Starting phenix.real_space_refine on Fri Jul 26 11:58:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/07_2024/8pdq_17618.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/07_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_17618/07_2024/8pdq_17618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/07_2024/8pdq_17618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/07_2024/8pdq_17618.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/07_2024/8pdq_17618.cif" } 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 18.03, per 1000 atoms: 0.54 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: 12.53 Conformation dependent library (CDL) restraints added in 6.0 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: 11.04 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: 3.949A 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: 11.54 Time building geometry restraints manager: 13.87 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: 6694 1.46 - 1.58: 16021 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: 13663 120.48 - 127.24: 11542 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: 153 0.110 - 0.137: 83 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: 169683 Warning: very small nonbonded interaction distances. Nonbonded interactions: 282186 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 282181 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: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.220 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 93.260 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.240 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.700 ------------------------------------------------------------------------------- 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 : 3.469 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: 0.7546 (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: 0.4314 time to fit residues: 327.1390 Evaluate side-chains 415 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 3.279 ------------------------------------------------------------------------------- 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: 9.9990 chunk 300 optimal weight: 0.6980 chunk 166 optimal weight: 0.5980 chunk 102 optimal weight: 0.2980 chunk 202 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 310 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 188 optimal weight: 0.0040 chunk 231 optimal weight: 0.6980 chunk 359 optimal weight: 4.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- 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 284 GLN V 306 GLN Y 7 HIS ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 284 GLN 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33792 Z= 0.167 Angle : 0.498 8.622 45881 Z= 0.269 Chirality : 0.039 0.131 5412 Planarity : 0.003 0.026 5555 Dihedral : 11.857 74.043 5621 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.60 % Allowed : 7.51 % Favored : 91.89 % 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: 0.90 (0.13), residues: 4004 helix: 1.45 (0.10), residues: 2530 sheet: -1.28 (0.29), residues: 231 loop : -0.71 (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 A 7 PHE 0.011 0.001 PHE Y 224 TYR 0.012 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 453 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 432 time to evaluate : 3.231 Fit side-chains REVERT: A 129 LYS cc_start: 0.7572 (ttmt) cc_final: 0.6972 (ttpp) REVERT: A 272 MET cc_start: 0.7252 (mmm) cc_final: 0.6849 (mmm) REVERT: C 129 LYS cc_start: 0.7555 (ttmt) cc_final: 0.6989 (ttpp) REVERT: C 272 MET cc_start: 0.7436 (mmm) cc_final: 0.6871 (mmm) REVERT: G 129 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7068 (mttp) REVERT: J 129 LYS cc_start: 0.7454 (ttpt) cc_final: 0.6999 (mttp) REVERT: J 272 MET cc_start: 0.7264 (mmm) cc_final: 0.6978 (mmm) REVERT: M 249 MET cc_start: 0.7917 (mmm) cc_final: 0.7573 (mmm) REVERT: M 258 MET cc_start: 0.7951 (tpp) cc_final: 0.7741 (mmm) REVERT: P 272 MET cc_start: 0.7544 (mmm) cc_final: 0.7092 (mmm) REVERT: P 339 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7501 (mtp180) REVERT: S 272 MET cc_start: 0.7329 (mmm) cc_final: 0.6885 (mmm) REVERT: S 339 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7253 (mtp180) REVERT: V 339 ARG cc_start: 0.7772 (mmm-85) cc_final: 0.7514 (mtp180) REVERT: Y 272 MET cc_start: 0.7302 (mmm) cc_final: 0.7032 (mmm) REVERT: Y 339 ARG cc_start: 0.7707 (mmm-85) cc_final: 0.7460 (mtp180) REVERT: 1 129 LYS cc_start: 0.7509 (ttmt) cc_final: 0.6879 (ttpp) REVERT: 4 129 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7025 (ttpp) REVERT: 4 341 ARG cc_start: 0.7396 (mtm180) cc_final: 0.7195 (mtm180) outliers start: 21 outliers final: 13 residues processed: 443 average time/residue: 0.4602 time to fit residues: 337.6054 Evaluate side-chains 395 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 382 time to evaluate : 3.904 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 99 optimal weight: 8.9990 chunk 360 optimal weight: 0.0980 chunk 389 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 HIS ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 33792 Z= 0.376 Angle : 0.589 7.461 45881 Z= 0.307 Chirality : 0.043 0.138 5412 Planarity : 0.004 0.047 5555 Dihedral : 11.205 74.811 5621 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.50 % Allowed : 8.52 % Favored : 89.99 % 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: 0.71 (0.13), residues: 4004 helix: 1.28 (0.10), residues: 2519 sheet: -1.40 (0.28), residues: 231 loop : -0.71 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP 4 123 HIS 0.006 0.001 HIS A 275 PHE 0.020 0.002 PHE 1 169 TYR 0.022 0.002 TYR P 23 ARG 0.005 0.001 ARG G 27 *********************** 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: 52 poor density : 396 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7385 (mmm) cc_final: 0.7017 (mmm) REVERT: C 129 LYS cc_start: 0.7723 (ttmt) cc_final: 0.7123 (ttpp) REVERT: C 272 MET cc_start: 0.7535 (mmm) cc_final: 0.6840 (mmm) REVERT: G 125 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: G 129 LYS cc_start: 0.7701 (ttmt) cc_final: 0.7236 (mttp) REVERT: G 283 LYS cc_start: 0.8045 (tppt) cc_final: 0.7841 (ttpt) REVERT: J 135 MET cc_start: 0.7122 (ttm) cc_final: 0.6852 (tpp) REVERT: J 272 MET cc_start: 0.7493 (mmm) cc_final: 0.7227 (mmm) REVERT: M 249 MET cc_start: 0.7984 (mmm) cc_final: 0.7411 (mmm) REVERT: M 272 MET cc_start: 0.7544 (mmm) cc_final: 0.7141 (mmm) REVERT: P 135 MET cc_start: 0.7346 (tpp) cc_final: 0.6564 (tpp) REVERT: P 339 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7598 (mtt180) REVERT: S 272 MET cc_start: 0.7331 (mmm) cc_final: 0.6919 (mmm) REVERT: S 339 ARG cc_start: 0.7669 (mmm-85) cc_final: 0.7303 (mtp180) REVERT: V 125 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: V 135 MET cc_start: 0.7543 (tpp) cc_final: 0.7123 (tpp) REVERT: Y 125 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: Y 283 LYS cc_start: 0.8059 (tppt) cc_final: 0.7821 (ttpt) REVERT: 1 125 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: 1 272 MET cc_start: 0.7482 (mmm) cc_final: 0.7178 (mmm) REVERT: 4 125 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6934 (mp0) REVERT: 4 272 MET cc_start: 0.7332 (mmm) cc_final: 0.6878 (mmm) REVERT: 4 283 LYS cc_start: 0.8249 (tppt) cc_final: 0.7999 (ttpt) REVERT: 4 341 ARG cc_start: 0.7537 (mtm180) cc_final: 0.7146 (mtm180) outliers start: 52 outliers final: 37 residues processed: 433 average time/residue: 0.4429 time to fit residues: 316.7923 Evaluate side-chains 421 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 379 time to evaluate : 3.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL 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 134 THR Chi-restraints excluded: chain C residue 190 VAL 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 176 ILE Chi-restraints excluded: chain G residue 190 VAL 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 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 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 31 THR Chi-restraints excluded: chain 1 residue 125 GLU Chi-restraints excluded: chain 1 residue 134 THR Chi-restraints excluded: chain 1 residue 190 VAL 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 235 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 0.2980 chunk 270 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 241 optimal weight: 0.7980 chunk 361 optimal weight: 0.7980 chunk 382 optimal weight: 0.5980 chunk 188 optimal weight: 4.9990 chunk 342 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 7 HIS V 7 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33792 Z= 0.167 Angle : 0.465 5.772 45881 Z= 0.252 Chirality : 0.038 0.139 5412 Planarity : 0.003 0.056 5555 Dihedral : 10.979 74.071 5621 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.38 % Allowed : 10.27 % Favored : 88.35 % 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: 1.14 (0.14), residues: 4004 helix: 1.64 (0.10), residues: 2530 sheet: -1.37 (0.30), residues: 231 loop : -0.60 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP 4 123 HIS 0.004 0.001 HIS V 15 PHE 0.012 0.002 PHE C 169 TYR 0.013 0.001 TYR P 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 448 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 400 time to evaluate : 3.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.8249 (tpp) cc_final: 0.7973 (mmm) REVERT: A 272 MET cc_start: 0.7422 (mmm) cc_final: 0.7104 (mmm) REVERT: C 129 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7039 (ttpp) REVERT: C 272 MET cc_start: 0.7565 (mmm) cc_final: 0.6919 (mmm) REVERT: G 125 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: G 129 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7119 (mttp) REVERT: G 272 MET cc_start: 0.7399 (mmm) cc_final: 0.7009 (mmm) REVERT: J 129 LYS cc_start: 0.7544 (ttpt) cc_final: 0.7098 (mttp) REVERT: J 272 MET cc_start: 0.7482 (mmm) cc_final: 0.7045 (mmm) REVERT: M 249 MET cc_start: 0.7993 (mmm) cc_final: 0.7254 (mmm) REVERT: M 272 MET cc_start: 0.7552 (mmm) cc_final: 0.7141 (mmm) REVERT: M 279 GLN cc_start: 0.7108 (mm-40) cc_final: 0.6522 (mm-40) REVERT: M 345 THR cc_start: 0.8180 (m) cc_final: 0.7730 (m) REVERT: P 125 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: P 339 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7386 (mtm-85) REVERT: S 125 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: S 272 MET cc_start: 0.7392 (mmm) cc_final: 0.7032 (mmm) REVERT: S 339 ARG cc_start: 0.7490 (mmm-85) cc_final: 0.7181 (mtp180) REVERT: V 125 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: V 135 MET cc_start: 0.7663 (tpp) cc_final: 0.7265 (tpp) REVERT: V 272 MET cc_start: 0.7558 (mmm) cc_final: 0.7246 (mmm) REVERT: Y 125 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: 1 125 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: 1 272 MET cc_start: 0.7592 (mmm) cc_final: 0.7319 (mmm) REVERT: 4 10 ASP cc_start: 0.7728 (m-30) cc_final: 0.7226 (m-30) REVERT: 4 125 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: 4 272 MET cc_start: 0.7415 (mmm) cc_final: 0.6843 (mmm) REVERT: 4 283 LYS cc_start: 0.8104 (tppt) cc_final: 0.7866 (ttpt) outliers start: 48 outliers final: 24 residues processed: 437 average time/residue: 0.4191 time to fit residues: 301.7136 Evaluate side-chains 415 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 384 time to evaluate : 3.785 ------------------------------------------------------------------------------- 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 C residue 125 GLU Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain G residue 125 GLU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain M residue 125 GLU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 235 SER 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 235 SER Chi-restraints excluded: chain S residue 125 GLU Chi-restraints excluded: chain S residue 176 ILE 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 125 GLU Chi-restraints excluded: chain 1 residue 235 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 0.8980 chunk 217 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 285 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 326 optimal weight: 0.0570 chunk 264 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 195 optimal weight: 0.6980 chunk 343 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- 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** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS 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: 0.7846 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33792 Z= 0.177 Angle : 0.462 7.510 45881 Z= 0.246 Chirality : 0.038 0.133 5412 Planarity : 0.003 0.041 5555 Dihedral : 10.900 74.105 5621 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.01 % Allowed : 11.25 % Favored : 86.74 % 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: 1.32 (0.14), residues: 4004 helix: 1.80 (0.10), residues: 2530 sheet: -1.35 (0.31), residues: 231 loop : -0.56 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 4 123 HIS 0.003 0.001 HIS S 15 PHE 0.013 0.002 PHE 1 169 TYR 0.012 0.001 TYR G 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 478 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 408 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7066 (ttpp) REVERT: C 272 MET cc_start: 0.7590 (mmm) cc_final: 0.6988 (mmm) REVERT: G 125 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: G 129 LYS cc_start: 0.7548 (ttmt) cc_final: 0.7076 (mttp) REVERT: G 272 MET cc_start: 0.7411 (mmm) cc_final: 0.7055 (mmm) REVERT: J 129 LYS cc_start: 0.7495 (ttpt) cc_final: 0.7049 (mttp) REVERT: J 135 MET cc_start: 0.7523 (tpp) cc_final: 0.6947 (tpp) REVERT: J 272 MET cc_start: 0.7463 (mmm) cc_final: 0.7074 (mmm) REVERT: M 272 MET cc_start: 0.7559 (mmm) cc_final: 0.7186 (mmm) REVERT: P 125 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: P 135 MET cc_start: 0.7317 (tpp) cc_final: 0.6940 (tpp) REVERT: P 339 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7376 (mtm-85) REVERT: S 125 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: S 272 MET cc_start: 0.7344 (mmm) cc_final: 0.6932 (mmm) REVERT: S 339 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.7198 (mtp180) REVERT: V 125 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6809 (mp0) REVERT: V 135 MET cc_start: 0.7747 (tpp) cc_final: 0.7378 (tpp) REVERT: V 272 MET cc_start: 0.7542 (mmm) cc_final: 0.7234 (mmm) REVERT: V 339 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7498 (mtp180) REVERT: Y 10 ASP cc_start: 0.7777 (m-30) cc_final: 0.7397 (m-30) REVERT: Y 125 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: Y 283 LYS cc_start: 0.7899 (tppt) cc_final: 0.7563 (mttp) REVERT: 1 125 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: 1 272 MET cc_start: 0.7526 (mmm) cc_final: 0.7228 (mmm) REVERT: 4 125 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7532 (mp0) REVERT: 4 272 MET cc_start: 0.7402 (mmm) cc_final: 0.6961 (mmm) outliers start: 70 outliers final: 47 residues processed: 459 average time/residue: 0.4286 time to fit residues: 326.0484 Evaluate side-chains 446 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 392 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 282 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 125 GLU 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 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 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 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 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 282 LEU 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 190 VAL 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: 0.7980 chunk 75 optimal weight: 4.9990 chunk 224 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 383 optimal weight: 0.6980 chunk 318 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 126 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** 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: 0.7860 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33792 Z= 0.203 Angle : 0.470 5.628 45881 Z= 0.249 Chirality : 0.039 0.133 5412 Planarity : 0.003 0.027 5555 Dihedral : 10.861 74.220 5621 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.90 % Allowed : 12.49 % Favored : 85.62 % 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: 1.38 (0.13), residues: 4004 helix: 1.77 (0.10), residues: 2552 sheet: -1.39 (0.32), residues: 231 loop : -0.36 (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 J 169 TYR 0.020 0.001 TYR A 23 ARG 0.002 0.000 ARG S 185 *********************** 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 477 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 411 time to evaluate : 3.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7702 (ttmt) cc_final: 0.7095 (ttpp) REVERT: C 135 MET cc_start: 0.7606 (tpp) cc_final: 0.7199 (tpp) REVERT: C 272 MET cc_start: 0.7593 (mmm) cc_final: 0.7025 (mmm) REVERT: G 125 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: G 129 LYS cc_start: 0.7580 (ttmt) cc_final: 0.7097 (mttp) REVERT: G 272 MET cc_start: 0.7454 (mmm) cc_final: 0.7106 (mmm) REVERT: J 129 LYS cc_start: 0.7507 (ttpt) cc_final: 0.7062 (mttp) REVERT: J 135 MET cc_start: 0.7565 (tpp) cc_final: 0.7030 (tpp) REVERT: J 272 MET cc_start: 0.7446 (mmm) cc_final: 0.7029 (mmm) REVERT: M 135 MET cc_start: 0.7587 (tpp) cc_final: 0.6993 (tpp) REVERT: M 272 MET cc_start: 0.7600 (mmm) cc_final: 0.7159 (mmm) REVERT: P 125 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: P 135 MET cc_start: 0.7424 (tpp) cc_final: 0.7178 (tpp) REVERT: P 339 ARG cc_start: 0.7790 (mmm-85) cc_final: 0.7451 (mtp180) REVERT: S 125 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: S 272 MET cc_start: 0.7353 (mmm) cc_final: 0.6931 (mmm) REVERT: S 339 ARG cc_start: 0.7515 (mmm-85) cc_final: 0.7223 (mtp180) REVERT: V 125 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: V 135 MET cc_start: 0.7841 (tpp) cc_final: 0.7448 (tpp) REVERT: V 272 MET cc_start: 0.7546 (mmm) cc_final: 0.7242 (mmm) REVERT: V 339 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7512 (mtp180) REVERT: Y 10 ASP cc_start: 0.7777 (m-30) cc_final: 0.7412 (m-30) REVERT: Y 125 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: 1 125 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.6950 (mp0) REVERT: 1 272 MET cc_start: 0.7523 (mmm) cc_final: 0.7276 (mmm) REVERT: 4 10 ASP cc_start: 0.7731 (m-30) cc_final: 0.7224 (m-30) REVERT: 4 125 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: 4 129 LYS cc_start: 0.7595 (ttmt) cc_final: 0.7350 (ttmm) REVERT: 4 272 MET cc_start: 0.7423 (mmm) cc_final: 0.6990 (mmm) outliers start: 66 outliers final: 48 residues processed: 458 average time/residue: 0.4385 time to fit residues: 332.9235 Evaluate side-chains 456 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 401 time to evaluate : 3.540 ------------------------------------------------------------------------------- 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 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 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 342 VAL 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 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 190 VAL 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: 1.9990 chunk 43 optimal weight: 0.9980 chunk 218 optimal weight: 0.6980 chunk 279 optimal weight: 7.9990 chunk 216 optimal weight: 0.2980 chunk 322 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 381 optimal weight: 0.9980 chunk 238 optimal weight: 1.9990 chunk 232 optimal weight: 0.9980 chunk 176 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7844 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33792 Z= 0.178 Angle : 0.460 5.848 45881 Z= 0.244 Chirality : 0.038 0.134 5412 Planarity : 0.003 0.021 5555 Dihedral : 10.872 74.096 5621 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.87 % Allowed : 13.29 % Favored : 84.84 % 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: 1.50 (0.14), residues: 4004 helix: 1.88 (0.10), residues: 2552 sheet: -1.39 (0.32), residues: 231 loop : -0.34 (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 0.013 0.002 PHE 1 169 TYR 0.014 0.001 TYR 4 23 ARG 0.002 0.000 ARG S 185 *********************** 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 473 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 408 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7075 (ttpp) REVERT: C 135 MET cc_start: 0.7610 (tpp) cc_final: 0.7164 (tpp) REVERT: C 272 MET cc_start: 0.7603 (mmm) cc_final: 0.6996 (mmm) REVERT: G 125 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: G 129 LYS cc_start: 0.7569 (ttmt) cc_final: 0.7077 (mttp) REVERT: G 272 MET cc_start: 0.7503 (mmm) cc_final: 0.7166 (mmm) REVERT: J 129 LYS cc_start: 0.7486 (ttpt) cc_final: 0.7039 (mttp) REVERT: J 135 MET cc_start: 0.7568 (tpp) cc_final: 0.7012 (tpp) REVERT: J 272 MET cc_start: 0.7475 (mmm) cc_final: 0.7081 (mmm) REVERT: M 135 MET cc_start: 0.7560 (tpp) cc_final: 0.6989 (tpp) REVERT: M 272 MET cc_start: 0.7535 (mmm) cc_final: 0.7089 (mmm) REVERT: P 125 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: P 135 MET cc_start: 0.7438 (tpp) cc_final: 0.6884 (tpp) REVERT: P 339 ARG cc_start: 0.7747 (mmm-85) cc_final: 0.7399 (mtp180) REVERT: S 125 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: S 272 MET cc_start: 0.7362 (mmm) cc_final: 0.7128 (mmm) REVERT: S 339 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.7209 (mtp180) REVERT: V 125 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: V 135 MET cc_start: 0.7810 (tpp) cc_final: 0.7428 (tpp) REVERT: V 272 MET cc_start: 0.7591 (mmm) cc_final: 0.7261 (mmm) REVERT: V 339 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7511 (mtp180) REVERT: Y 10 ASP cc_start: 0.7822 (m-30) cc_final: 0.7460 (m-30) REVERT: Y 125 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: 1 125 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: 1 272 MET cc_start: 0.7548 (mmm) cc_final: 0.7326 (mmm) REVERT: 4 125 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: 4 129 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7354 (ttmm) REVERT: 4 283 LYS cc_start: 0.8126 (tppt) cc_final: 0.7826 (ttpt) outliers start: 65 outliers final: 53 residues processed: 454 average time/residue: 0.4163 time to fit residues: 313.3635 Evaluate side-chains 461 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 401 time to evaluate : 3.592 ------------------------------------------------------------------------------- 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 125 GLU 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 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 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 190 VAL Chi-restraints excluded: chain Y residue 235 SER Chi-restraints excluded: chain Y residue 282 LEU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 0.5980 chunk 152 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 242 optimal weight: 0.9980 chunk 260 optimal weight: 0.5980 chunk 188 optimal weight: 0.0980 chunk 35 optimal weight: 7.9990 chunk 300 optimal weight: 0.0020 overall best weight: 0.4188 ------------------------------------------------------------------------------- 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** S 7 HIS ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 33792 Z= 0.142 Angle : 0.448 9.072 45881 Z= 0.237 Chirality : 0.037 0.132 5412 Planarity : 0.003 0.021 5555 Dihedral : 10.918 73.863 5621 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.93 % Allowed : 13.69 % 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: 1.69 (0.14), residues: 4004 helix: 2.04 (0.10), residues: 2552 sheet: -1.37 (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 0.005 0.001 HIS A 275 PHE 0.011 0.001 PHE 1 169 TYR 0.011 0.001 TYR Y 338 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 491 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 424 time to evaluate : 3.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 10 ASP cc_start: 0.7714 (m-30) cc_final: 0.7404 (m-30) REVERT: C 129 LYS cc_start: 0.7638 (ttmt) cc_final: 0.7026 (ttpp) REVERT: C 135 MET cc_start: 0.7535 (tpp) cc_final: 0.7134 (tpp) REVERT: G 125 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: G 129 LYS cc_start: 0.7463 (ttmt) cc_final: 0.7013 (mttp) REVERT: G 272 MET cc_start: 0.7507 (mmm) cc_final: 0.7232 (mmm) REVERT: J 129 LYS cc_start: 0.7433 (ttpt) cc_final: 0.7024 (mttp) REVERT: J 135 MET cc_start: 0.7544 (tpp) cc_final: 0.7035 (tpp) REVERT: J 272 MET cc_start: 0.7516 (mmm) cc_final: 0.7282 (mmm) REVERT: M 135 MET cc_start: 0.7534 (tpp) cc_final: 0.6944 (tpp) REVERT: M 272 MET cc_start: 0.7572 (mmm) cc_final: 0.7117 (mmm) REVERT: M 345 THR cc_start: 0.8117 (m) cc_final: 0.7663 (m) REVERT: P 125 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: P 135 MET cc_start: 0.7436 (tpp) cc_final: 0.7100 (tpp) REVERT: P 339 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7427 (mtp180) REVERT: S 10 ASP cc_start: 0.7633 (m-30) cc_final: 0.7301 (m-30) REVERT: S 272 MET cc_start: 0.7440 (mmm) cc_final: 0.7224 (mmm) REVERT: S 339 ARG cc_start: 0.7448 (mmm-85) cc_final: 0.7167 (mtp180) REVERT: V 125 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: V 135 MET cc_start: 0.7809 (tpp) cc_final: 0.7479 (tpp) REVERT: V 272 MET cc_start: 0.7626 (mmm) cc_final: 0.7302 (mmm) REVERT: V 339 ARG cc_start: 0.7734 (mmm-85) cc_final: 0.7466 (mtp180) REVERT: Y 10 ASP cc_start: 0.7755 (m-30) cc_final: 0.7378 (m-30) REVERT: Y 125 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: Y 129 LYS cc_start: 0.7306 (ttmm) cc_final: 0.7000 (mttp) REVERT: Y 135 MET cc_start: 0.7249 (tpp) cc_final: 0.6847 (tpp) REVERT: Y 283 LYS cc_start: 0.8084 (tppt) cc_final: 0.7604 (mttp) REVERT: Y 339 ARG cc_start: 0.7680 (mmm-85) cc_final: 0.7378 (mtp180) REVERT: 1 125 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: 1 272 MET cc_start: 0.7552 (mmm) cc_final: 0.7348 (mmm) REVERT: 1 283 LYS cc_start: 0.8130 (tppt) cc_final: 0.7694 (mttm) REVERT: 4 125 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: 4 129 LYS cc_start: 0.7559 (ttmt) cc_final: 0.7167 (mttp) REVERT: 4 283 LYS cc_start: 0.8171 (tppt) cc_final: 0.7845 (ttpt) outliers start: 67 outliers final: 56 residues processed: 472 average time/residue: 0.4131 time to fit residues: 323.6181 Evaluate side-chains 468 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 406 time to evaluate : 3.518 ------------------------------------------------------------------------------- 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 125 GLU 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 190 VAL 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 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 282 LEU 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 282 LEU Chi-restraints excluded: chain V residue 342 VAL 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 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 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: 6.9990 chunk 355 optimal weight: 0.9980 chunk 214 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 336 optimal weight: 0.8980 chunk 354 optimal weight: 0.0170 overall best weight: 0.9822 ------------------------------------------------------------------------------- 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33792 Z= 0.213 Angle : 0.485 7.760 45881 Z= 0.251 Chirality : 0.039 0.132 5412 Planarity : 0.003 0.032 5555 Dihedral : 10.887 74.220 5621 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.84 % Allowed : 14.21 % Favored : 83.95 % 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: 1.59 (0.14), residues: 4004 helix: 1.96 (0.10), residues: 2552 sheet: -1.45 (0.33), residues: 231 loop : -0.30 (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 G 56 PHE 0.016 0.002 PHE J 169 TYR 0.014 0.001 TYR G 23 ARG 0.002 0.000 ARG S 185 *********************** 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 471 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 407 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 LYS cc_start: 0.7643 (ttmt) cc_final: 0.7032 (ttpp) REVERT: C 135 MET cc_start: 0.7567 (tpp) cc_final: 0.7172 (tpp) REVERT: G 125 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: G 129 LYS cc_start: 0.7584 (ttmt) cc_final: 0.7098 (mttp) REVERT: G 272 MET cc_start: 0.7493 (mmm) cc_final: 0.7230 (mmm) REVERT: J 129 LYS cc_start: 0.7489 (ttpt) cc_final: 0.7049 (mttp) REVERT: J 135 MET cc_start: 0.7609 (tpp) cc_final: 0.7092 (tpp) REVERT: J 272 MET cc_start: 0.7464 (mmm) cc_final: 0.7218 (mmm) REVERT: M 135 MET cc_start: 0.7566 (tpp) cc_final: 0.7022 (tpp) REVERT: M 272 MET cc_start: 0.7563 (mmm) cc_final: 0.7363 (mmm) REVERT: P 125 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: P 135 MET cc_start: 0.7452 (tpp) cc_final: 0.7161 (tpp) REVERT: P 339 ARG cc_start: 0.7743 (mmm-85) cc_final: 0.7470 (mtp180) REVERT: S 272 MET cc_start: 0.7437 (mmm) cc_final: 0.7218 (mmm) REVERT: S 339 ARG cc_start: 0.7496 (mmm-85) cc_final: 0.7212 (mtp180) REVERT: V 125 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: V 135 MET cc_start: 0.7818 (tpp) cc_final: 0.7500 (tpp) REVERT: V 272 MET cc_start: 0.7601 (mmm) cc_final: 0.7284 (mmm) REVERT: V 339 ARG cc_start: 0.7800 (mmm-85) cc_final: 0.7524 (mtp180) REVERT: Y 10 ASP cc_start: 0.7829 (m-30) cc_final: 0.7448 (m-30) REVERT: Y 125 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: Y 129 LYS cc_start: 0.7348 (ttmm) cc_final: 0.7035 (mttp) REVERT: Y 135 MET cc_start: 0.7402 (tpp) cc_final: 0.7109 (tpp) REVERT: Y 283 LYS cc_start: 0.8098 (tppt) cc_final: 0.7886 (ttpt) REVERT: 1 125 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: 1 258 MET cc_start: 0.8295 (mmm) cc_final: 0.8025 (mmm) REVERT: 1 272 MET cc_start: 0.7548 (mmm) cc_final: 0.7337 (mmm) REVERT: 1 283 LYS cc_start: 0.8102 (tppt) cc_final: 0.7722 (mttm) REVERT: 4 125 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: 4 129 LYS cc_start: 0.7596 (ttmt) cc_final: 0.7199 (mttp) REVERT: 4 283 LYS cc_start: 0.8164 (tppt) cc_final: 0.7872 (ttpt) outliers start: 64 outliers final: 55 residues processed: 451 average time/residue: 0.4229 time to fit residues: 318.7582 Evaluate side-chains 467 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 406 time to evaluate : 3.664 ------------------------------------------------------------------------------- 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 125 GLU 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 282 LEU 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 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 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 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: 0.6980 chunk 376 optimal weight: 0.9990 chunk 229 optimal weight: 6.9990 chunk 178 optimal weight: 0.0670 chunk 261 optimal weight: 6.9990 chunk 394 optimal weight: 0.0770 chunk 363 optimal weight: 0.4980 chunk 314 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 192 optimal weight: 0.3980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS ** C 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33792 Z= 0.137 Angle : 0.457 7.791 45881 Z= 0.240 Chirality : 0.037 0.135 5412 Planarity : 0.003 0.021 5555 Dihedral : 10.913 73.810 5621 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.52 % Allowed : 14.61 % Favored : 83.86 % 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: 1.74 (0.14), residues: 4004 helix: 2.09 (0.10), residues: 2563 sheet: -1.37 (0.34), residues: 231 loop : -0.32 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP 4 123 HIS 0.004 0.001 HIS M 15 PHE 0.010 0.001 PHE P 169 TYR 0.011 0.001 TYR G 23 ARG 0.003 0.000 ARG V 78 ********************** 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 473 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 420 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.7631 (m-30) cc_final: 0.7168 (m-30) REVERT: C 10 ASP cc_start: 0.7799 (m-30) cc_final: 0.7385 (m-30) REVERT: C 129 LYS cc_start: 0.7596 (ttmt) cc_final: 0.6976 (ttpp) REVERT: C 135 MET cc_start: 0.7576 (tpp) cc_final: 0.7221 (tpp) REVERT: G 125 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: G 129 LYS cc_start: 0.7453 (ttmt) cc_final: 0.7011 (mttp) REVERT: J 129 LYS cc_start: 0.7415 (ttpt) cc_final: 0.7011 (mttp) REVERT: J 135 MET cc_start: 0.7522 (tpp) cc_final: 0.7103 (tpp) REVERT: J 272 MET cc_start: 0.7491 (mmm) cc_final: 0.7278 (mmm) REVERT: M 135 MET cc_start: 0.7505 (tpp) cc_final: 0.7229 (tpp) REVERT: M 272 MET cc_start: 0.7542 (mmm) cc_final: 0.7289 (mmt) REVERT: M 345 THR cc_start: 0.8050 (m) cc_final: 0.7584 (m) REVERT: P 10 ASP cc_start: 0.7720 (m-30) cc_final: 0.7280 (m-30) REVERT: P 125 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: P 135 MET cc_start: 0.7345 (tpp) cc_final: 0.6856 (tpp) REVERT: P 339 ARG cc_start: 0.7700 (mmm-85) cc_final: 0.7427 (mtp180) REVERT: S 272 MET cc_start: 0.7436 (mmm) cc_final: 0.7149 (mmm) REVERT: S 339 ARG cc_start: 0.7411 (mmm-85) cc_final: 0.7170 (mtp180) REVERT: V 125 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6832 (mp0) REVERT: V 135 MET cc_start: 0.7735 (tpp) cc_final: 0.7424 (tpp) REVERT: V 272 MET cc_start: 0.7610 (mmm) cc_final: 0.7287 (mmm) REVERT: V 339 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7440 (mtp180) REVERT: Y 125 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: Y 129 LYS cc_start: 0.7277 (ttmm) cc_final: 0.6982 (mttp) REVERT: Y 135 MET cc_start: 0.7222 (tpp) cc_final: 0.6937 (tpp) REVERT: Y 339 ARG cc_start: 0.7665 (mmm-85) cc_final: 0.7368 (mtp180) REVERT: 1 125 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: 1 258 MET cc_start: 0.8223 (mmm) cc_final: 0.7986 (mmm) REVERT: 1 283 LYS cc_start: 0.8008 (tppt) cc_final: 0.7697 (mttm) REVERT: 4 129 LYS cc_start: 0.7513 (ttmt) cc_final: 0.7126 (mttp) REVERT: 4 283 LYS cc_start: 0.8090 (tppt) cc_final: 0.7812 (ttpt) outliers start: 53 outliers final: 44 residues processed: 454 average time/residue: 0.4218 time to fit residues: 317.0423 Evaluate side-chains 455 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 406 time to evaluate : 3.511 ------------------------------------------------------------------------------- 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 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 282 LEU Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain G residue 7 HIS 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 282 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain J residue 176 ILE 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 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 282 LEU 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 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 282 LEU 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 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 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: 0.3980 chunk 334 optimal weight: 0.0050 chunk 96 optimal weight: 0.5980 chunk 289 optimal weight: 1.9990 chunk 46 optimal weight: 0.0070 chunk 87 optimal weight: 0.9980 chunk 314 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 323 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.3812 ------------------------------------------------------------------------------- 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** ** 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** P 216 GLN ** P 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 216 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.172720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.146482 restraints weight = 40554.650| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.37 r_work: 0.3338 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2111 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= 0.138 Angle : 0.451 7.550 45881 Z= 0.234 Chirality : 0.037 0.127 5412 Planarity : 0.003 0.021 5555 Dihedral : 11.011 73.813 5621 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.50 % Allowed : 14.82 % Favored : 83.69 % 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: 1.81 (0.14), residues: 4004 helix: 2.15 (0.10), residues: 2563 sheet: -1.36 (0.34), residues: 231 loop : -0.28 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 123 HIS 0.004 0.001 HIS M 15 PHE 0.011 0.001 PHE P 169 TYR 0.012 0.001 TYR 1 23 ARG 0.003 0.000 ARG C 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6853.65 seconds wall clock time: 124 minutes 6.11 seconds (7446.11 seconds total)