Starting phenix.real_space_refine on Sat Dec 16 00:15:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/12_2023/8pdq_17618.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/12_2023/8pdq_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_17618/12_2023/8pdq_17618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/12_2023/8pdq_17618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/12_2023/8pdq_17618.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdq_17618/12_2023/8pdq_17618.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 143 5.16 5 C 20702 2.51 5 N 5709 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 10": "OD1" <-> "OD2" Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "B ASP 10": "OD1" <-> "OD2" Residue "C ASP 10": "OD1" <-> "OD2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "D ASP 10": "OD1" <-> "OD2" Residue "G ASP 10": "OD1" <-> "OD2" Residue "G TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G ASP 290": "OD1" <-> "OD2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "H ASP 10": "OD1" <-> "OD2" Residue "J ASP 10": "OD1" <-> "OD2" Residue "J TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J ARG 132": "NH1" <-> "NH2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J ASP 290": "OD1" <-> "OD2" Residue "J GLU 298": "OE1" <-> "OE2" Residue "J GLU 352": "OE1" <-> "OE2" Residue "J TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 360": "OE1" <-> "OE2" Residue "K ASP 10": "OD1" <-> "OD2" Residue "M ASP 10": "OD1" <-> "OD2" Residue "M TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M ARG 132": "NH1" <-> "NH2" Residue "M GLU 181": "OE1" <-> "OE2" Residue "M ASP 290": "OD1" <-> "OD2" Residue "M GLU 298": "OE1" <-> "OE2" Residue "M GLU 352": "OE1" <-> "OE2" Residue "M TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "N ASP 10": "OD1" <-> "OD2" Residue "P ASP 10": "OD1" <-> "OD2" Residue "P TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 89": "OE1" <-> "OE2" Residue "P GLU 109": "OE1" <-> "OE2" Residue "P ARG 132": "NH1" <-> "NH2" Residue "P GLU 181": "OE1" <-> "OE2" Residue "P ASP 290": "OD1" <-> "OD2" Residue "P GLU 298": "OE1" <-> "OE2" Residue "P GLU 352": "OE1" <-> "OE2" Residue "P TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 360": "OE1" <-> "OE2" Residue "Q ASP 10": "OD1" <-> "OD2" Residue "S ASP 10": "OD1" <-> "OD2" Residue "S TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 89": "OE1" <-> "OE2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "S ARG 132": "NH1" <-> "NH2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S ASP 290": "OD1" <-> "OD2" Residue "S GLU 298": "OE1" <-> "OE2" Residue "S GLU 352": "OE1" <-> "OE2" Residue "S TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 360": "OE1" <-> "OE2" Residue "T ASP 10": "OD1" <-> "OD2" Residue "V ASP 10": "OD1" <-> "OD2" Residue "V TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 20": "OE1" <-> "OE2" Residue "V TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 89": "OE1" <-> "OE2" Residue "V GLU 109": "OE1" <-> "OE2" Residue "V ARG 132": "NH1" <-> "NH2" Residue "V GLU 181": "OE1" <-> "OE2" Residue "V ASP 290": "OD1" <-> "OD2" Residue "V GLU 298": "OE1" <-> "OE2" Residue "V GLU 352": "OE1" <-> "OE2" Residue "V TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 360": "OE1" <-> "OE2" Residue "W ASP 10": "OD1" <-> "OD2" Residue "Y ASP 10": "OD1" <-> "OD2" Residue "Y TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 20": "OE1" <-> "OE2" Residue "Y TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 89": "OE1" <-> "OE2" Residue "Y GLU 109": "OE1" <-> "OE2" Residue "Y ARG 132": "NH1" <-> "NH2" Residue "Y GLU 181": "OE1" <-> "OE2" Residue "Y ASP 290": "OD1" <-> "OD2" Residue "Y GLU 298": "OE1" <-> "OE2" Residue "Y GLU 352": "OE1" <-> "OE2" Residue "Y TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 360": "OE1" <-> "OE2" Residue "Z ASP 10": "OD1" <-> "OD2" Residue "1 ASP 10": "OD1" <-> "OD2" Residue "1 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 20": "OE1" <-> "OE2" Residue "1 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 89": "OE1" <-> "OE2" Residue "1 GLU 109": "OE1" <-> "OE2" Residue "1 ARG 132": "NH1" <-> "NH2" Residue "1 GLU 181": "OE1" <-> "OE2" Residue "1 ASP 290": "OD1" <-> "OD2" Residue "1 GLU 298": "OE1" <-> "OE2" Residue "1 GLU 352": "OE1" <-> "OE2" Residue "1 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 360": "OE1" <-> "OE2" Residue "2 ASP 10": "OD1" <-> "OD2" Residue "4 ASP 10": "OD1" <-> "OD2" Residue "4 TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 20": "OE1" <-> "OE2" Residue "4 TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 89": "OE1" <-> "OE2" Residue "4 GLU 109": "OE1" <-> "OE2" Residue "4 ARG 132": "NH1" <-> "NH2" Residue "4 GLU 181": "OE1" <-> "OE2" Residue "4 ASP 290": "OD1" <-> "OD2" Residue "4 GLU 298": "OE1" <-> "OE2" Residue "4 GLU 352": "OE1" <-> "OE2" Residue "4 TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 360": "OE1" <-> "OE2" Residue "5 ASP 10": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 19.36, per 1000 atoms: 0.58 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: 14.79 Conformation dependent library (CDL) restraints added in 7.1 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: 10.87 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 188 Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 250 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU A 273 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU B 14 " --> pdb=" O ILE B 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN C 150 " --> pdb=" O PRO C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 188 Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.950A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 250 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU C 273 " --> pdb=" O ASN C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU D 14 " --> pdb=" O ILE D 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 removed outlier: 3.549A pdb=" N GLN G 150 " --> pdb=" O PRO G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 188 Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 250 Processing helix chain 'G' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU G 273 " --> pdb=" O ASN G 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 280 Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'H' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU H 14 " --> pdb=" O ILE H 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 removed outlier: 3.547A pdb=" N GLN J 150 " --> pdb=" O PRO J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 188 Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER J 222 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 250 Processing helix chain 'J' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 274 removed outlier: 3.636A pdb=" N LEU J 273 " --> pdb=" O ASN J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 297 through 300' Processing helix chain 'J' and resid 301 through 306 Processing helix chain 'J' and resid 318 through 332 Processing helix chain 'J' and resid 344 through 361 Processing helix chain 'K' and resid 10 through 14 removed outlier: 3.578A pdb=" N LEU K 14 " --> pdb=" O ILE K 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 20 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL M 124 " --> pdb=" O GLU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN M 150 " --> pdb=" O PRO M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS M 171 " --> pdb=" O LEU M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 188 Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 250 Processing helix chain 'M' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU M 273 " --> pdb=" O ASN M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 275 through 280 Processing helix chain 'M' and resid 281 through 296 Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 301 through 306 Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'N' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU N 14 " --> pdb=" O ILE N 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 37 through 39 No H-bonds generated for 'chain 'P' and resid 37 through 39' Processing helix chain 'P' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 75 Processing helix chain 'P' and resid 75 through 86 Processing helix chain 'P' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL P 124 " --> pdb=" O GLU P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN P 150 " --> pdb=" O PRO P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 175 through 188 Processing helix chain 'P' and resid 191 through 198 Processing helix chain 'P' and resid 202 through 217 Processing helix chain 'P' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER P 222 " --> pdb=" O VAL P 218 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 250 Processing helix chain 'P' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG P 260 " --> pdb=" O GLN P 256 " (cutoff:3.500A) Processing helix chain 'P' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU P 273 " --> pdb=" O ASN P 270 " (cutoff:3.500A) Processing helix chain 'P' and resid 275 through 280 Processing helix chain 'P' and resid 281 through 296 Processing helix chain 'P' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY P 300 " --> pdb=" O PRO P 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 297 through 300' Processing helix chain 'P' and resid 301 through 306 Processing helix chain 'P' and resid 318 through 332 Processing helix chain 'P' and resid 344 through 361 Processing helix chain 'Q' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU Q 14 " --> pdb=" O ILE Q 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 20 Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 51 removed outlier: 4.010A pdb=" N LEU S 47 " --> pdb=" O GLU S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL S 124 " --> pdb=" O GLU S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN S 150 " --> pdb=" O PRO S 147 " (cutoff:3.500A) Processing helix chain 'S' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS S 171 " --> pdb=" O LEU S 167 " (cutoff:3.500A) Processing helix chain 'S' and resid 175 through 188 Processing helix chain 'S' and resid 191 through 198 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 250 Processing helix chain 'S' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU S 273 " --> pdb=" O ASN S 270 " (cutoff:3.500A) Processing helix chain 'S' and resid 275 through 280 Processing helix chain 'S' and resid 281 through 296 Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 301 through 306 Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'T' and resid 10 through 14 removed outlier: 3.576A pdb=" N LEU T 14 " --> pdb=" O ILE T 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 20 Processing helix chain 'V' and resid 37 through 39 No H-bonds generated for 'chain 'V' and resid 37 through 39' Processing helix chain 'V' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 61 through 75 Processing helix chain 'V' and resid 75 through 86 Processing helix chain 'V' and resid 120 through 142 removed outlier: 3.725A pdb=" N VAL V 124 " --> pdb=" O GLU V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN V 150 " --> pdb=" O PRO V 147 " (cutoff:3.500A) Processing helix chain 'V' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS V 171 " --> pdb=" O LEU V 167 " (cutoff:3.500A) Processing helix chain 'V' and resid 175 through 188 Processing helix chain 'V' and resid 191 through 198 Processing helix chain 'V' and resid 202 through 217 Processing helix chain 'V' and resid 218 through 233 removed outlier: 3.950A pdb=" N SER V 222 " --> pdb=" O VAL V 218 " (cutoff:3.500A) Processing helix chain 'V' and resid 238 through 250 Processing helix chain 'V' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG V 260 " --> pdb=" O GLN V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU V 273 " --> pdb=" O ASN V 270 " (cutoff:3.500A) Processing helix chain 'V' and resid 275 through 280 Processing helix chain 'V' and resid 281 through 296 Processing helix chain 'V' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY V 300 " --> pdb=" O PRO V 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 297 through 300' Processing helix chain 'V' and resid 301 through 306 Processing helix chain 'V' and resid 318 through 332 Processing helix chain 'V' and resid 344 through 361 Processing helix chain 'W' and resid 10 through 14 removed outlier: 3.578A pdb=" N LEU W 14 " --> pdb=" O ILE W 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 20 Processing helix chain 'Y' and resid 37 through 39 No H-bonds generated for 'chain 'Y' and resid 37 through 39' Processing helix chain 'Y' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU Y 47 " --> pdb=" O GLU Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 61 through 75 Processing helix chain 'Y' and resid 75 through 86 Processing helix chain 'Y' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL Y 124 " --> pdb=" O GLU Y 120 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN Y 150 " --> pdb=" O PRO Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 156 through 171 removed outlier: 3.979A pdb=" N LYS Y 171 " --> pdb=" O LEU Y 167 " (cutoff:3.500A) Processing helix chain 'Y' and resid 175 through 188 Processing helix chain 'Y' and resid 191 through 198 Processing helix chain 'Y' and resid 202 through 217 Processing helix chain 'Y' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER Y 222 " --> pdb=" O VAL Y 218 " (cutoff:3.500A) Processing helix chain 'Y' and resid 238 through 250 Processing helix chain 'Y' and resid 256 through 268 removed outlier: 3.756A pdb=" N ARG Y 260 " --> pdb=" O GLN Y 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU Y 273 " --> pdb=" O ASN Y 270 " (cutoff:3.500A) Processing helix chain 'Y' and resid 275 through 280 Processing helix chain 'Y' and resid 281 through 296 Processing helix chain 'Y' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY Y 300 " --> pdb=" O PRO Y 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 297 through 300' Processing helix chain 'Y' and resid 301 through 306 Processing helix chain 'Y' and resid 318 through 332 Processing helix chain 'Y' and resid 344 through 361 Processing helix chain 'Z' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU Z 14 " --> pdb=" O ILE Z 11 " (cutoff:3.500A) Processing helix chain '1' and resid 9 through 20 Processing helix chain '1' and resid 37 through 39 No H-bonds generated for 'chain '1' and resid 37 through 39' Processing helix chain '1' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU 1 47 " --> pdb=" O GLU 1 43 " (cutoff:3.500A) Processing helix chain '1' and resid 61 through 75 Processing helix chain '1' and resid 75 through 86 Processing helix chain '1' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL 1 124 " --> pdb=" O GLU 1 120 " (cutoff:3.500A) Processing helix chain '1' and resid 147 through 151 removed outlier: 3.549A pdb=" N GLN 1 150 " --> pdb=" O PRO 1 147 " (cutoff:3.500A) Processing helix chain '1' and resid 156 through 171 removed outlier: 3.978A pdb=" N LYS 1 171 " --> pdb=" O LEU 1 167 " (cutoff:3.500A) Processing helix chain '1' and resid 175 through 188 Processing helix chain '1' and resid 191 through 198 Processing helix chain '1' and resid 202 through 217 Processing helix chain '1' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER 1 222 " --> pdb=" O VAL 1 218 " (cutoff:3.500A) Processing helix chain '1' and resid 238 through 250 Processing helix chain '1' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG 1 260 " --> pdb=" O GLN 1 256 " (cutoff:3.500A) Processing helix chain '1' and resid 270 through 274 removed outlier: 3.635A pdb=" N LEU 1 273 " --> pdb=" O ASN 1 270 " (cutoff:3.500A) Processing helix chain '1' and resid 275 through 280 Processing helix chain '1' and resid 281 through 296 Processing helix chain '1' and resid 297 through 300 removed outlier: 3.644A pdb=" N GLY 1 300 " --> pdb=" O PRO 1 297 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 297 through 300' Processing helix chain '1' and resid 301 through 306 Processing helix chain '1' and resid 318 through 332 Processing helix chain '1' and resid 344 through 361 Processing helix chain '2' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU 2 14 " --> pdb=" O ILE 2 11 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 20 Processing helix chain '4' and resid 37 through 39 No H-bonds generated for 'chain '4' and resid 37 through 39' Processing helix chain '4' and resid 40 through 51 removed outlier: 4.009A pdb=" N LEU 4 47 " --> pdb=" O GLU 4 43 " (cutoff:3.500A) Processing helix chain '4' and resid 61 through 75 Processing helix chain '4' and resid 75 through 86 Processing helix chain '4' and resid 120 through 142 removed outlier: 3.726A pdb=" N VAL 4 124 " --> pdb=" O GLU 4 120 " (cutoff:3.500A) Processing helix chain '4' and resid 147 through 151 removed outlier: 3.548A pdb=" N GLN 4 150 " --> pdb=" O PRO 4 147 " (cutoff:3.500A) Processing helix chain '4' and resid 156 through 171 removed outlier: 3.980A pdb=" N LYS 4 171 " --> pdb=" O LEU 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 175 through 188 Processing helix chain '4' and resid 191 through 198 Processing helix chain '4' and resid 202 through 217 Processing helix chain '4' and resid 218 through 233 removed outlier: 3.949A pdb=" N SER 4 222 " --> pdb=" O VAL 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 238 through 250 Processing helix chain '4' and resid 256 through 268 removed outlier: 3.755A pdb=" N ARG 4 260 " --> pdb=" O GLN 4 256 " (cutoff:3.500A) Processing helix chain '4' and resid 270 through 274 removed outlier: 3.636A pdb=" N LEU 4 273 " --> pdb=" O ASN 4 270 " (cutoff:3.500A) Processing helix chain '4' and resid 275 through 280 Processing helix chain '4' and resid 281 through 296 Processing helix chain '4' and resid 297 through 300 removed outlier: 3.643A pdb=" N GLY 4 300 " --> pdb=" O PRO 4 297 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 297 through 300' Processing helix chain '4' and resid 301 through 306 Processing helix chain '4' and resid 318 through 332 Processing helix chain '4' and resid 344 through 361 Processing helix chain '5' and resid 10 through 14 removed outlier: 3.577A pdb=" N LEU 5 14 " --> pdb=" O ILE 5 11 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU A 111 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'C' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU C 111 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'G' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'G' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU G 111 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'J' and resid 32 through 35 removed outlier: 6.468A pdb=" N THR J 33 " --> pdb=" O VAL J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'J' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU J 111 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'M' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'M' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU M 111 " --> pdb=" O LEU M 100 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'P' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR P 33 " --> pdb=" O VAL P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'P' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU P 111 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'S' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'S' and resid 96 through 104 removed outlier: 7.737A pdb=" N LEU S 111 " --> pdb=" O LEU S 100 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'V' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR V 33 " --> pdb=" O VAL V 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'V' and resid 96 through 104 removed outlier: 7.737A pdb=" N LEU V 111 " --> pdb=" O LEU V 100 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Y' and resid 32 through 35 removed outlier: 6.466A pdb=" N THR Y 33 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'Y' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU Y 111 " --> pdb=" O LEU Y 100 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '1' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR 1 33 " --> pdb=" O VAL 1 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain '1' and resid 96 through 104 removed outlier: 7.737A pdb=" N LEU 1 111 " --> pdb=" O LEU 1 100 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '4' and resid 32 through 35 removed outlier: 6.467A pdb=" N THR 4 33 " --> pdb=" O VAL 4 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain '4' and resid 96 through 104 removed outlier: 7.738A pdb=" N LEU 4 111 " --> pdb=" O LEU 4 100 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5346 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 11.15 Time building geometry restraints manager: 15.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10681 1.34 - 1.46: 6692 1.46 - 1.58: 16023 1.58 - 1.69: 143 1.69 - 1.81: 253 Bond restraints: 33792 Sorted by residual: bond pdb=" CA ILE J 203 " pdb=" CB ILE J 203 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.33e-01 bond pdb=" CA ILE Y 203 " pdb=" CB ILE Y 203 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.09e-01 bond pdb=" CA ILE M 203 " pdb=" CB ILE M 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.78e-01 bond pdb=" CA ILE S 203 " pdb=" CB ILE S 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.55e-01 bond pdb=" CA ILE 4 203 " pdb=" CB ILE 4 203 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.45e-01 ... (remaining 33787 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.95: 1024 106.95 - 113.72: 19432 113.72 - 120.48: 13658 120.48 - 127.24: 11547 127.24 - 134.01: 220 Bond angle restraints: 45881 Sorted by residual: angle pdb=" N GLU Y 125 " pdb=" CA GLU Y 125 " pdb=" CB GLU Y 125 " ideal model delta sigma weight residual 110.28 113.47 -3.19 1.55e+00 4.16e-01 4.24e+00 angle pdb=" N GLU J 125 " pdb=" CA GLU J 125 " pdb=" CB GLU J 125 " ideal model delta sigma weight residual 110.28 113.46 -3.18 1.55e+00 4.16e-01 4.21e+00 angle pdb=" N GLU P 125 " pdb=" CA GLU P 125 " pdb=" CB GLU P 125 " ideal model delta sigma weight residual 110.28 113.45 -3.17 1.55e+00 4.16e-01 4.19e+00 angle pdb=" N GLU C 125 " pdb=" CA GLU C 125 " pdb=" CB GLU C 125 " ideal model delta sigma weight residual 110.28 113.44 -3.16 1.55e+00 4.16e-01 4.17e+00 angle pdb=" N GLU A 125 " pdb=" CA GLU A 125 " pdb=" CB GLU A 125 " ideal model delta sigma weight residual 110.28 113.44 -3.16 1.55e+00 4.16e-01 4.16e+00 ... (remaining 45876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 18198 15.55 - 31.10: 1877 31.10 - 46.65: 550 46.65 - 62.20: 99 62.20 - 77.75: 132 Dihedral angle restraints: 20856 sinusoidal: 9075 harmonic: 11781 Sorted by residual: dihedral pdb=" CA LEU G 52 " pdb=" C LEU G 52 " pdb=" N TYR G 53 " pdb=" CA TYR G 53 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU 4 52 " pdb=" C LEU 4 52 " pdb=" N TYR 4 53 " pdb=" CA TYR 4 53 " ideal model delta harmonic sigma weight residual 180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU Y 52 " pdb=" C LEU Y 52 " pdb=" N TYR Y 53 " pdb=" CA TYR Y 53 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 20853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3117 0.027 - 0.055: 1345 0.055 - 0.082: 714 0.082 - 0.110: 152 0.110 - 0.137: 84 Chirality restraints: 5412 Sorted by residual: chirality pdb=" CA THR C 157 " pdb=" N THR C 157 " pdb=" C THR C 157 " pdb=" CB THR C 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.71e-01 chirality pdb=" CA THR S 157 " pdb=" N THR S 157 " pdb=" C THR S 157 " pdb=" CB THR S 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA THR V 157 " pdb=" N THR V 157 " pdb=" C THR V 157 " pdb=" CB THR V 157 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.69e-01 ... (remaining 5409 not shown) Planarity restraints: 5555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C U 73 " 0.027 2.00e-02 2.50e+03 1.35e-02 4.11e+00 pdb=" N1 C U 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C U 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C U 73 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C U 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C U 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C U 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C U 73 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C U 73 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C X 73 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.05e+00 pdb=" N1 C X 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C X 73 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C X 73 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C X 73 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C X 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C X 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C X 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C X 73 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C O 73 " 0.027 2.00e-02 2.50e+03 1.34e-02 4.03e+00 pdb=" N1 C O 73 " -0.027 2.00e-02 2.50e+03 pdb=" C2 C O 73 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C O 73 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C O 73 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C O 73 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C O 73 " 0.008 2.00e-02 2.50e+03 pdb=" C5 C O 73 " -0.000 2.00e-02 2.50e+03 pdb=" C6 C O 73 " -0.006 2.00e-02 2.50e+03 ... (remaining 5552 not shown) Histogram of nonbonded interaction distances: 0.24 - 1.17: 77 1.17 - 2.10: 231 2.10 - 3.03: 21000 3.03 - 3.97: 91195 3.97 - 4.90: 169684 Warning: very small nonbonded interaction distances. Nonbonded interactions: 282187 Sorted by model distance: nonbonded pdb=" NH1 ARG M 78 " pdb=" CZ TYR P 23 " model vdw 0.235 3.340 nonbonded pdb=" NH1 ARG C 78 " pdb=" CZ TYR G 23 " model vdw 0.235 3.340 nonbonded pdb=" NH1 ARG S 78 " pdb=" CZ TYR V 23 " model vdw 0.236 3.340 nonbonded pdb=" CZ TYR A 23 " pdb=" NH1 ARG 4 78 " model vdw 0.236 3.340 nonbonded pdb=" NH1 ARG P 78 " pdb=" CZ TYR S 23 " model vdw 0.236 3.340 ... (remaining 282182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '3' selection = chain '6' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain '1' selection = chain '4' selection = chain 'A' selection = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'V' selection = chain 'Y' } ncs_group { reference = chain '2' selection = chain '5' selection = chain 'B' selection = chain 'D' selection = chain 'H' selection = chain 'K' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.370 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: 15.290 Check model and map are aligned: 0.480 Set scattering table: 0.280 Process input model: 98.070 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.250 ------------------------------------------------------------------------------- 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 : 4.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.4460 time to fit residues: 342.1472 Evaluate side-chains 415 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 415 time to evaluate : 3.754 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 7.9990 chunk 300 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 102 optimal weight: 0.2980 chunk 202 optimal weight: 0.6980 chunk 160 optimal weight: 1.9990 chunk 310 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 231 optimal weight: 0.6980 chunk 359 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 306 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 306 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 306 GLN ** V 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 306 GLN Y 7 HIS ** Y 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 306 GLN ** 1 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 306 GLN ** 4 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 306 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33792 Z= 0.186 Angle : 0.505 8.886 45881 Z= 0.273 Chirality : 0.039 0.131 5412 Planarity : 0.003 0.029 5555 Dihedral : 11.831 74.061 5621 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.60 % Allowed : 7.28 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4004 helix: 1.39 (0.10), residues: 2530 sheet: -1.29 (0.28), residues: 231 loop : -0.74 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.004 0.001 HIS V 56 PHE 0.012 0.002 PHE 1 169 TYR 0.011 0.001 TYR M 53 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 442 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 421 time to evaluate : 4.018 Fit side-chains outliers start: 21 outliers final: 14 residues processed: 432 average time/residue: 0.4408 time to fit residues: 312.6118 Evaluate side-chains 399 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 385 time to evaluate : 3.673 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2874 time to fit residues: 12.7396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 0.0980 chunk 111 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 244 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 360 optimal weight: 0.7980 chunk 389 optimal weight: 3.9990 chunk 320 optimal weight: 4.9990 chunk 357 optimal weight: 0.9980 chunk 122 optimal weight: 0.0470 chunk 289 optimal weight: 0.8980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 279 GLN 1 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 33792 Z= 0.160 Angle : 0.464 5.827 45881 Z= 0.250 Chirality : 0.038 0.132 5412 Planarity : 0.003 0.065 5555 Dihedral : 11.322 73.979 5621 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.72 % Allowed : 8.43 % Favored : 90.85 % 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: 1.17 (0.14), residues: 4004 helix: 1.65 (0.10), residues: 2530 sheet: -1.26 (0.30), residues: 231 loop : -0.56 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP 4 123 HIS 0.004 0.001 HIS V 7 PHE 0.012 0.001 PHE P 169 TYR 0.025 0.001 TYR Y 23 ARG 0.004 0.000 ARG V 78 *********************** 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 438 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 413 time to evaluate : 4.374 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 429 average time/residue: 0.4357 time to fit residues: 306.1233 Evaluate side-chains 396 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 385 time to evaluate : 3.779 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2949 time to fit residues: 11.2685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 361 optimal weight: 0.6980 chunk 382 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 342 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 7 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 33792 Z= 0.297 Angle : 0.528 11.419 45881 Z= 0.277 Chirality : 0.041 0.132 5412 Planarity : 0.004 0.039 5555 Dihedral : 10.991 74.558 5621 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.24 % Allowed : 9.55 % Favored : 89.21 % 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: 1.08 (0.13), residues: 4004 helix: 1.56 (0.10), residues: 2530 sheet: -1.32 (0.30), residues: 231 loop : -0.56 (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 275 PHE 0.019 0.002 PHE J 169 TYR 0.022 0.002 TYR C 23 ARG 0.005 0.000 ARG A 78 *********************** 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 439 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 396 time to evaluate : 4.540 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 421 average time/residue: 0.4374 time to fit residues: 304.3904 Evaluate side-chains 402 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 380 time to evaluate : 3.864 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2980 time to fit residues: 17.7502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 0.0770 chunk 217 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 285 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 326 optimal weight: 0.1980 chunk 264 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 343 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 overall best weight: 0.5340 ------------------------------------------------------------------------------- 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 1 7 HIS 4 148 GLN ** 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: 0.7818 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33792 Z= 0.156 Angle : 0.458 7.150 45881 Z= 0.247 Chirality : 0.038 0.137 5412 Planarity : 0.003 0.049 5555 Dihedral : 10.892 73.967 5621 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.83 % Allowed : 11.13 % Favored : 88.03 % 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: 1.36 (0.14), residues: 4004 helix: 1.81 (0.10), residues: 2530 sheet: -1.34 (0.32), residues: 231 loop : -0.48 (0.18), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 123 HIS 0.004 0.001 HIS M 275 PHE 0.011 0.001 PHE P 169 TYR 0.023 0.001 TYR S 23 ARG 0.003 0.000 ARG 4 78 *********************** 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 450 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 421 time to evaluate : 3.841 Fit side-chains outliers start: 29 outliers final: 14 residues processed: 444 average time/residue: 0.4346 time to fit residues: 319.4541 Evaluate side-chains 407 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 393 time to evaluate : 3.658 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2887 time to fit residues: 12.8402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 75 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 383 optimal weight: 4.9990 chunk 318 optimal weight: 0.0000 chunk 177 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 201 optimal weight: 1.9990 overall best weight: 0.5122 ------------------------------------------------------------------------------- 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 Y 216 GLN 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: 0.7813 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 33792 Z= 0.151 Angle : 0.446 5.673 45881 Z= 0.238 Chirality : 0.038 0.130 5412 Planarity : 0.003 0.022 5555 Dihedral : 10.897 73.938 5621 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.58 % Allowed : 13.26 % Favored : 86.16 % 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: 1.54 (0.14), residues: 4004 helix: 1.89 (0.10), residues: 2552 sheet: -1.31 (0.33), residues: 231 loop : -0.28 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 123 HIS 0.004 0.001 HIS P 15 PHE 0.012 0.001 PHE P 169 TYR 0.013 0.001 TYR 4 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 437 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 417 time to evaluate : 3.785 Fit side-chains outliers start: 20 outliers final: 10 residues processed: 420 average time/residue: 0.4477 time to fit residues: 309.5568 Evaluate side-chains 412 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 402 time to evaluate : 3.654 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2972 time to fit residues: 10.8385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 0.0570 chunk 43 optimal weight: 0.6980 chunk 218 optimal weight: 0.0170 chunk 279 optimal weight: 10.0000 chunk 216 optimal weight: 0.0270 chunk 322 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 381 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 232 optimal weight: 0.5980 chunk 176 optimal weight: 3.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1980 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= 0.130 Angle : 0.440 8.383 45881 Z= 0.234 Chirality : 0.037 0.128 5412 Planarity : 0.003 0.022 5555 Dihedral : 10.941 73.744 5621 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.37 % Allowed : 13.98 % Favored : 85.64 % 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: 1.75 (0.14), residues: 4004 helix: 2.05 (0.10), residues: 2552 sheet: -1.30 (0.34), residues: 231 loop : -0.19 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP S 123 HIS 0.004 0.001 HIS 4 15 PHE 0.010 0.001 PHE P 169 TYR 0.016 0.001 TYR C 23 ARG 0.003 0.000 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8008 Ramachandran restraints generated. 4004 Oldfield, 0 Emsley, 4004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 428 time to evaluate : 4.124 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 432 average time/residue: 0.4457 time to fit residues: 316.5034 Evaluate side-chains 417 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 411 time to evaluate : 3.875 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3055 time to fit residues: 8.8076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 0.9980 chunk 152 optimal weight: 0.6980 chunk 227 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 260 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 300 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ** 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** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33792 Z= 0.229 Angle : 0.489 5.607 45881 Z= 0.255 Chirality : 0.039 0.153 5412 Planarity : 0.003 0.036 5555 Dihedral : 10.866 74.312 5621 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.32 % Allowed : 14.87 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.14), residues: 4004 helix: 1.93 (0.10), residues: 2552 sheet: -1.41 (0.33), residues: 231 loop : -0.17 (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 0.017 0.002 PHE J 169 TYR 0.016 0.001 TYR C 23 ARG 0.002 0.000 ARG G 27 *********************** 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 430 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 419 time to evaluate : 3.884 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 424 average time/residue: 0.4415 time to fit residues: 308.4085 Evaluate side-chains 414 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 408 time to evaluate : 3.537 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2936 time to fit residues: 8.2255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 0.8980 chunk 365 optimal weight: 4.9990 chunk 333 optimal weight: 4.9990 chunk 355 optimal weight: 1.9990 chunk 214 optimal weight: 0.0060 chunk 154 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 321 optimal weight: 0.0980 chunk 336 optimal weight: 3.9990 chunk 354 optimal weight: 0.0970 overall best weight: 0.3594 ------------------------------------------------------------------------------- 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** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN S 7 HIS V 216 GLN ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 7 HIS ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2005 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= 0.141 Angle : 0.461 8.890 45881 Z= 0.242 Chirality : 0.037 0.134 5412 Planarity : 0.003 0.021 5555 Dihedral : 10.880 73.820 5621 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.40 % Allowed : 14.79 % Favored : 84.81 % 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: 1.77 (0.14), residues: 4004 helix: 2.05 (0.10), residues: 2552 sheet: -1.34 (0.34), residues: 231 loop : -0.15 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 123 HIS 0.004 0.001 HIS P 15 PHE 0.010 0.001 PHE P 169 TYR 0.013 0.001 TYR C 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 433 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 419 time to evaluate : 3.772 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 423 average time/residue: 0.4442 time to fit residues: 309.2424 Evaluate side-chains 416 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 406 time to evaluate : 3.638 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2857 time to fit residues: 10.7916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 0.0050 chunk 376 optimal weight: 0.6980 chunk 229 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 394 optimal weight: 3.9990 chunk 363 optimal weight: 1.9990 chunk 314 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 192 optimal weight: 3.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- 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 275 HIS ** C 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN P 216 GLN ** S 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 216 GLN ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33792 Z= 0.260 Angle : 0.518 8.216 45881 Z= 0.268 Chirality : 0.040 0.134 5412 Planarity : 0.003 0.040 5555 Dihedral : 10.849 74.396 5621 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.09 % Allowed : 15.10 % Favored : 84.81 % 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: 1.52 (0.14), residues: 4004 helix: 1.85 (0.10), residues: 2552 sheet: -1.48 (0.33), residues: 231 loop : -0.20 (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 C 275 PHE 0.016 0.002 PHE 1 169 TYR 0.016 0.001 TYR C 23 ARG 0.002 0.000 ARG G 27 ********************** 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 408 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 405 time to evaluate : 3.723 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 406 average time/residue: 0.4622 time to fit residues: 309.8815 Evaluate side-chains 402 residues out of total 3476 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 400 time to evaluate : 3.909 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3050 time to fit residues: 6.4286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 0.8980 chunk 334 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 chunk 289 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 314 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 GLN ** V 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142588 restraints weight = 40498.941| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.38 r_work: 0.3247 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33792 Z= 0.197 Angle : 0.490 6.904 45881 Z= 0.256 Chirality : 0.039 0.147 5412 Planarity : 0.003 0.024 5555 Dihedral : 10.848 74.152 5621 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.17 % Allowed : 15.19 % Favored : 84.64 % 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: 1.91 (0.10), residues: 2552 sheet: -1.45 (0.33), residues: 231 loop : -0.19 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 123 HIS 0.003 0.001 HIS M 15 PHE 0.014 0.002 PHE J 169 TYR 0.016 0.001 TYR 4 23 ARG 0.002 0.000 ARG S 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6840.56 seconds wall clock time: 126 minutes 6.91 seconds (7566.91 seconds total)