Starting phenix.real_space_refine on Fri Mar 22 11:05:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/03_2024/8pdq_17618.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/03_2024/8pdq_17618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/03_2024/8pdq_17618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/03_2024/8pdq_17618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/03_2024/8pdq_17618.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/03_2024/8pdq_17618.pdb" } resolution = 3.1 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= 0.000 sd= 0.038 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: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 143 5.16 5 C 20702 2.51 5 N 5709 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 10": "OD1" <-> "OD2" Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "B ASP 10": "OD1" <-> "OD2" Residue "C ASP 10": "OD1" <-> "OD2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "D ASP 10": "OD1" <-> "OD2" Residue "G ASP 10": "OD1" <-> "OD2" Residue "G TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G ASP 290": "OD1" <-> "OD2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "H ASP 10": "OD1" <-> "OD2" Residue "J ASP 10": "OD1" <-> "OD2" Residue "J TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J ARG 132": "NH1" <-> "NH2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J ASP 290": "OD1" <-> "OD2" Residue "J GLU 298": "OE1" <-> "OE2" Residue "J GLU 352": "OE1" <-> "OE2" Residue "J TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 360": "OE1" <-> "OE2" Residue "K ASP 10": "OD1" <-> "OD2" Residue "M ASP 10": "OD1" <-> "OD2" Residue "M TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M GLU 181": "OE1" <-> "OE2" Residue "M ASP 290": "OD1" <-> "OD2" Residue "M GLU 298": "OE1" <-> "OE2" Residue "M GLU 352": "OE1" <-> "OE2" Residue "M TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "N ASP 10": "OD1" <-> "OD2" Residue "P ASP 10": "OD1" <-> "OD2" Residue "P TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 89": "OE1" <-> "OE2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "P GLU 181": "OE1" <-> "OE2" Residue "P ASP 290": "OD1" <-> "OD2" Residue "P GLU 298": "OE1" <-> "OE2" Residue "P GLU 352": "OE1" <-> "OE2" Residue "P TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 360": "OE1" <-> "OE2" Residue "Q ASP 10": "OD1" <-> "OD2" Residue "S ASP 10": "OD1" <-> "OD2" Residue "S TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "S ARG 132": "NH1" <-> "NH2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S ASP 290": "OD1" <-> "OD2" Residue "S GLU 298": "OE1" <-> "OE2" Residue "S GLU 352": "OE1" <-> "OE2" Residue "S TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 360": "OE1" <-> "OE2" Residue "T ASP 10": "OD1" <-> "OD2" Residue "V ASP 10": "OD1" <-> "OD2" Residue "V TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 20": "OE1" <-> "OE2" Residue "V TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 89": "OE1" <-> "OE2" Residue "V GLU 109": "OE1" <-> "OE2" Residue "V ARG 132": "NH1" <-> "NH2" Residue "V GLU 181": "OE1" <-> "OE2" Residue "V ASP 290": "OD1" <-> "OD2" Residue "V GLU 298": "OE1" <-> "OE2" Residue "V GLU 352": "OE1" <-> "OE2" Residue "V TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 360": "OE1" <-> "OE2" Residue "W ASP 10": "OD1" <-> "OD2" Residue "Y ASP 10": "OD1" <-> "OD2" Residue "Y TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 20": "OE1" <-> "OE2" Residue "Y TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 89": "OE1" <-> "OE2" Residue "Y GLU 109": "OE1" <-> "OE2" Residue "Y ARG 132": "NH1" <-> "NH2" Residue "Y GLU 181": "OE1" <-> "OE2" Residue "Y ASP 290": "OD1" <-> "OD2" Residue "Y GLU 298": "OE1" <-> "OE2" Residue "Y GLU 352": "OE1" <-> "OE2" Residue "Y TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 360": "OE1" <-> "OE2" Residue "Z ASP 10": "OD1" <-> "OD2" Residue "1 ASP 10": "OD1" <-> "OD2" Residue "1 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 20": "OE1" <-> "OE2" Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 89": "OE1" <-> "OE2" Residue "1 GLU 109": "OE1" <-> "OE2" Residue "1 ARG 132": "NH1" <-> "NH2" Residue "1 GLU 181": "OE1" <-> "OE2" Residue "1 ASP 290": "OD1" <-> "OD2" Residue "1 GLU 298": "OE1" <-> "OE2" Residue "1 GLU 352": "OE1" <-> "OE2" Residue "1 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 360": "OE1" <-> "OE2" Residue "2 ASP 10": "OD1" <-> "OD2" Residue "4 ASP 10": "OD1" <-> "OD2" Residue "4 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 20": "OE1" <-> "OE2" Residue "4 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 89": "OE1" <-> "OE2" Residue "4 GLU 109": "OE1" <-> "OE2" Residue "4 ARG 132": "NH1" <-> "NH2" Residue "4 GLU 181": "OE1" <-> "OE2" Residue "4 ASP 290": "OD1" <-> "OD2" Residue "4 GLU 298": "OE1" <-> "OE2" Residue "4 GLU 352": "OE1" <-> "OE2" Residue "4 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 360": "OE1" <-> "OE2" Residue "5 ASP 10": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33176 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "C" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "G" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "J" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "L" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "M" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "O" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "P" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "S" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "U" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "V" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "X" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "Y" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "Z" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "0" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "1" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "2" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "3" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "4" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2815 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 1 Chain: "5" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 16.57, per 1000 atoms: 0.50 Number of scatterers: 33176 At special positions: 0 Unit cell: (197.4, 199.5, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 P 77 15.00 O 6545 8.00 N 5709 7.00 C 20702 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: 13.19 Conformation dependent library (CDL) restraints added in 5.5 seconds 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7568 Finding SS restraints... Secondary structure from input PDB file: 242 helices and 22 sheets defined 68.4% alpha, 5.1% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 11.25 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU A 273 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN C 150 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.950A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 250 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU C 273 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU D 14 " --> pdb=" O ILE D 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 removed outlier: 3.549A pdb=" N GLN G 150 " --> pdb=" O PRO G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 188 Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 250 Processing helix chain 'G' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU G 273 " --> pdb=" O ASN G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 280 Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU H 14 " --> pdb=" O ILE H 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 removed outlier: 3.547A pdb=" N GLN J 150 " --> pdb=" O PRO J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 188 Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER J 222 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 250 Processing helix chain 'J' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 274 removed outlier: 3.636A pdb=" N LEU J 273 " --> pdb=" O ASN J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 297 through 300' Processing helix chain 'J' and resid 301 through 306 Processing helix chain 'J' and resid 318 through 332 Processing helix chain 'J' and resid 344 through 361 Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.578A pdb=" N LEU K 14 " --> pdb=" O ILE K 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 20 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL M 124 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN M 150 " --> pdb=" O PRO M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 188 Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 250 Processing helix chain 'M' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU M 273 " --> pdb=" O ASN M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 280 Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 301 through 306 Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'N' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU N 14 " --> pdb=" O ILE N 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL P 124 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN P 150 " --> pdb=" O PRO P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 188 Processing helix chain 'P' and resid 191 through 198 Processing helix chain 'P' and resid 202 through 217 Processing helix chain 'P' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER P 222 " --> pdb=" O VAL P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 250 Processing helix chain 'P' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG P 260 " --> pdb=" O GLN P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU P 273 " --> pdb=" O ASN P 270 " (cutoff:3.500A) Processing helix chain 'P' and resid 275 through 280 Processing helix chain 'P' and resid 281 through 296 Processing helix chain 'P' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY P 300 " --> pdb=" O PRO P 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 297 through 300' Processing helix chain 'P' and resid 301 through 306 Processing helix chain 'P' and resid 318 through 332 Processing helix chain 'P' and resid 344 through 361 Processing helix chain 'Q' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU Q 14 " --> pdb=" O ILE Q 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 20 Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 51 removed outlier: 4.010A pdb=" N LEU S 47 " --> pdb=" O GLU S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN S 150 " --> pdb=" O PRO S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS S 171 " --> pdb=" O LEU S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 188 Processing helix chain 'S' and resid 191 through 198 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 250 Processing helix chain 'S' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU S 273 " --> pdb=" O ASN S 270 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 280 Processing helix chain 'S' and resid 281 through 296 Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 301 through 306 Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'T' and resid 10 through 14 removed outlier: 3.576A pdb=" N LEU T 14 " --> pdb=" O ILE T 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 20 Processing helix chain 'V' and resid 37 through 39 No H-bonds generated for 'chain 'V' and resid 37 through 39' Processing helix chain 'V' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 75 Processing helix chain 'V' and resid 75 through 86 Processing helix chain 'V' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL V 124 " --> pdb=" O GLU V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN V 150 " --> pdb=" O PRO V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 175 through 188 Processing helix chain 'V' and resid 191 through 198 Processing helix chain 'V' and resid 202 through 217 Processing helix chain 'V' and resid 218 through 233 removed outlier: 3.950A pdb=" N SER V 222 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 250 Processing helix chain 'V' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG V 260 " --> pdb=" O GLN V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU V 273 " --> pdb=" O ASN V 270 " (cutoff:3.500A) Processing helix chain 'V' and resid 275 through 280 Processing helix chain 'V' and resid 281 through 296 Processing helix chain 'V' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY V 300 " --> pdb=" O PRO V 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 297 through 300' Processing helix chain 'V' and resid 301 through 306 Processing helix chain 'V' and resid 318 through 332 Processing helix chain 'V' and resid 344 through 361 Processing helix chain 'W' and resid 10 through 14 removed outlier: 3.578A pdb=" N LEU W 14 " --> pdb=" O ILE W 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 20 Processing helix chain 'Y' and resid 37 through 39 No H-bonds generated for 'chain 'Y' and resid 37 through 39' Processing helix chain 'Y' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU Y 47 " --> pdb=" O GLU Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 75 Processing helix chain 'Y' and resid 75 through 86 Processing helix chain 'Y' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL Y 124 " --> pdb=" O GLU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN Y 150 " --> pdb=" O PRO Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 188 Processing helix chain 'Y' and resid 191 through 198 Processing helix chain 'Y' and resid 202 through 217 Processing helix chain 'Y' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER Y 222 " --> pdb=" O VAL Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 238 through 250 Processing helix chain 'Y' and resid 256 through 268 removed outlier: 3.756A pdb=" N ARG Y 260 " --> pdb=" O GLN Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU Y 273 " --> pdb=" O ASN Y 270 " (cutoff:3.500A) Processing helix chain 'Y' and resid 275 through 280 Processing helix chain 'Y' and resid 281 through 296 Processing helix chain 'Y' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY Y 300 " --> pdb=" O PRO Y 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 297 through 300' Processing helix chain 'Y' and resid 301 through 306 Processing helix chain 'Y' and resid 318 through 332 Processing helix chain 'Y' and resid 344 through 361 Processing helix chain 'Z' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU Z 14 " --> pdb=" O ILE Z 11 " (cutoff:3.500A) Processing helix chain '1' and resid 9 through 20 Processing helix chain '1' and resid 37 through 39 No H-bonds generated for 'chain '1' and resid 37 through 39' Processing helix chain '1' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU 1 47 " --> pdb=" O GLU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 61 through 75 Processing helix chain '1' and resid 75 through 86 Processing helix chain '1' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL 1 124 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 151 removed outlier: 3.549A pdb=" N GLN 1 150 " --> pdb=" O PRO 1 147 " (cutoff:3.500A) Processing helix chain '1' and resid 156 through 171 removed outlier: 3.978A pdb=" N LYS 1 171 " --> pdb=" O LEU 1 167 " (cutoff:3.500A) Processing helix chain '1' and resid 175 through 188 Processing helix chain '1' and resid 191 through 198 Processing helix chain '1' and resid 202 through 217 Processing helix chain '1' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER 1 222 " --> pdb=" O VAL 1 218 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 250 Processing helix chain '1' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG 1 260 " --> pdb=" O GLN 1 256 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU 1 273 " --> pdb=" O ASN 1 270 " (cutoff:3.500A) Processing helix chain '1' and resid 275 through 280 Processing helix chain '1' and resid 281 through 296 Processing helix chain '1' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY 1 300 " --> pdb=" O PRO 1 297 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 297 through 300' Processing helix chain '1' and resid 301 through 306 Processing helix chain '1' and resid 318 through 332 Processing helix chain '1' and resid 344 through 361 Processing helix chain '2' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU 2 14 " --> pdb=" O ILE 2 11 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 20 Processing helix chain '4' and resid 37 through 39 No H-bonds generated for 'chain '4' and resid 37 through 39' Processing helix chain '4' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU 4 47 " --> pdb=" O GLU 4 43 " (cutoff:3.500A) Processing helix chain '4' and resid 61 through 75 Processing helix chain '4' and resid 75 through 86 Processing helix chain '4' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL 4 124 " --> pdb=" O GLU 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN 4 150 " --> pdb=" O PRO 4 147 " (cutoff:3.500A) Processing helix chain '4' and resid 156 through 171 removed outlier: 3.980A pdb=" N LYS 4 171 " --> pdb=" O LEU 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 175 through 188 Processing helix chain '4' and resid 191 through 198 Processing helix chain '4' and resid 202 through 217 Processing helix chain '4' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER 4 222 " --> pdb=" O VAL 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 250 Processing helix chain '4' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG 4 260 " --> pdb=" O GLN 4 256 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 274 removed outlier: 3.636A pdb=" N LEU 4 273 " --> pdb=" O ASN 4 270 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 280 Processing helix chain '4' and resid 281 through 296 Processing helix chain '4' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY 4 300 " --> pdb=" O PRO 4 297 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 297 through 300' Processing helix chain '4' and resid 301 through 306 Processing helix chain '4' and resid 318 through 332 Processing helix chain '4' and resid 344 through 361 Processing helix chain '5' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU 5 14 " --> pdb=" O ILE 5 11 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU A 111 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'C' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU C 111 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'G' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU G 111 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'J' and resid 32 through 35 removed outlier: 6.468A pdb=" N THR J 33 " --> pdb=" O VAL J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'J' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU J 111 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'M' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'M' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU M 111 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'P' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR P 33 " --> pdb=" O VAL P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'P' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU P 111 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'S' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'S' and resid 96 through 104 removed outlier: 7.737A pdb=" N LEU S 111 " --> pdb=" O LEU S 100 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'V' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR V 33 " --> pdb=" O VAL V 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'V' and resid 96 through 104 removed outlier: 7.737A pdb=" N LEU V 111 " --> pdb=" O LEU V 100 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Y' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR Y 33 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'Y' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU Y 111 " --> pdb=" O LEU Y 100 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '1' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR 1 33 " --> pdb=" O VAL 1 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain '1' and resid 96 through 104 removed outlier: 7.737A pdb=" N LEU 1 111 " --> pdb=" O LEU 1 100 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '4' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR 4 33 " --> pdb=" O VAL 4 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain '4' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU 4 111 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 11.67 Time building geometry restraints manager: 14.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10681 1.34 - 1.46: 6692 1.46 - 1.58: 16023 1.58 - 1.69: 143 1.69 - 1.81: 253 Bond restraints: 33792 Sorted by residual: bond pdb=" CA ILE J 203 " pdb=" CB ILE J 203 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.33e-01 bond pdb=" CA ILE Y 203 " pdb=" CB ILE Y 203 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.09e-01 bond pdb=" CA ILE M 203 " pdb=" CB ILE M 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.78e-01 bond pdb=" CA ILE S 203 " pdb=" CB ILE S 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.55e-01 bond pdb=" CA ILE 4 203 " pdb=" CB ILE 4 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.45e-01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.95: 1024 106.95 - 113.72: 19432 113.72 - 120.48: 13658 120.48 - 127.24: 11547 127.24 - 134.01: 220 Bond angle restraints: 45881 Sorted by residual: angle pdb=" N GLU Y 125 " pdb=" CA GLU Y 125 " pdb=" CB GLU Y 125 " ideal model delta sigma weight residual 110.28 113.47 -3.19 1.55e+00 4.16e-01 4.24e+00 angle pdb=" N GLU J 125 " pdb=" CA GLU J 125 " pdb=" CB GLU J 125 " ideal model delta sigma weight residual 110.28 113.46 -3.18 1.55e+00 4.16e-01 4.21e+00 angle pdb=" N GLU P 125 " pdb=" CA GLU P 125 " pdb=" CB GLU P 125 " ideal model delta sigma weight residual 110.28 113.45 -3.17 1.55e+00 4.16e-01 4.19e+00 angle pdb=" N GLU C 125 " pdb=" CA GLU C 125 " pdb=" CB GLU C 125 " ideal model delta sigma weight residual 110.28 113.44 -3.16 1.55e+00 4.16e-01 4.17e+00 angle pdb=" N GLU A 125 " pdb=" CA GLU A 125 " pdb=" CB GLU A 125 " ideal model delta sigma weight residual 110.28 113.44 -3.16 1.55e+00 4.16e-01 4.16e+00 ... (remaining 45876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 18198 15.55 - 31.10: 1877 31.10 - 46.65: 550 46.65 - 62.20: 99 62.20 - 77.75: 132 Dihedral angle restraints: 20856 sinusoidal: 9075 harmonic: 11781 Sorted by residual: dihedral pdb=" CA LEU G 52 " pdb=" C LEU G 52 " pdb=" N TYR G 53 " pdb=" CA TYR G 53 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU 4 52 " pdb=" C LEU 4 52 " pdb=" N TYR 4 53 " pdb=" CA TYR 4 53 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU Y 52 " pdb=" C LEU Y 52 " pdb=" N TYR Y 53 " pdb=" CA TYR Y 53 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3117 0.027 - 0.055: 1345 0.055 - 0.082: 714 0.082 - 0.110: 152 0.110 - 0.137: 84 Chirality restraints: 5412 Sorted by residual: chirality pdb=" CA THR C 157 " pdb=" N THR C 157 " pdb=" C THR C 157 " pdb=" CB THR C 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA THR S 157 " pdb=" N THR S 157 " pdb=" C THR S 157 " pdb=" CB THR S 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA THR V 157 " pdb=" N THR V 157 " pdb=" C THR V 157 " pdb=" CB THR V 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 5409 not shown) Planarity restraints: 5555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C U 73 " 0.027 2.00e-02 2.50e+03 1.35e-02 4.11e+00 pdb=" N1 C U 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C U 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C U 73 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C U 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C U 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C U 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C U 73 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C U 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C X 73 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.05e+00 pdb=" N1 C X 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C X 73 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C X 73 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C X 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C X 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C X 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C X 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C X 73 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 73 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.03e+00 pdb=" N1 C O 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C O 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C O 73 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C O 73 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C O 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C O 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C O 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C O 73 " -0.006 2.00e-02 2.50e+03 ... (remaining 5552 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.17: 77 1.17 - 2.10: 231 2.10 - 3.03: 21000 3.03 - 3.97: 91195 3.97 - 4.90: 169684 Warning: very small nonbonded interaction distances. Nonbonded interactions: 282187 Sorted by model distance: nonbonded pdb=" NH1 ARG M 78 " pdb=" CZ TYR P 23 " model vdw 0.235 3.340 nonbonded pdb=" NH1 ARG C 78 " pdb=" CZ TYR G 23 " model vdw 0.235 3.340 nonbonded pdb=" NH1 ARG S 78 " pdb=" CZ TYR V 23 " model vdw 0.236 3.340 nonbonded pdb=" CZ TYR A 23 " pdb=" NH1 ARG 4 78 " model vdw 0.236 3.340 nonbonded pdb=" NH1 ARG P 78 " pdb=" CZ TYR S 23 " model vdw 0.236 3.340 ... (remaining 282182 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 '0' selection = chain '3' selection = chain '6' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain '1' selection = chain '4' selection = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain '2' selection = chain '5' selection = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 15.170 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 91.090 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 33792 Z= 0.246 Angle : 0.566 5.976 45881 Z= 0.324 Chirality : 0.040 0.137 5412 Planarity : 0.004 0.040 5555 Dihedral : 15.289 77.749 13288 Min Nonbonded Distance : 0.235 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.13), residues: 4004 helix: 0.83 (0.10), residues: 2486 sheet: -1.25 (0.27), residues: 231 loop : -0.91 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 123 HIS 0.003 0.001 HIS S 15 PHE 0.014 0.002 PHE M 169 TYR 0.013 0.001 TYR C 69 ARG 0.003 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7610 (ttmt) cc_final: 0.7017 (ttpp) REVERT: G 129 LYS cc_start: 0.7603 (ttmt) cc_final: 0.7105 (mttp) REVERT: M 113 MET cc_start: 0.7771 (mmt) cc_final: 0.7547 (mmt) REVERT: M 249 MET cc_start: 0.8216 (mmm) cc_final: 0.7451 (mmm) REVERT: P 129 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7158 (ttpp) REVERT: P 249 MET cc_start: 0.8193 (mmm) cc_final: 0.7702 (mmm) REVERT: P 258 MET cc_start: 0.8107 (tpp) cc_final: 0.7799 (tpp) REVERT: P 339 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7502 (mtp180) REVERT: S 339 ARG cc_start: 0.7629 (mmm-85) cc_final: 0.7285 (mtp180) REVERT: V 339 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7565 (mtp180) REVERT: 1 201 MET cc_start: 0.7967 (ptt) cc_final: 0.7508 (ptt) REVERT: 4 249 MET cc_start: 0.8255 (mmm) cc_final: 0.7994 (mmm) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.4429 time to fit residues: 333.6201 Evaluate side-chains 415 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 202 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 359 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 306 GLN Y 7 HIS ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN ** 1 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 306 GLN ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 306 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33792 Z= 0.187 Angle : 0.505 8.792 45881 Z= 0.273 Chirality : 0.039 0.131 5412 Planarity : 0.003 0.029 5555 Dihedral : 11.837 74.062 5621 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.58 % Allowed : 7.28 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.13), residues: 4004 helix: 1.39 (0.10), residues: 2530 sheet: -1.29 (0.28), residues: 231 loop : -0.74 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.004 0.001 HIS V 56 PHE 0.012 0.002 PHE 1 169 TYR 0.011 0.001 TYR Y 338 ARG 0.005 0.000 ARG S 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 419 time to evaluate : 3.049 Fit side-chains REVERT: A 129 LYS cc_start: 0.7594 (ttmt) cc_final: 0.6995 (ttpp) REVERT: A 272 MET cc_start: 0.7246 (mmm) cc_final: 0.6838 (mmm) REVERT: C 129 LYS cc_start: 0.7552 (ttmt) cc_final: 0.6977 (ttpp) REVERT: C 272 MET cc_start: 0.7409 (mmm) cc_final: 0.6842 (mmm) REVERT: G 129 LYS cc_start: 0.7566 (ttmt) cc_final: 0.7068 (mttp) REVERT: J 272 MET cc_start: 0.7253 (mmm) cc_final: 0.6967 (mmm) REVERT: M 249 MET cc_start: 0.7981 (mmm) cc_final: 0.7611 (mmm) REVERT: P 129 LYS cc_start: 0.7622 (ttmt) cc_final: 0.7065 (ttpp) REVERT: P 272 MET cc_start: 0.7525 (mmm) cc_final: 0.7073 (mmm) REVERT: P 339 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7522 (mtp180) REVERT: S 135 MET cc_start: 0.6910 (ttm) cc_final: 0.6634 (tpp) REVERT: S 339 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7226 (mtp180) REVERT: V 339 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7533 (mtp180) REVERT: Y 61 TYR cc_start: 0.8541 (m-80) cc_final: 0.8235 (m-80) REVERT: Y 272 MET cc_start: 0.7291 (mmm) cc_final: 0.6602 (mmm) REVERT: Y 339 ARG cc_start: 0.7694 (mmm-85) cc_final: 0.7439 (mtp180) REVERT: 1 129 LYS cc_start: 0.7523 (ttmt) cc_final: 0.6897 (ttpp) REVERT: 1 272 MET cc_start: 0.7432 (mmm) cc_final: 0.7009 (mmm) outliers start: 20 outliers final: 14 residues processed: 430 average time/residue: 0.4281 time to fit residues: 300.0265 Evaluate side-chains 399 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 385 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 235 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 360 optimal weight: 0.0980 chunk 389 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 357 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 289 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 HIS P 279 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 33792 Z= 0.306 Angle : 0.544 6.422 45881 Z= 0.286 Chirality : 0.042 0.134 5412 Planarity : 0.004 0.055 5555 Dihedral : 11.219 74.583 5621 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.58 % Allowed : 8.29 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4004 helix: 1.36 (0.10), residues: 2530 sheet: -1.38 (0.29), residues: 231 loop : -0.64 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP 4 123 HIS 0.004 0.001 HIS V 7 PHE 0.018 0.002 PHE 1 169 TYR 0.026 0.002 TYR A 23 ARG 0.004 0.001 ARG S 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 393 time to evaluate : 3.619 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7384 (mmm) cc_final: 0.7027 (mmm) REVERT: C 23 TYR cc_start: 0.7419 (m-80) cc_final: 0.6996 (m-80) REVERT: C 129 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7096 (ttpp) REVERT: C 272 MET cc_start: 0.7531 (mmm) cc_final: 0.6826 (mmm) REVERT: G 125 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: G 129 LYS cc_start: 0.7629 (ttmt) cc_final: 0.7161 (mttp) REVERT: G 272 MET cc_start: 0.7278 (mmm) cc_final: 0.6865 (mmm) REVERT: G 283 LYS cc_start: 0.7965 (tppt) cc_final: 0.7731 (ttpt) REVERT: J 135 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6816 (tpp) REVERT: J 272 MET cc_start: 0.7522 (mmm) cc_final: 0.6859 (mmm) REVERT: M 249 MET cc_start: 0.7974 (mmm) cc_final: 0.7380 (mmm) REVERT: M 272 MET cc_start: 0.7585 (mmm) cc_final: 0.7213 (mmm) REVERT: P 135 MET cc_start: 0.7323 (tpp) cc_final: 0.6530 (tpp) REVERT: P 339 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7449 (mtm-85) REVERT: S 125 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: S 272 MET cc_start: 0.7322 (mmm) cc_final: 0.6923 (mmm) REVERT: S 339 ARG cc_start: 0.7617 (mmm-85) cc_final: 0.7274 (mtp180) REVERT: V 125 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: V 272 MET cc_start: 0.7541 (mmm) cc_final: 0.7215 (mmm) REVERT: Y 125 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: Y 283 LYS cc_start: 0.8011 (tppt) cc_final: 0.7807 (ttpt) REVERT: 1 125 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6931 (mp0) REVERT: 1 272 MET cc_start: 0.7442 (mmm) cc_final: 0.7009 (mmm) REVERT: 4 94 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7965 (mp) REVERT: 4 125 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.6903 (mp0) REVERT: 4 272 MET cc_start: 0.7326 (mmm) cc_final: 0.6869 (mmm) REVERT: 4 283 LYS cc_start: 0.8220 (tppt) cc_final: 0.7957 (ttpt) outliers start: 55 outliers final: 36 residues processed: 429 average time/residue: 0.4598 time to fit residues: 325.2658 Evaluate side-chains 424 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 380 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 125 GLU Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain Y residue 31 THR Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 263 VAL Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 125 GLU Chi-restraints excluded: chain 4 residue 134 THR Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 361 optimal weight: 0.9990 chunk 382 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 342 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 7 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 33792 Z= 0.235 Angle : 0.494 5.928 45881 Z= 0.263 Chirality : 0.040 0.139 5412 Planarity : 0.003 0.039 5555 Dihedral : 10.976 74.350 5621 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.75 % Allowed : 10.36 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4004 helix: 1.55 (0.10), residues: 2530 sheet: -1.39 (0.30), residues: 231 loop : -0.63 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 4 123 HIS 0.003 0.001 HIS P 7 PHE 0.015 0.002 PHE J 169 TYR 0.022 0.001 TYR A 23 ARG 0.003 0.000 ARG S 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 401 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7417 (mmm) cc_final: 0.7087 (mmm) REVERT: C 129 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7080 (ttpp) REVERT: C 272 MET cc_start: 0.7558 (mmm) cc_final: 0.6911 (mmm) REVERT: G 125 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7378 (mp0) REVERT: G 129 LYS cc_start: 0.7654 (ttmt) cc_final: 0.7193 (mttp) REVERT: G 272 MET cc_start: 0.7399 (mmm) cc_final: 0.7000 (mmm) REVERT: G 283 LYS cc_start: 0.7950 (tppt) cc_final: 0.7748 (ttpt) REVERT: J 272 MET cc_start: 0.7448 (mmm) cc_final: 0.6995 (mmm) REVERT: M 249 MET cc_start: 0.7999 (mmm) cc_final: 0.7256 (mmm) REVERT: M 272 MET cc_start: 0.7558 (mmm) cc_final: 0.7166 (mmm) REVERT: P 125 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: P 339 ARG cc_start: 0.7833 (mmm-85) cc_final: 0.7415 (mtm-85) REVERT: S 125 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: S 135 MET cc_start: 0.7114 (OUTLIER) cc_final: 0.6649 (tpp) REVERT: S 272 MET cc_start: 0.7382 (mmm) cc_final: 0.7015 (mmm) REVERT: S 339 ARG cc_start: 0.7536 (mmm-85) cc_final: 0.7228 (mtp180) REVERT: V 125 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: V 135 MET cc_start: 0.7642 (tpp) cc_final: 0.7280 (tpp) REVERT: V 272 MET cc_start: 0.7562 (mmm) cc_final: 0.7246 (mmm) REVERT: Y 125 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6643 (mp0) REVERT: 1 125 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: 1 272 MET cc_start: 0.7442 (mmm) cc_final: 0.7012 (mmm) REVERT: 4 10 ASP cc_start: 0.7812 (m-30) cc_final: 0.7377 (m-30) REVERT: 4 125 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: 4 272 MET cc_start: 0.7408 (mmm) cc_final: 0.6834 (mmm) REVERT: 4 283 LYS cc_start: 0.8128 (tppt) cc_final: 0.7889 (ttpt) outliers start: 61 outliers final: 34 residues processed: 441 average time/residue: 0.4413 time to fit residues: 319.9500 Evaluate side-chains 428 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 386 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain J residue 22 GLN Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain S residue 125 GLU Chi-restraints excluded: chain S residue 135 MET Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain 1 residue 31 THR Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 4 residue 125 GLU Chi-restraints excluded: chain 4 residue 134 THR Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 0.0010 chunk 217 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 326 optimal weight: 0.0970 chunk 264 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 343 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 33792 Z= 0.159 Angle : 0.455 7.580 45881 Z= 0.245 Chirality : 0.038 0.137 5412 Planarity : 0.003 0.051 5555 Dihedral : 10.918 74.018 5621 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.01 % Allowed : 11.62 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.14), residues: 4004 helix: 1.79 (0.10), residues: 2530 sheet: -1.33 (0.31), residues: 231 loop : -0.62 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 4 123 HIS 0.004 0.001 HIS A 275 PHE 0.011 0.001 PHE P 169 TYR 0.025 0.001 TYR S 23 ARG 0.003 0.000 ARG S 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 422 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7664 (ttmt) cc_final: 0.7051 (ttpp) REVERT: C 272 MET cc_start: 0.7593 (mmm) cc_final: 0.6978 (mmm) REVERT: G 125 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: G 129 LYS cc_start: 0.7594 (ttmt) cc_final: 0.7127 (mttp) REVERT: G 272 MET cc_start: 0.7435 (mmm) cc_final: 0.7068 (mmm) REVERT: J 129 LYS cc_start: 0.7493 (ttpt) cc_final: 0.7048 (mttp) REVERT: J 135 MET cc_start: 0.7609 (tpp) cc_final: 0.7017 (tpp) REVERT: J 272 MET cc_start: 0.7453 (mmm) cc_final: 0.7063 (mmm) REVERT: M 125 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6977 (mp0) REVERT: M 272 MET cc_start: 0.7616 (mmm) cc_final: 0.7269 (mmm) REVERT: M 345 THR cc_start: 0.8136 (m) cc_final: 0.7678 (m) REVERT: P 125 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7265 (mp0) REVERT: P 135 MET cc_start: 0.7325 (tpp) cc_final: 0.6932 (tpp) REVERT: P 339 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7364 (mtm-85) REVERT: S 272 MET cc_start: 0.7356 (mmm) cc_final: 0.6945 (mmm) REVERT: S 339 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7185 (mtp180) REVERT: V 125 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: V 135 MET cc_start: 0.7695 (tpp) cc_final: 0.7325 (tpp) REVERT: V 272 MET cc_start: 0.7547 (mmm) cc_final: 0.7239 (mmm) REVERT: V 339 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7495 (mtp180) REVERT: Y 10 ASP cc_start: 0.7762 (m-30) cc_final: 0.7404 (m-30) REVERT: Y 125 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: 1 125 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: 1 272 MET cc_start: 0.7425 (mmm) cc_final: 0.7070 (mmm) REVERT: 4 125 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: 4 272 MET cc_start: 0.7403 (mmm) cc_final: 0.6957 (mmm) outliers start: 70 outliers final: 43 residues processed: 474 average time/residue: 0.4261 time to fit residues: 333.3637 Evaluate side-chains 446 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 396 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 22 GLN Chi-restraints excluded: chain 4 residue 125 GLU Chi-restraints excluded: chain 4 residue 134 THR Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 4.9990 chunk 344 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 383 optimal weight: 4.9990 chunk 318 optimal weight: 0.6980 chunk 177 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS V 7 HIS 1 7 HIS ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 33792 Z= 0.199 Angle : 0.469 5.637 45881 Z= 0.248 Chirality : 0.039 0.133 5412 Planarity : 0.003 0.027 5555 Dihedral : 10.879 74.182 5621 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.90 % Allowed : 12.83 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.14), residues: 4004 helix: 1.77 (0.10), residues: 2552 sheet: -1.37 (0.32), residues: 231 loop : -0.38 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.004 0.001 HIS M 275 PHE 0.016 0.002 PHE 1 169 TYR 0.014 0.001 TYR V 23 ARG 0.003 0.000 ARG S 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 413 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7053 (ttpp) REVERT: C 272 MET cc_start: 0.7601 (mmm) cc_final: 0.7016 (mmm) REVERT: G 125 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: G 129 LYS cc_start: 0.7549 (ttmt) cc_final: 0.7084 (mttp) REVERT: G 272 MET cc_start: 0.7448 (mmm) cc_final: 0.7105 (mmm) REVERT: G 283 LYS cc_start: 0.7947 (tppt) cc_final: 0.7741 (ttpt) REVERT: J 129 LYS cc_start: 0.7505 (ttpt) cc_final: 0.7062 (mttp) REVERT: J 135 MET cc_start: 0.7528 (tpp) cc_final: 0.6999 (tpp) REVERT: J 272 MET cc_start: 0.7434 (mmm) cc_final: 0.7015 (mmm) REVERT: M 125 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: M 135 MET cc_start: 0.7561 (tpp) cc_final: 0.6933 (tpp) REVERT: M 272 MET cc_start: 0.7555 (mmm) cc_final: 0.7228 (mmm) REVERT: P 125 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: P 135 MET cc_start: 0.7439 (tpp) cc_final: 0.7162 (tpp) REVERT: P 339 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7377 (mtm-85) REVERT: S 272 MET cc_start: 0.7351 (mmm) cc_final: 0.7113 (mmm) REVERT: S 339 ARG cc_start: 0.7487 (mmm-85) cc_final: 0.7187 (mtp180) REVERT: V 125 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: V 135 MET cc_start: 0.7794 (tpp) cc_final: 0.7419 (tpp) REVERT: V 272 MET cc_start: 0.7551 (mmm) cc_final: 0.7254 (mmm) REVERT: V 339 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7521 (mtp180) REVERT: Y 10 ASP cc_start: 0.7790 (m-30) cc_final: 0.7418 (m-30) REVERT: Y 125 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: Y 272 MET cc_start: 0.7383 (mmm) cc_final: 0.7086 (mmm) REVERT: 1 125 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6944 (mp0) REVERT: 1 272 MET cc_start: 0.7436 (mmm) cc_final: 0.7088 (mmm) REVERT: 4 10 ASP cc_start: 0.7755 (m-30) cc_final: 0.7254 (m-30) REVERT: 4 125 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: 4 272 MET cc_start: 0.7426 (mmm) cc_final: 0.6990 (mmm) outliers start: 66 outliers final: 49 residues processed: 457 average time/residue: 0.4227 time to fit residues: 318.4716 Evaluate side-chains 457 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 401 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 181 GLU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 22 GLN Chi-restraints excluded: chain 4 residue 125 GLU Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 279 optimal weight: 9.9990 chunk 216 optimal weight: 2.9990 chunk 322 optimal weight: 0.0570 chunk 213 optimal weight: 0.0870 chunk 381 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 232 optimal weight: 0.9990 chunk 176 optimal weight: 5.9990 overall best weight: 1.0282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33792 Z= 0.216 Angle : 0.480 5.964 45881 Z= 0.253 Chirality : 0.039 0.133 5412 Planarity : 0.003 0.028 5555 Dihedral : 10.868 74.276 5621 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.87 % Allowed : 13.41 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.14), residues: 4004 helix: 1.78 (0.10), residues: 2552 sheet: -1.41 (0.32), residues: 231 loop : -0.35 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.003 0.001 HIS S 15 PHE 0.015 0.002 PHE 1 169 TYR 0.015 0.001 TYR G 23 ARG 0.003 0.000 ARG Y 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 410 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7671 (ttmt) cc_final: 0.7048 (ttpp) REVERT: C 272 MET cc_start: 0.7600 (mmm) cc_final: 0.7024 (mmm) REVERT: G 125 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: G 129 LYS cc_start: 0.7574 (ttmt) cc_final: 0.7103 (mttp) REVERT: G 272 MET cc_start: 0.7500 (mmm) cc_final: 0.7154 (mmm) REVERT: G 283 LYS cc_start: 0.7939 (tppt) cc_final: 0.7737 (ttpt) REVERT: J 129 LYS cc_start: 0.7513 (ttpt) cc_final: 0.7062 (mttp) REVERT: J 135 MET cc_start: 0.7572 (tpp) cc_final: 0.7051 (tpp) REVERT: J 272 MET cc_start: 0.7440 (mmm) cc_final: 0.7025 (mmm) REVERT: M 125 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: M 135 MET cc_start: 0.7606 (tpp) cc_final: 0.7046 (tpp) REVERT: M 272 MET cc_start: 0.7590 (mmm) cc_final: 0.7285 (mmm) REVERT: P 125 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: P 135 MET cc_start: 0.7430 (tpp) cc_final: 0.7205 (tpp) REVERT: P 339 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7453 (mtp180) REVERT: S 125 GLU cc_start: 0.7394 (mp0) cc_final: 0.6554 (mp0) REVERT: S 272 MET cc_start: 0.7359 (mmm) cc_final: 0.7123 (mmm) REVERT: S 339 ARG cc_start: 0.7509 (mmm-85) cc_final: 0.7213 (mtp180) REVERT: V 125 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7041 (mp0) REVERT: V 135 MET cc_start: 0.7825 (tpp) cc_final: 0.7450 (tpp) REVERT: V 272 MET cc_start: 0.7601 (mmm) cc_final: 0.7261 (mmm) REVERT: V 339 ARG cc_start: 0.7798 (mmm-85) cc_final: 0.7520 (mtp180) REVERT: Y 10 ASP cc_start: 0.7792 (m-30) cc_final: 0.7435 (m-30) REVERT: Y 125 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6916 (mp0) REVERT: Y 135 MET cc_start: 0.7609 (tpp) cc_final: 0.7003 (tpp) REVERT: 1 125 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.6940 (mp0) REVERT: 1 272 MET cc_start: 0.7466 (mmm) cc_final: 0.7119 (mmm) REVERT: 4 10 ASP cc_start: 0.7771 (m-30) cc_final: 0.7263 (m-30) REVERT: 4 125 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: 4 283 LYS cc_start: 0.8178 (tppt) cc_final: 0.7927 (ttpt) outliers start: 65 outliers final: 50 residues processed: 454 average time/residue: 0.4209 time to fit residues: 315.9862 Evaluate side-chains 462 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 405 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 181 GLU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 22 GLN Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 22 GLN Chi-restraints excluded: chain 4 residue 125 GLU Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 3.9990 chunk 152 optimal weight: 0.0270 chunk 227 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 242 optimal weight: 0.6980 chunk 260 optimal weight: 0.1980 chunk 188 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS V 7 HIS 1 7 HIS ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33792 Z= 0.142 Angle : 0.451 8.650 45881 Z= 0.239 Chirality : 0.037 0.134 5412 Planarity : 0.003 0.021 5555 Dihedral : 10.920 73.858 5621 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.84 % Allowed : 13.78 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.14), residues: 4004 helix: 1.98 (0.10), residues: 2552 sheet: -1.36 (0.33), residues: 231 loop : -0.31 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 4 123 HIS 0.004 0.001 HIS 4 15 PHE 0.010 0.001 PHE P 169 TYR 0.012 0.001 TYR 4 23 ARG 0.002 0.000 ARG S 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 428 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 10 ASP cc_start: 0.7713 (m-30) cc_final: 0.7381 (m-30) REVERT: C 129 LYS cc_start: 0.7597 (ttmt) cc_final: 0.6976 (ttpp) REVERT: C 272 MET cc_start: 0.7621 (mmm) cc_final: 0.7341 (mmt) REVERT: G 125 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: G 129 LYS cc_start: 0.7532 (ttmt) cc_final: 0.7061 (mttp) REVERT: G 272 MET cc_start: 0.7509 (mmm) cc_final: 0.7232 (mmm) REVERT: J 129 LYS cc_start: 0.7440 (ttpt) cc_final: 0.7012 (mttp) REVERT: J 135 MET cc_start: 0.7551 (tpp) cc_final: 0.7038 (tpp) REVERT: J 272 MET cc_start: 0.7499 (mmm) cc_final: 0.7268 (mmm) REVERT: M 135 MET cc_start: 0.7601 (tpp) cc_final: 0.7009 (tpp) REVERT: M 201 MET cc_start: 0.7976 (ptt) cc_final: 0.7766 (ptm) REVERT: M 272 MET cc_start: 0.7559 (mmm) cc_final: 0.7344 (mmm) REVERT: M 345 THR cc_start: 0.8087 (m) cc_final: 0.7618 (m) REVERT: P 125 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: P 135 MET cc_start: 0.7471 (tpp) cc_final: 0.6956 (tpp) REVERT: P 339 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7417 (mtp180) REVERT: S 125 GLU cc_start: 0.7371 (mp0) cc_final: 0.6585 (mp0) REVERT: S 272 MET cc_start: 0.7441 (mmm) cc_final: 0.7225 (mmm) REVERT: S 339 ARG cc_start: 0.7451 (mmm-85) cc_final: 0.7163 (mtp180) REVERT: V 125 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: V 135 MET cc_start: 0.7784 (tpp) cc_final: 0.7480 (tpp) REVERT: V 272 MET cc_start: 0.7609 (mmm) cc_final: 0.7290 (mmm) REVERT: V 339 ARG cc_start: 0.7761 (mmm-85) cc_final: 0.7483 (mtp180) REVERT: Y 10 ASP cc_start: 0.7764 (m-30) cc_final: 0.7405 (m-30) REVERT: Y 125 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: Y 129 LYS cc_start: 0.7314 (ttmm) cc_final: 0.6992 (mttp) REVERT: Y 135 MET cc_start: 0.7674 (tpp) cc_final: 0.7160 (tpp) REVERT: 1 125 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: 1 272 MET cc_start: 0.7471 (mmm) cc_final: 0.7152 (mmm) REVERT: 4 283 LYS cc_start: 0.8151 (tppt) cc_final: 0.7878 (ttpt) outliers start: 64 outliers final: 49 residues processed: 471 average time/residue: 0.4107 time to fit residues: 320.0569 Evaluate side-chains 465 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 411 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 282 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 282 LEU Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 22 GLN Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 282 LEU Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 3.9990 chunk 365 optimal weight: 4.9990 chunk 333 optimal weight: 5.9990 chunk 355 optimal weight: 0.8980 chunk 214 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 279 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 321 optimal weight: 3.9990 chunk 336 optimal weight: 0.8980 chunk 354 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS V 216 GLN ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 216 GLN ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33792 Z= 0.330 Angle : 0.549 6.809 45881 Z= 0.283 Chirality : 0.041 0.135 5412 Planarity : 0.004 0.044 5555 Dihedral : 10.896 74.658 5621 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.87 % Allowed : 14.30 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4004 helix: 1.69 (0.10), residues: 2552 sheet: -1.52 (0.32), residues: 231 loop : -0.36 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP 4 261 HIS 0.003 0.001 HIS J 275 PHE 0.018 0.002 PHE 1 169 TYR 0.018 0.002 TYR S 69 ARG 0.003 0.000 ARG M 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 408 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7699 (ttmt) cc_final: 0.7072 (ttpp) REVERT: C 272 MET cc_start: 0.7618 (mmm) cc_final: 0.7038 (mmm) REVERT: G 125 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: G 129 LYS cc_start: 0.7613 (ttmt) cc_final: 0.7142 (mttp) REVERT: G 272 MET cc_start: 0.7498 (mmm) cc_final: 0.7153 (mmm) REVERT: J 135 MET cc_start: 0.7634 (tpp) cc_final: 0.7124 (tpp) REVERT: J 272 MET cc_start: 0.7440 (mmm) cc_final: 0.7027 (mmm) REVERT: M 135 MET cc_start: 0.7614 (tpp) cc_final: 0.7085 (tpp) REVERT: P 125 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: P 339 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7492 (mtp180) REVERT: S 125 GLU cc_start: 0.7437 (mp0) cc_final: 0.6654 (mp0) REVERT: S 272 MET cc_start: 0.7376 (mmm) cc_final: 0.7142 (mmm) REVERT: S 339 ARG cc_start: 0.7567 (mmm-85) cc_final: 0.7281 (mtp180) REVERT: V 125 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6957 (mp0) REVERT: V 135 MET cc_start: 0.7813 (tpp) cc_final: 0.7444 (tpp) REVERT: V 272 MET cc_start: 0.7551 (mmm) cc_final: 0.7213 (mmm) REVERT: V 339 ARG cc_start: 0.7874 (mmm-85) cc_final: 0.7568 (mtp180) REVERT: Y 125 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: Y 135 MET cc_start: 0.7727 (tpp) cc_final: 0.7273 (tpp) REVERT: 1 125 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: 1 272 MET cc_start: 0.7441 (mmm) cc_final: 0.7080 (mmm) REVERT: 4 283 LYS cc_start: 0.8182 (tppt) cc_final: 0.7873 (ttpt) outliers start: 65 outliers final: 55 residues processed: 450 average time/residue: 0.4188 time to fit residues: 309.7627 Evaluate side-chains 461 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 401 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 181 GLU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 282 LEU Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 22 GLN Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 22 GLN Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 282 LEU Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 0.0870 chunk 376 optimal weight: 0.5980 chunk 229 optimal weight: 7.9990 chunk 178 optimal weight: 0.0170 chunk 261 optimal weight: 9.9990 chunk 394 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 314 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 242 optimal weight: 0.7980 chunk 192 optimal weight: 0.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN V 7 HIS ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 33792 Z= 0.155 Angle : 0.484 9.608 45881 Z= 0.253 Chirality : 0.038 0.139 5412 Planarity : 0.003 0.022 5555 Dihedral : 10.919 73.933 5621 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.70 % Allowed : 14.56 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 4004 helix: 1.94 (0.10), residues: 2552 sheet: -1.45 (0.33), residues: 231 loop : -0.32 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 123 HIS 0.004 0.001 HIS M 15 PHE 0.012 0.001 PHE P 169 TYR 0.016 0.001 TYR Y 23 ARG 0.003 0.000 ARG S 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 415 time to evaluate : 3.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7610 (ttmt) cc_final: 0.6981 (ttpp) REVERT: C 135 MET cc_start: 0.7518 (tpp) cc_final: 0.7248 (tpp) REVERT: C 272 MET cc_start: 0.7612 (mmm) cc_final: 0.7337 (mmt) REVERT: G 125 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: G 129 LYS cc_start: 0.7531 (ttmt) cc_final: 0.7063 (mttp) REVERT: G 283 LYS cc_start: 0.8143 (tppt) cc_final: 0.7811 (ttpt) REVERT: J 129 LYS cc_start: 0.7464 (ttpt) cc_final: 0.7028 (mttp) REVERT: J 135 MET cc_start: 0.7530 (tpp) cc_final: 0.7124 (tpp) REVERT: J 272 MET cc_start: 0.7479 (mmm) cc_final: 0.7247 (mmm) REVERT: M 135 MET cc_start: 0.7573 (tpp) cc_final: 0.7078 (tpp) REVERT: M 272 MET cc_start: 0.7642 (mmm) cc_final: 0.7274 (mmm) REVERT: P 125 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: P 339 ARG cc_start: 0.7744 (mmm-85) cc_final: 0.7394 (mtp180) REVERT: S 125 GLU cc_start: 0.7378 (mp0) cc_final: 0.6625 (mp0) REVERT: S 272 MET cc_start: 0.7453 (mmm) cc_final: 0.7231 (mmm) REVERT: S 339 ARG cc_start: 0.7490 (mmm-85) cc_final: 0.7198 (mtp180) REVERT: V 125 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: V 135 MET cc_start: 0.7748 (tpp) cc_final: 0.7454 (tpp) REVERT: V 272 MET cc_start: 0.7589 (mmm) cc_final: 0.7268 (mmm) REVERT: V 339 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7503 (mtp180) REVERT: Y 10 ASP cc_start: 0.7831 (m-30) cc_final: 0.7423 (m-30) REVERT: Y 125 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: Y 135 MET cc_start: 0.7663 (tpp) cc_final: 0.7260 (tpp) REVERT: 1 125 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.6993 (mp0) REVERT: 1 272 MET cc_start: 0.7475 (mmm) cc_final: 0.7147 (mmm) REVERT: 1 283 LYS cc_start: 0.8121 (tppt) cc_final: 0.7687 (mttm) REVERT: 4 10 ASP cc_start: 0.7811 (m-30) cc_final: 0.7342 (m-30) REVERT: 4 283 LYS cc_start: 0.8153 (tppt) cc_final: 0.7841 (ttpt) outliers start: 59 outliers final: 50 residues processed: 455 average time/residue: 0.4166 time to fit residues: 313.3385 Evaluate side-chains 458 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 403 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 235 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 235 SER Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain P residue 22 GLN Chi-restraints excluded: chain P residue 125 GLU Chi-restraints excluded: chain P residue 176 ILE Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 235 SER Chi-restraints excluded: chain P residue 282 LEU Chi-restraints excluded: chain P residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 342 VAL Chi-restraints excluded: chain V residue 125 GLU Chi-restraints excluded: chain V residue 176 ILE Chi-restraints excluded: chain V residue 181 GLU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 235 SER Chi-restraints excluded: chain V residue 342 VAL Chi-restraints excluded: chain Y residue 125 GLU Chi-restraints excluded: chain Y residue 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 342 VAL Chi-restraints excluded: chain 1 residue 22 GLN Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 190 VAL Chi-restraints excluded: chain 1 residue 235 SER Chi-restraints excluded: chain 1 residue 342 VAL Chi-restraints excluded: chain 4 residue 22 GLN Chi-restraints excluded: chain 4 residue 176 ILE Chi-restraints excluded: chain 4 residue 190 VAL Chi-restraints excluded: chain 4 residue 235 SER Chi-restraints excluded: chain 4 residue 282 LEU Chi-restraints excluded: chain 4 residue 342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 0.0020 chunk 334 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 289 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 314 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 323 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS C 284 GLN ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN P 216 GLN ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.168108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.140925 restraints weight = 40517.297| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.43 r_work: 0.3261 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33792 Z= 0.244 Angle : 0.519 8.730 45881 Z= 0.266 Chirality : 0.040 0.131 5412 Planarity : 0.003 0.034 5555 Dihedral : 10.957 74.348 5621 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.67 % Allowed : 14.70 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.14), residues: 4004 helix: 1.85 (0.10), residues: 2552 sheet: -1.51 (0.33), residues: 231 loop : -0.35 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.004 0.001 HIS A 56 PHE 0.017 0.002 PHE J 169 TYR 0.015 0.001 TYR 4 69 ARG 0.002 0.000 ARG S 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6795.60 seconds wall clock time: 124 minutes 3.29 seconds (7443.29 seconds total)