 0.7921 (t0) cc_final: 0.7522 (t0) REVERT: O 92 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7493 (t70) REVERT: R 72 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8281 (pttp) REVERT: R 170 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6965 (p0) REVERT: S 40 ASN cc_start: 0.7805 (p0) cc_final: 0.7511 (p0) REVERT: T 18 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7183 (mt-10) REVERT: T 69 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.6989 (t0) REVERT: U 21 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8069 (tm-30) REVERT: U 54 LYS cc_start: 0.9085 (mmmm) cc_final: 0.8774 (mmmt) REVERT: V 53 PRO cc_start: 0.6642 (Cg_endo) cc_final: 0.6275 (Cg_exo) REVERT: V 58 ARG cc_start: 0.6949 (mmp80) cc_final: 0.6138 (ptp-170) REVERT: V 62 MET cc_start: 0.8747 (ttm) cc_final: 0.8464 (ttp) REVERT: W 78 ASN cc_start: 0.8920 (t0) cc_final: 0.8708 (m-40) outliers start: 128 outliers final: 101 residues processed: 515 average time/residue: 0.3409 time to fit residues: 269.9968 Evaluate side-chains 514 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 405 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain B residue 24 ILE 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 170 ASP 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 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 25 LEU 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 142 LEU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 170 ASP 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 29 SER 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 87 ASN Chi-restraints excluded: chain F residue 90 ASP 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 196 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 59 ASN 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 74 THR 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 87 ASN Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 LEU 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 58 ARG Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 42 LEU Chi-restraints excluded: chain M residue 48 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 N residue 196 VAL Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 109 TYR 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 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 161 SER Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain S residue 22 THR 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 123 VAL Chi-restraints excluded: chain T residue 142 LEU 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 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 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 W residue 71 THR Chi-restraints excluded: chain W residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 8.9990 chunk 267 optimal weight: 20.0000 chunk 163 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 280 optimal weight: 10.0000 chunk 258 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.9017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 22444 Z= 0.362 Angle : 0.836 12.220 30566 Z= 0.422 Chirality : 0.050 0.277 3753 Planarity : 0.007 0.068 3918 Dihedral : 5.716 56.945 3090 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 24.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 5.45 % Allowed : 32.58 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2862 helix: 0.74 (0.15), residues: 1023 sheet: -0.73 (0.18), residues: 843 loop : -0.81 (0.21), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 112 HIS 0.006 0.002 HIS K 90 PHE 0.031 0.003 PHE O 115 TYR 0.027 0.002 TYR G 109 ARG 0.016 0.001 ARG T 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 525 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 397 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.8267 (mmp80) cc_final: 0.7960 (mmm160) REVERT: B 74 MET cc_start: 0.8844 (mmm) cc_final: 0.8440 (mmt) REVERT: D 24 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8561 (tt) REVERT: F 90 ASP cc_start: 0.8007 (m-30) cc_final: 0.7609 (m-30) REVERT: G 17 MET cc_start: 0.5000 (tpt) cc_final: 0.3576 (tpt) REVERT: G 75 GLU cc_start: 0.8486 (tp30) cc_final: 0.8041 (mp0) REVERT: J 19 ARG cc_start: 0.9210 (mmt180) cc_final: 0.8459 (ppt170) REVERT: J 62 MET cc_start: 0.6122 (tpp) cc_final: 0.5276 (tpp) REVERT: J 102 LEU cc_start: 0.8560 (mp) cc_final: 0.7871 (tt) REVERT: J 142 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7418 (mm) REVERT: J 170 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.4616 (t70) REVERT: K 17 MET cc_start: 0.4410 (tpp) cc_final: 0.0571 (pmm) REVERT: L 26 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6875 (mt-10) REVERT: M 52 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7197 (mp) REVERT: N 26 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: N 74 MET cc_start: 0.9369 (mmt) cc_final: 0.9117 (mmt) REVERT: N 79 ASP cc_start: 0.9264 (t0) cc_final: 0.8981 (t0) REVERT: O 61 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7911 (mp0) REVERT: O 109 TYR cc_start: 0.7557 (OUTLIER) cc_final: 0.5670 (t80) REVERT: R 72 LYS cc_start: 0.8646 (ptmt) cc_final: 0.8384 (pttt) REVERT: R 170 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7299 (p0) REVERT: S 40 ASN cc_start: 0.7894 (p0) cc_final: 0.7647 (p0) REVERT: T 18 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7377 (mt-10) REVERT: T 69 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7117 (t0) REVERT: U 42 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9196 (tp) REVERT: U 54 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8808 (mmmt) REVERT: V 53 PRO cc_start: 0.6750 (Cg_endo) cc_final: 0.6348 (Cg_exo) REVERT: V 58 ARG cc_start: 0.7037 (mmp80) cc_final: 0.6047 (ptp90) REVERT: V 62 MET cc_start: 0.8790 (ttm) cc_final: 0.8552 (ttm) REVERT: W 47 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7716 (mm) REVERT: W 78 ASN cc_start: 0.8725 (t0) cc_final: 0.7875 (t0) outliers start: 128 outliers final: 97 residues processed: 483 average time/residue: 0.3286 time to fit residues: 246.8143 Evaluate side-chains 483 residues out of total 2349 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 376 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 THR Chi-restraints excluded: chain A residue 92 ASP 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 61 ILE Chi-restraints excluded: chain B residue 78 LEU 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 71 THR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 97 ILE Chi-restraints excluded: chain D residue 24 ILE Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 38 ASP 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 D residue 170 ASP 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 109 TYR Chi-restraints excluded: chain F residue 29 SER 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 87 ASN 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 74 THR Chi-restraints excluded: chain I residue 79 VAL Chi-restraints excluded: chain J residue 87 ASN Chi-restraints excluded: chain J residue 93 LEU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 129 VAL Chi-restraints excluded: chain J residue 142 LEU 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 L residue 46 VAL Chi-restraints excluded: chain L residue 58 ARG Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 148 THR Chi-restraints excluded: chain L residue 190 GLU Chi-restraints excluded: chain M residue 17 MET Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain M residue 52 LEU 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 122 ILE Chi-restraints excluded: chain N residue 129 VAL Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 109 TYR Chi-restraints excluded: chain Q residue 22 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 R residue 137 ASP Chi-restraints excluded: chain R residue 142 LEU Chi-restraints excluded: chain R residue 156 ILE Chi-restraints excluded: chain R residue 161 SER Chi-restraints excluded: chain R residue 170 ASP Chi-restraints excluded: chain S residue 22 THR 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 123 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 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 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 W residue 37 LEU Chi-restraints excluded: chain W residue 47 ILE Chi-restraints excluded: chain W residue 71 THR Chi-restraints excluded: chain W residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 1.9990 chunk 238 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 206 optimal weight: 0.1980 chunk 33 optimal weight: 8.9990 chunk 62 optimal weight: 0.0470 chunk 224 optimal weight: 20.0000 chunk 93 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 ASN E 40 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 ASN ** Q 59 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 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.120270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098101 restraints weight = 79908.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.100873 restraints weight = 52665.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.102926 restraints weight = 38914.866| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.9036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22444 Z= 0.220 Angle : 0.759 12.520 30566 Z= 0.373 Chirality : 0.049 0.322 3753 Planarity : 0.006 0.056 3918 Dihedral : 5.368 58.025 3090 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 4.26 % Allowed : 33.69 % Favored : 62.05 % 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: -0.11 (0.16), residues: 2862 helix: 1.13 (0.16), residues: 1023 sheet: -0.48 (0.18), residues: 825 loop : -0.81 (0.21), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 112 HIS 0.004 0.001 HIS T 155 PHE 0.024 0.003 PHE O 115 TYR 0.022 0.001 TYR I 109 ARG 0.014 0.001 ARG L 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5679.76 seconds wall clock time: 104 minutes 1.73 seconds (6241.73 seconds total)