Starting phenix.real_space_refine on Sun Apr 7 05:58:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/04_2024/8oou_17031.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/04_2024/8oou_17031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/04_2024/8oou_17031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/04_2024/8oou_17031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/04_2024/8oou_17031.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oou_17031/04_2024/8oou_17031.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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 140 5.49 5 S 320 5.16 5 C 38620 2.51 5 N 10660 2.21 5 O 12060 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 15": "OD1" <-> "OD2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 155": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ASP 155": "OD1" <-> "OD2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C GLU 297": "OE1" <-> "OE2" Residue "D ASP 15": "OD1" <-> "OD2" Residue "D PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D GLU 130": "OE1" <-> "OE2" Residue "D ASP 155": "OD1" <-> "OD2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "E GLU 297": "OE1" <-> "OE2" Residue "F ASP 15": "OD1" <-> "OD2" Residue "F PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "F ASP 155": "OD1" <-> "OD2" Residue "F ASP 221": "OD1" <-> "OD2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G ASP 155": "OD1" <-> "OD2" Residue "G ASP 221": "OD1" <-> "OD2" Residue "G GLU 297": "OE1" <-> "OE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H GLU 130": "OE1" <-> "OE2" Residue "H ASP 155": "OD1" <-> "OD2" Residue "H ASP 221": "OD1" <-> "OD2" Residue "H GLU 297": "OE1" <-> "OE2" Residue "I ASP 15": "OD1" <-> "OD2" Residue "I PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I GLU 130": "OE1" <-> "OE2" Residue "I ASP 155": "OD1" <-> "OD2" Residue "I ASP 221": "OD1" <-> "OD2" Residue "I GLU 297": "OE1" <-> "OE2" Residue "J ASP 15": "OD1" <-> "OD2" Residue "J PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "J ASP 155": "OD1" <-> "OD2" Residue "J ASP 221": "OD1" <-> "OD2" Residue "J GLU 297": "OE1" <-> "OE2" Residue "K ASP 15": "OD1" <-> "OD2" Residue "K PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 128": "OE1" <-> "OE2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K ASP 155": "OD1" <-> "OD2" Residue "K ASP 221": "OD1" <-> "OD2" Residue "K GLU 297": "OE1" <-> "OE2" Residue "L ASP 15": "OD1" <-> "OD2" Residue "L PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L GLU 130": "OE1" <-> "OE2" Residue "L ASP 155": "OD1" <-> "OD2" Residue "L ASP 221": "OD1" <-> "OD2" Residue "L GLU 297": "OE1" <-> "OE2" Residue "M ASP 15": "OD1" <-> "OD2" Residue "M PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 128": "OE1" <-> "OE2" Residue "M GLU 130": "OE1" <-> "OE2" Residue "M ASP 155": "OD1" <-> "OD2" Residue "M ASP 221": "OD1" <-> "OD2" Residue "M GLU 297": "OE1" <-> "OE2" Residue "N ASP 15": "OD1" <-> "OD2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 128": "OE1" <-> "OE2" Residue "N GLU 130": "OE1" <-> "OE2" Residue "N ASP 155": "OD1" <-> "OD2" Residue "N ASP 221": "OD1" <-> "OD2" Residue "N GLU 297": "OE1" <-> "OE2" Residue "O ASP 15": "OD1" <-> "OD2" Residue "O PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 128": "OE1" <-> "OE2" Residue "O GLU 130": "OE1" <-> "OE2" Residue "O ASP 155": "OD1" <-> "OD2" Residue "O ASP 221": "OD1" <-> "OD2" Residue "O GLU 297": "OE1" <-> "OE2" Residue "P ASP 15": "OD1" <-> "OD2" Residue "P PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 128": "OE1" <-> "OE2" Residue "P GLU 130": "OE1" <-> "OE2" Residue "P ASP 155": "OD1" <-> "OD2" Residue "P ASP 221": "OD1" <-> "OD2" Residue "P GLU 297": "OE1" <-> "OE2" Residue "Q ASP 15": "OD1" <-> "OD2" Residue "Q PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "Q GLU 130": "OE1" <-> "OE2" Residue "Q ASP 155": "OD1" <-> "OD2" Residue "Q ASP 221": "OD1" <-> "OD2" Residue "Q GLU 297": "OE1" <-> "OE2" Residue "R ASP 15": "OD1" <-> "OD2" Residue "R PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "R GLU 130": "OE1" <-> "OE2" Residue "R ASP 155": "OD1" <-> "OD2" Residue "R ASP 221": "OD1" <-> "OD2" Residue "R GLU 297": "OE1" <-> "OE2" Residue "S ASP 15": "OD1" <-> "OD2" Residue "S PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 128": "OE1" <-> "OE2" Residue "S GLU 130": "OE1" <-> "OE2" Residue "S ASP 155": "OD1" <-> "OD2" Residue "S ASP 221": "OD1" <-> "OD2" Residue "S GLU 297": "OE1" <-> "OE2" Residue "T ASP 15": "OD1" <-> "OD2" Residue "T PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 128": "OE1" <-> "OE2" Residue "T GLU 130": "OE1" <-> "OE2" Residue "T ASP 155": "OD1" <-> "OD2" Residue "T ASP 221": "OD1" <-> "OD2" Residue "T GLU 297": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 61800 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "U" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1400 Classifications: {'RNA': 70} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 60} Link IDs: {'rna2p': 10, 'rna3p': 59} Chain: "B" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "C" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "D" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "E" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "F" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "G" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "H" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "I" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "J" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "K" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "e" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1400 Classifications: {'RNA': 70} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 60} Link IDs: {'rna2p': 10, 'rna3p': 59} Chain: "L" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "M" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "N" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "O" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "P" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "Q" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "R" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "S" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Chain: "T" Number of atoms: 2950 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Conformer: "B" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} bond proxies already assigned to first conformer: 2982 Time building chain proxies: 43.49, per 1000 atoms: 0.70 Number of scatterers: 61800 At special positions: 0 Unit cell: (186.635, 186.635, 175.185, 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 320 16.00 P 140 15.00 O 12060 8.00 N 10660 7.00 C 38620 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: 18.60 Conformation dependent library (CDL) restraints added in 16.9 seconds 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13920 Finding SS restraints... Secondary structure from input PDB file: 480 helices and 60 sheets defined 71.4% alpha, 5.3% beta 0 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 15.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 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 53 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 143 Processing helix chain 'A' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE A 220 " --> pdb=" O HIS A 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 249 through 251 No H-bonds generated for 'chain 'A' and resid 249 through 251' Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU A 282 " --> pdb=" O GLN A 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE A 300 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 53 Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 143 Processing helix chain 'B' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 248 Processing helix chain 'B' and resid 249 through 251 No H-bonds generated for 'chain 'B' and resid 249 through 251' Processing helix chain 'B' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU B 282 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE B 300 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE B 378 " --> pdb=" O GLU B 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 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 53 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 143 Processing helix chain 'C' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE C 220 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE C 300 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER C 310 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 Processing helix chain 'D' and resid 9 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 53 Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 120 through 143 Processing helix chain 'D' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE D 160 " --> pdb=" O CYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE D 220 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU D 282 " --> pdb=" O GLN D 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE D 300 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 368 Processing helix chain 'D' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE D 378 " --> pdb=" O GLU D 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'E' and resid 9 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 53 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 143 Processing helix chain 'E' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE E 160 " --> pdb=" O CYS E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE E 220 " --> pdb=" O HIS E 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU E 282 " --> pdb=" O GLN E 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE E 300 " --> pdb=" O GLU E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU E 359 " --> pdb=" O GLU E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 368 Processing helix chain 'E' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE E 378 " --> pdb=" O GLU E 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'F' and resid 9 through 20 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 40 through 53 Processing helix chain 'F' and resid 61 through 75 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 120 through 143 Processing helix chain 'F' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE F 160 " --> pdb=" O CYS F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 178 through 189 Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 201 through 216 Processing helix chain 'F' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE F 220 " --> pdb=" O HIS F 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP F 221 " --> pdb=" O PRO F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 248 Processing helix chain 'F' and resid 249 through 251 No H-bonds generated for 'chain 'F' and resid 249 through 251' Processing helix chain 'F' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG F 259 " --> pdb=" O GLN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU F 282 " --> pdb=" O GLN F 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE F 300 " --> pdb=" O GLU F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER F 310 " --> pdb=" O PRO F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 331 Processing helix chain 'F' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU F 359 " --> pdb=" O GLU F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 368 Processing helix chain 'F' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE F 378 " --> pdb=" O GLU F 374 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 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 53 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 143 Processing helix chain 'G' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE G 160 " --> pdb=" O CYS G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 178 through 189 Processing helix chain 'G' and resid 190 through 197 Processing helix chain 'G' and resid 201 through 216 Processing helix chain 'G' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE G 220 " --> pdb=" O HIS G 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP G 221 " --> pdb=" O PRO G 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 248 Processing helix chain 'G' and resid 249 through 251 No H-bonds generated for 'chain 'G' and resid 249 through 251' Processing helix chain 'G' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG G 259 " --> pdb=" O GLN G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU G 282 " --> pdb=" O GLN G 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE G 300 " --> pdb=" O GLU G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER G 310 " --> pdb=" O PRO G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 331 Processing helix chain 'G' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU G 359 " --> pdb=" O GLU G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 368 Processing helix chain 'G' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE G 378 " --> pdb=" O GLU G 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 Processing helix chain 'H' and resid 9 through 20 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 40 through 53 Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 120 through 143 Processing helix chain 'H' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE H 160 " --> pdb=" O CYS H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 178 through 189 Processing helix chain 'H' and resid 190 through 197 Processing helix chain 'H' and resid 201 through 216 Processing helix chain 'H' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE H 220 " --> pdb=" O HIS H 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP H 221 " --> pdb=" O PRO H 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 237 through 248 Processing helix chain 'H' and resid 249 through 251 No H-bonds generated for 'chain 'H' and resid 249 through 251' Processing helix chain 'H' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG H 259 " --> pdb=" O GLN H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU H 282 " --> pdb=" O GLN H 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE H 300 " --> pdb=" O GLU H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER H 310 " --> pdb=" O PRO H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 331 Processing helix chain 'H' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU H 359 " --> pdb=" O GLU H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 364 through 368 Processing helix chain 'H' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE H 378 " --> pdb=" O GLU H 374 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 6 Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 53 Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 143 Processing helix chain 'I' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE I 160 " --> pdb=" O CYS I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 174 No H-bonds generated for 'chain 'I' and resid 172 through 174' Processing helix chain 'I' and resid 178 through 189 Processing helix chain 'I' and resid 190 through 197 Processing helix chain 'I' and resid 201 through 216 Processing helix chain 'I' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE I 220 " --> pdb=" O HIS I 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP I 221 " --> pdb=" O PRO I 217 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 248 Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'I' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG I 259 " --> pdb=" O GLN I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 273 Processing helix chain 'I' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU I 282 " --> pdb=" O GLN I 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN I 283 " --> pdb=" O ALA I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE I 300 " --> pdb=" O GLU I 297 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER I 310 " --> pdb=" O PRO I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 331 Processing helix chain 'I' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS I 358 " --> pdb=" O ALA I 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU I 359 " --> pdb=" O GLU I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 364 through 368 Processing helix chain 'I' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE I 378 " --> pdb=" O GLU I 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 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 53 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 143 Processing helix chain 'J' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE J 160 " --> pdb=" O CYS J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 174 No H-bonds generated for 'chain 'J' and resid 172 through 174' Processing helix chain 'J' and resid 178 through 189 Processing helix chain 'J' and resid 190 through 197 Processing helix chain 'J' and resid 201 through 216 Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE J 220 " --> pdb=" O HIS J 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP J 221 " --> pdb=" O PRO J 217 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 248 Processing helix chain 'J' and resid 249 through 251 No H-bonds generated for 'chain 'J' and resid 249 through 251' Processing helix chain 'J' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG J 259 " --> pdb=" O GLN J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 273 Processing helix chain 'J' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU J 282 " --> pdb=" O GLN J 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN J 283 " --> pdb=" O ALA J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE J 300 " --> pdb=" O GLU J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER J 310 " --> pdb=" O PRO J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 317 through 331 Processing helix chain 'J' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS J 358 " --> pdb=" O ALA J 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU J 359 " --> pdb=" O GLU J 355 " (cutoff:3.500A) Processing helix chain 'J' and resid 364 through 368 Processing helix chain 'J' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE J 378 " --> pdb=" O GLU J 374 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 6 Processing helix chain 'K' and resid 9 through 20 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 53 Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 143 Processing helix chain 'K' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE K 160 " --> pdb=" O CYS K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 174 No H-bonds generated for 'chain 'K' and resid 172 through 174' Processing helix chain 'K' and resid 178 through 189 Processing helix chain 'K' and resid 190 through 197 Processing helix chain 'K' and resid 201 through 216 Processing helix chain 'K' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE K 220 " --> pdb=" O HIS K 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP K 221 " --> pdb=" O PRO K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 248 Processing helix chain 'K' and resid 249 through 251 No H-bonds generated for 'chain 'K' and resid 249 through 251' Processing helix chain 'K' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG K 259 " --> pdb=" O GLN K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 269 through 273 Processing helix chain 'K' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU K 282 " --> pdb=" O GLN K 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN K 283 " --> pdb=" O ALA K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE K 300 " --> pdb=" O GLU K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER K 310 " --> pdb=" O PRO K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 331 Processing helix chain 'K' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS K 358 " --> pdb=" O ALA K 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU K 359 " --> pdb=" O GLU K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 364 through 368 Processing helix chain 'K' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE K 378 " --> pdb=" O GLU K 374 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'L' and resid 9 through 20 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 40 through 53 Processing helix chain 'L' and resid 61 through 75 Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 120 through 143 Processing helix chain 'L' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE L 160 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 174 No H-bonds generated for 'chain 'L' and resid 172 through 174' Processing helix chain 'L' and resid 178 through 189 Processing helix chain 'L' and resid 190 through 197 Processing helix chain 'L' and resid 201 through 216 Processing helix chain 'L' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE L 220 " --> pdb=" O HIS L 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP L 221 " --> pdb=" O PRO L 217 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 248 Processing helix chain 'L' and resid 249 through 251 No H-bonds generated for 'chain 'L' and resid 249 through 251' Processing helix chain 'L' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG L 259 " --> pdb=" O GLN L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 269 through 273 Processing helix chain 'L' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU L 282 " --> pdb=" O GLN L 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN L 283 " --> pdb=" O ALA L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE L 300 " --> pdb=" O GLU L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER L 310 " --> pdb=" O PRO L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 317 through 331 Processing helix chain 'L' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS L 358 " --> pdb=" O ALA L 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU L 359 " --> pdb=" O GLU L 355 " (cutoff:3.500A) Processing helix chain 'L' and resid 364 through 368 Processing helix chain 'L' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE L 378 " --> pdb=" O GLU L 374 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 6 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 53 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 143 Processing helix chain 'M' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE M 160 " --> pdb=" O CYS M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 174 No H-bonds generated for 'chain 'M' and resid 172 through 174' Processing helix chain 'M' and resid 178 through 189 Processing helix chain 'M' and resid 190 through 197 Processing helix chain 'M' and resid 201 through 216 Processing helix chain 'M' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE M 220 " --> pdb=" O HIS M 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP M 221 " --> pdb=" O PRO M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 248 Processing helix chain 'M' and resid 249 through 251 No H-bonds generated for 'chain 'M' and resid 249 through 251' Processing helix chain 'M' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG M 259 " --> pdb=" O GLN M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 269 through 273 Processing helix chain 'M' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU M 282 " --> pdb=" O GLN M 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN M 283 " --> pdb=" O ALA M 279 " (cutoff:3.500A) Processing helix chain 'M' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE M 300 " --> pdb=" O GLU M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER M 310 " --> pdb=" O PRO M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 317 through 331 Processing helix chain 'M' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS M 358 " --> pdb=" O ALA M 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU M 359 " --> pdb=" O GLU M 355 " (cutoff:3.500A) Processing helix chain 'M' and resid 364 through 368 Processing helix chain 'M' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE M 378 " --> pdb=" O GLU M 374 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'N' and resid 9 through 20 Processing helix chain 'N' and resid 37 through 39 No H-bonds generated for 'chain 'N' and resid 37 through 39' Processing helix chain 'N' and resid 40 through 53 Processing helix chain 'N' and resid 61 through 75 Processing helix chain 'N' and resid 75 through 86 Processing helix chain 'N' and resid 120 through 143 Processing helix chain 'N' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE N 160 " --> pdb=" O CYS N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 174 No H-bonds generated for 'chain 'N' and resid 172 through 174' Processing helix chain 'N' and resid 178 through 189 Processing helix chain 'N' and resid 190 through 197 Processing helix chain 'N' and resid 201 through 216 Processing helix chain 'N' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE N 220 " --> pdb=" O HIS N 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP N 221 " --> pdb=" O PRO N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 248 Processing helix chain 'N' and resid 249 through 251 No H-bonds generated for 'chain 'N' and resid 249 through 251' Processing helix chain 'N' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG N 259 " --> pdb=" O GLN N 255 " (cutoff:3.500A) Processing helix chain 'N' and resid 269 through 273 Processing helix chain 'N' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU N 282 " --> pdb=" O GLN N 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN N 283 " --> pdb=" O ALA N 279 " (cutoff:3.500A) Processing helix chain 'N' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE N 300 " --> pdb=" O GLU N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER N 310 " --> pdb=" O PRO N 307 " (cutoff:3.500A) Processing helix chain 'N' and resid 317 through 331 Processing helix chain 'N' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS N 358 " --> pdb=" O ALA N 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU N 359 " --> pdb=" O GLU N 355 " (cutoff:3.500A) Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE N 378 " --> pdb=" O GLU N 374 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 6 Processing helix chain 'O' and resid 9 through 20 Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'O' and resid 40 through 53 Processing helix chain 'O' and resid 61 through 75 Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 120 through 143 Processing helix chain 'O' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE O 160 " --> pdb=" O CYS O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 174 No H-bonds generated for 'chain 'O' and resid 172 through 174' Processing helix chain 'O' and resid 178 through 189 Processing helix chain 'O' and resid 190 through 197 Processing helix chain 'O' and resid 201 through 216 Processing helix chain 'O' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE O 220 " --> pdb=" O HIS O 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP O 221 " --> pdb=" O PRO O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 237 through 248 Processing helix chain 'O' and resid 249 through 251 No H-bonds generated for 'chain 'O' and resid 249 through 251' Processing helix chain 'O' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG O 259 " --> pdb=" O GLN O 255 " (cutoff:3.500A) Processing helix chain 'O' and resid 269 through 273 Processing helix chain 'O' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU O 282 " --> pdb=" O GLN O 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN O 283 " --> pdb=" O ALA O 279 " (cutoff:3.500A) Processing helix chain 'O' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE O 300 " --> pdb=" O GLU O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER O 310 " --> pdb=" O PRO O 307 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 331 Processing helix chain 'O' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS O 358 " --> pdb=" O ALA O 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU O 359 " --> pdb=" O GLU O 355 " (cutoff:3.500A) Processing helix chain 'O' and resid 364 through 368 Processing helix chain 'O' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE O 378 " --> pdb=" O GLU O 374 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 6 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 53 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 143 Processing helix chain 'P' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE P 160 " --> pdb=" O CYS P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 174 No H-bonds generated for 'chain 'P' and resid 172 through 174' Processing helix chain 'P' and resid 178 through 189 Processing helix chain 'P' and resid 190 through 197 Processing helix chain 'P' and resid 201 through 216 Processing helix chain 'P' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE P 220 " --> pdb=" O HIS P 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP P 221 " --> pdb=" O PRO P 217 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 248 Processing helix chain 'P' and resid 249 through 251 No H-bonds generated for 'chain 'P' and resid 249 through 251' Processing helix chain 'P' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG P 259 " --> pdb=" O GLN P 255 " (cutoff:3.500A) Processing helix chain 'P' and resid 269 through 273 Processing helix chain 'P' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU P 282 " --> pdb=" O GLN P 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN P 283 " --> pdb=" O ALA P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE P 300 " --> pdb=" O GLU P 297 " (cutoff:3.500A) Processing helix chain 'P' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER P 310 " --> pdb=" O PRO P 307 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 331 Processing helix chain 'P' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS P 358 " --> pdb=" O ALA P 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU P 359 " --> pdb=" O GLU P 355 " (cutoff:3.500A) Processing helix chain 'P' and resid 364 through 368 Processing helix chain 'P' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE P 378 " --> pdb=" O GLU P 374 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 6 Processing helix chain 'Q' and resid 9 through 20 Processing helix chain 'Q' and resid 37 through 39 No H-bonds generated for 'chain 'Q' and resid 37 through 39' Processing helix chain 'Q' and resid 40 through 53 Processing helix chain 'Q' and resid 61 through 75 Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 120 through 143 Processing helix chain 'Q' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE Q 160 " --> pdb=" O CYS Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 172 through 174 No H-bonds generated for 'chain 'Q' and resid 172 through 174' Processing helix chain 'Q' and resid 178 through 189 Processing helix chain 'Q' and resid 190 through 197 Processing helix chain 'Q' and resid 201 through 216 Processing helix chain 'Q' and resid 216 through 231 removed outlier: 3.888A pdb=" N ILE Q 220 " --> pdb=" O HIS Q 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP Q 221 " --> pdb=" O PRO Q 217 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 248 Processing helix chain 'Q' and resid 249 through 251 No H-bonds generated for 'chain 'Q' and resid 249 through 251' Processing helix chain 'Q' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG Q 259 " --> pdb=" O GLN Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 269 through 273 Processing helix chain 'Q' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU Q 282 " --> pdb=" O GLN Q 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN Q 283 " --> pdb=" O ALA Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE Q 300 " --> pdb=" O GLU Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER Q 310 " --> pdb=" O PRO Q 307 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 331 Processing helix chain 'Q' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS Q 358 " --> pdb=" O ALA Q 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU Q 359 " --> pdb=" O GLU Q 355 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 368 Processing helix chain 'Q' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE Q 378 " --> pdb=" O GLU Q 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 6 Processing helix chain 'R' and resid 9 through 20 Processing helix chain 'R' and resid 37 through 39 No H-bonds generated for 'chain 'R' and resid 37 through 39' Processing helix chain 'R' and resid 40 through 53 Processing helix chain 'R' and resid 61 through 75 Processing helix chain 'R' and resid 75 through 86 Processing helix chain 'R' and resid 120 through 143 Processing helix chain 'R' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE R 160 " --> pdb=" O CYS R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 174 No H-bonds generated for 'chain 'R' and resid 172 through 174' Processing helix chain 'R' and resid 178 through 189 Processing helix chain 'R' and resid 190 through 197 Processing helix chain 'R' and resid 201 through 216 Processing helix chain 'R' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE R 220 " --> pdb=" O HIS R 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP R 221 " --> pdb=" O PRO R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 237 through 248 Processing helix chain 'R' and resid 249 through 251 No H-bonds generated for 'chain 'R' and resid 249 through 251' Processing helix chain 'R' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG R 259 " --> pdb=" O GLN R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 269 through 273 Processing helix chain 'R' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU R 282 " --> pdb=" O GLN R 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN R 283 " --> pdb=" O ALA R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 301 removed outlier: 3.595A pdb=" N PHE R 300 " --> pdb=" O GLU R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER R 310 " --> pdb=" O PRO R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 331 Processing helix chain 'R' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS R 358 " --> pdb=" O ALA R 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU R 359 " --> pdb=" O GLU R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 364 through 368 Processing helix chain 'R' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE R 378 " --> pdb=" O GLU R 374 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 6 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 53 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 143 Processing helix chain 'S' and resid 155 through 171 removed outlier: 3.660A pdb=" N ILE S 160 " --> pdb=" O CYS S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 172 through 174 No H-bonds generated for 'chain 'S' and resid 172 through 174' Processing helix chain 'S' and resid 178 through 189 Processing helix chain 'S' and resid 190 through 197 Processing helix chain 'S' and resid 201 through 216 Processing helix chain 'S' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE S 220 " --> pdb=" O HIS S 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP S 221 " --> pdb=" O PRO S 217 " (cutoff:3.500A) Processing helix chain 'S' and resid 237 through 248 Processing helix chain 'S' and resid 249 through 251 No H-bonds generated for 'chain 'S' and resid 249 through 251' Processing helix chain 'S' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG S 259 " --> pdb=" O GLN S 255 " (cutoff:3.500A) Processing helix chain 'S' and resid 269 through 273 Processing helix chain 'S' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU S 282 " --> pdb=" O GLN S 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN S 283 " --> pdb=" O ALA S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 296 through 301 removed outlier: 3.593A pdb=" N PHE S 300 " --> pdb=" O GLU S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER S 310 " --> pdb=" O PRO S 307 " (cutoff:3.500A) Processing helix chain 'S' and resid 317 through 331 Processing helix chain 'S' and resid 343 through 360 removed outlier: 3.693A pdb=" N LYS S 358 " --> pdb=" O ALA S 354 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU S 359 " --> pdb=" O GLU S 355 " (cutoff:3.500A) Processing helix chain 'S' and resid 364 through 368 Processing helix chain 'S' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE S 378 " --> pdb=" O GLU S 374 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 6 Processing helix chain 'T' and resid 9 through 20 Processing helix chain 'T' and resid 37 through 39 No H-bonds generated for 'chain 'T' and resid 37 through 39' Processing helix chain 'T' and resid 40 through 53 Processing helix chain 'T' and resid 61 through 75 Processing helix chain 'T' and resid 75 through 86 Processing helix chain 'T' and resid 120 through 143 Processing helix chain 'T' and resid 155 through 171 removed outlier: 3.659A pdb=" N ILE T 160 " --> pdb=" O CYS T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 172 through 174 No H-bonds generated for 'chain 'T' and resid 172 through 174' Processing helix chain 'T' and resid 178 through 189 Processing helix chain 'T' and resid 190 through 197 Processing helix chain 'T' and resid 201 through 216 Processing helix chain 'T' and resid 216 through 231 removed outlier: 3.887A pdb=" N ILE T 220 " --> pdb=" O HIS T 216 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP T 221 " --> pdb=" O PRO T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 237 through 248 Processing helix chain 'T' and resid 249 through 251 No H-bonds generated for 'chain 'T' and resid 249 through 251' Processing helix chain 'T' and resid 255 through 267 removed outlier: 3.827A pdb=" N ARG T 259 " --> pdb=" O GLN T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 269 through 273 Processing helix chain 'T' and resid 274 through 295 removed outlier: 4.755A pdb=" N GLU T 282 " --> pdb=" O GLN T 278 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLN T 283 " --> pdb=" O ALA T 279 " (cutoff:3.500A) Processing helix chain 'T' and resid 296 through 301 removed outlier: 3.594A pdb=" N PHE T 300 " --> pdb=" O GLU T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 306 through 313 removed outlier: 3.738A pdb=" N SER T 310 " --> pdb=" O PRO T 307 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 331 Processing helix chain 'T' and resid 343 through 360 removed outlier: 3.692A pdb=" N LYS T 358 " --> pdb=" O ALA T 354 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU T 359 " --> pdb=" O GLU T 355 " (cutoff:3.500A) Processing helix chain 'T' and resid 364 through 368 Processing helix chain 'T' and resid 374 through 379 removed outlier: 3.751A pdb=" N ILE T 378 " --> pdb=" O GLU T 374 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG A 27 " --> pdb=" O HIS A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE A 33 " --> pdb=" O ASN A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG B 27 " --> pdb=" O HIS B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE B 33 " --> pdb=" O ASN B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 104 Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG C 27 " --> pdb=" O HIS C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE C 33 " --> pdb=" O ASN C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 104 Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG D 27 " --> pdb=" O HIS D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE D 33 " --> pdb=" O ASN D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 97 through 104 Processing sheet with id=AB4, first strand: chain 'E' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG E 27 " --> pdb=" O HIS E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE E 33 " --> pdb=" O ASN E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 97 through 104 Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG F 27 " --> pdb=" O HIS F 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE F 33 " --> pdb=" O ASN F 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 97 through 104 Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG G 27 " --> pdb=" O HIS G 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'G' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE G 33 " --> pdb=" O ASN G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 97 through 104 Processing sheet with id=AC4, first strand: chain 'H' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG H 27 " --> pdb=" O HIS H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE H 33 " --> pdb=" O ASN H 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 97 through 104 Processing sheet with id=AC7, first strand: chain 'I' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG I 27 " --> pdb=" O HIS I 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'I' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE I 33 " --> pdb=" O ASN I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 97 through 104 Processing sheet with id=AD1, first strand: chain 'J' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG J 27 " --> pdb=" O HIS J 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE J 33 " --> pdb=" O ASN J 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 97 through 104 Processing sheet with id=AD4, first strand: chain 'K' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG K 27 " --> pdb=" O HIS K 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'K' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE K 33 " --> pdb=" O ASN K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 97 through 104 Processing sheet with id=AD7, first strand: chain 'L' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG L 27 " --> pdb=" O HIS L 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'L' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE L 33 " --> pdb=" O ASN L 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'L' and resid 97 through 104 Processing sheet with id=AE1, first strand: chain 'M' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG M 27 " --> pdb=" O HIS M 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'M' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE M 33 " --> pdb=" O ASN M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'M' and resid 97 through 104 Processing sheet with id=AE4, first strand: chain 'N' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG N 27 " --> pdb=" O HIS N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'N' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE N 33 " --> pdb=" O ASN N 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'N' and resid 97 through 104 Processing sheet with id=AE7, first strand: chain 'O' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG O 27 " --> pdb=" O HIS O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'O' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE O 33 " --> pdb=" O ASN O 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'O' and resid 97 through 104 Processing sheet with id=AF1, first strand: chain 'P' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG P 27 " --> pdb=" O HIS P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'P' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE P 33 " --> pdb=" O ASN P 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'P' and resid 97 through 104 Processing sheet with id=AF4, first strand: chain 'Q' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG Q 27 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'Q' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE Q 33 " --> pdb=" O ASN Q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'Q' and resid 97 through 104 Processing sheet with id=AF7, first strand: chain 'R' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG R 27 " --> pdb=" O HIS R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'R' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE R 33 " --> pdb=" O ASN R 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'R' and resid 97 through 104 Processing sheet with id=AG1, first strand: chain 'S' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG S 27 " --> pdb=" O HIS S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'S' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE S 33 " --> pdb=" O ASN S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'S' and resid 97 through 104 Processing sheet with id=AG4, first strand: chain 'T' and resid 27 through 28 removed outlier: 6.767A pdb=" N ARG T 27 " --> pdb=" O HIS T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'T' and resid 33 through 35 removed outlier: 6.739A pdb=" N ILE T 33 " --> pdb=" O ASN T 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'T' and resid 97 through 104 3580 hydrogen bonds defined for protein. 9940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 20.61 Time building geometry restraints manager: 20.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.54: 62048 1.54 - 1.86: 1012 1.86 - 2.18: 0 2.18 - 2.50: 0 2.50 - 2.82: 18 Bond restraints: 63078 Sorted by residual: bond pdb=" O3' C U1014 " pdb=" P C U1015 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1014 " pdb=" P C e1015 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C U1049 " pdb=" P C U1050 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1049 " pdb=" P C e1050 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.52e+03 bond pdb=" O3' C e1007 " pdb=" P C e1008 " ideal model delta sigma weight residual 1.607 2.818 -1.211 1.50e-02 4.44e+03 6.51e+03 ... (remaining 63073 not shown) Histogram of bond angle deviations from ideal: 75.63 - 90.70: 36 90.70 - 105.77: 1320 105.77 - 120.84: 66566 120.84 - 135.92: 17672 135.92 - 150.99: 18 Bond angle restraints: 85612 Sorted by residual: angle pdb=" O3' C e1014 " pdb=" P C e1015 " pdb=" O5' C e1015 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C U1014 " pdb=" P C U1015 " pdb=" O5' C U1015 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C U1049 " pdb=" P C U1050 " pdb=" O5' C U1050 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C e1049 " pdb=" P C e1050 " pdb=" O5' C e1050 " ideal model delta sigma weight residual 104.00 75.63 28.37 1.50e+00 4.44e-01 3.58e+02 angle pdb=" O3' C e1028 " pdb=" P C e1029 " pdb=" O5' C e1029 " ideal model delta sigma weight residual 104.00 75.64 28.36 1.50e+00 4.44e-01 3.57e+02 ... (remaining 85607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 35058 17.76 - 35.53: 2776 35.53 - 53.29: 400 53.29 - 71.05: 160 71.05 - 88.81: 180 Dihedral angle restraints: 38574 sinusoidal: 16754 harmonic: 21820 Sorted by residual: dihedral pdb=" CA ARG O 338 " pdb=" C ARG O 338 " pdb=" N GLY O 339 " pdb=" CA GLY O 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG T 338 " pdb=" C ARG T 338 " pdb=" N GLY T 339 " pdb=" CA GLY T 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ARG E 338 " pdb=" C ARG E 338 " pdb=" N GLY E 339 " pdb=" CA GLY E 339 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 38571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 5780 0.034 - 0.069: 2960 0.069 - 0.103: 740 0.103 - 0.137: 320 0.137 - 0.172: 20 Chirality restraints: 9820 Sorted by residual: chirality pdb=" CB VAL S 284 " pdb=" CA VAL S 284 " pdb=" CG1 VAL S 284 " pdb=" CG2 VAL S 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB VAL N 284 " pdb=" CA VAL N 284 " pdb=" CG1 VAL N 284 " pdb=" CG2 VAL N 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CB VAL D 284 " pdb=" CA VAL D 284 " pdb=" CG1 VAL D 284 " pdb=" CG2 VAL D 284 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 9817 not shown) Planarity restraints: 10520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 149 " 0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR L 149 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR L 149 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR L 149 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR L 149 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR L 149 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR L 149 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 149 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 149 " -0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR G 149 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR G 149 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR G 149 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR G 149 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR G 149 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR G 149 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 149 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 149 " 0.005 2.00e-02 2.50e+03 1.11e-02 2.44e+00 pdb=" CG TYR B 149 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR B 149 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR B 149 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 149 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 149 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 149 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 149 " 0.002 2.00e-02 2.50e+03 ... (remaining 10517 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7168 2.74 - 3.28: 60942 3.28 - 3.82: 104240 3.82 - 4.36: 134256 4.36 - 4.90: 217416 Nonbonded interactions: 524022 Sorted by model distance: nonbonded pdb=" OE1 GLU G 297 " pdb=" OH TYR G 301 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU L 297 " pdb=" OH TYR L 301 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU B 297 " pdb=" OH TYR B 301 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU Q 297 " pdb=" OH TYR Q 301 " model vdw 2.203 2.440 nonbonded pdb=" OE1 GLU J 297 " pdb=" OH TYR J 301 " model vdw 2.204 2.440 ... (remaining 524017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'B' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'C' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'D' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'E' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'F' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'G' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'H' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'I' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'J' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'K' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'L' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'M' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'N' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'O' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'P' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'Q' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'R' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'S' and (resid 2 through 99 or resid 101 through 379)) selection = (chain 'T' and (resid 2 through 99 or resid 101 through 379)) } ncs_group { reference = chain 'U' selection = chain 'e' } 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=0.50 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: 4.050 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: 0.050 Extract box with map and model: 16.320 Check model and map are aligned: 0.680 Set scattering table: 0.410 Process input model: 165.280 Find NCS groups from input model: 3.300 Set up NCS constraints: 0.290 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:9.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.021 1.211 63078 Z= 1.282 Angle : 1.033 42.987 85612 Z= 0.504 Chirality : 0.044 0.172 9820 Planarity : 0.003 0.034 10520 Dihedral : 14.494 88.812 24654 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 0.71 (0.09), residues: 7540 helix: 0.86 (0.07), residues: 4720 sheet: 0.74 (0.22), residues: 440 loop : -0.15 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 260 HIS 0.006 0.001 HIS E 225 PHE 0.019 0.002 PHE S 219 TYR 0.022 0.002 TYR G 149 ARG 0.004 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 980 time to evaluate : 5.076 Fit side-chains REVERT: A 71 MET cc_start: 0.9205 (mtm) cc_final: 0.8963 (mtp) REVERT: B 50 MET cc_start: 0.9065 (mtm) cc_final: 0.8863 (mtm) REVERT: B 71 MET cc_start: 0.9158 (mtm) cc_final: 0.8768 (mtp) REVERT: C 64 LEU cc_start: 0.8985 (tt) cc_final: 0.8717 (tm) REVERT: E 71 MET cc_start: 0.9221 (mtm) cc_final: 0.8875 (mtp) REVERT: E 158 MET cc_start: 0.8922 (mmm) cc_final: 0.8718 (mmp) REVERT: E 343 ASN cc_start: 0.8234 (t0) cc_final: 0.7958 (t0) REVERT: F 71 MET cc_start: 0.9206 (mtm) cc_final: 0.8962 (mtp) REVERT: G 50 MET cc_start: 0.9066 (mtm) cc_final: 0.8863 (mtm) REVERT: G 71 MET cc_start: 0.9159 (mtm) cc_final: 0.8769 (mtp) REVERT: H 64 LEU cc_start: 0.8987 (tt) cc_final: 0.8717 (tm) REVERT: J 71 MET cc_start: 0.9221 (mtm) cc_final: 0.8877 (mtp) REVERT: J 158 MET cc_start: 0.8923 (mmm) cc_final: 0.8718 (mmp) REVERT: J 343 ASN cc_start: 0.8238 (t0) cc_final: 0.7958 (t0) REVERT: K 71 MET cc_start: 0.9209 (mtm) cc_final: 0.8967 (mtp) REVERT: L 50 MET cc_start: 0.9064 (mtm) cc_final: 0.8863 (mtm) REVERT: L 71 MET cc_start: 0.9156 (mtm) cc_final: 0.8770 (mtp) REVERT: M 64 LEU cc_start: 0.8989 (tt) cc_final: 0.8715 (tm) REVERT: O 71 MET cc_start: 0.9217 (mtm) cc_final: 0.8877 (mtp) REVERT: O 158 MET cc_start: 0.8925 (mmm) cc_final: 0.8722 (mmp) REVERT: O 343 ASN cc_start: 0.8238 (t0) cc_final: 0.7956 (t0) REVERT: P 71 MET cc_start: 0.9203 (mtm) cc_final: 0.8959 (mtp) REVERT: Q 50 MET cc_start: 0.9064 (mtm) cc_final: 0.8862 (mtm) REVERT: Q 71 MET cc_start: 0.9164 (mtm) cc_final: 0.8779 (mtp) REVERT: R 64 LEU cc_start: 0.8989 (tt) cc_final: 0.8718 (tm) REVERT: T 71 MET cc_start: 0.9219 (mtm) cc_final: 0.8875 (mtp) REVERT: T 158 MET cc_start: 0.8925 (mmm) cc_final: 0.8721 (mmp) REVERT: T 343 ASN cc_start: 0.8238 (t0) cc_final: 0.7957 (t0) outliers start: 0 outliers final: 4 residues processed: 980 average time/residue: 1.8305 time to fit residues: 2180.9219 Evaluate side-chains 788 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 784 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain P residue 96 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 636 optimal weight: 0.9980 chunk 571 optimal weight: 0.0050 chunk 317 optimal weight: 8.9990 chunk 195 optimal weight: 0.7980 chunk 385 optimal weight: 0.9990 chunk 305 optimal weight: 0.6980 chunk 590 optimal weight: 0.7980 chunk 228 optimal weight: 0.9990 chunk 359 optimal weight: 0.5980 chunk 439 optimal weight: 0.9980 chunk 684 optimal weight: 1.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 89 HIS B 26 GLN B 89 HIS ** B 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN D 26 GLN D 89 HIS D 356 GLN E 26 GLN E 89 HIS F 26 GLN F 89 HIS G 26 GLN G 89 HIS ** G 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 356 GLN I 26 GLN I 89 HIS I 151 HIS I 356 GLN J 26 GLN J 89 HIS K 26 GLN K 89 HIS L 26 GLN L 89 HIS ** L 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 356 GLN N 26 GLN N 89 HIS N 356 GLN O 26 GLN O 89 HIS P 26 GLN P 89 HIS Q 26 GLN Q 89 HIS ** Q 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 HIS R 356 GLN S 26 GLN S 89 HIS S 151 HIS S 356 GLN T 26 GLN T 89 HIS Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 63078 Z= 0.178 Angle : 0.507 5.401 85612 Z= 0.275 Chirality : 0.040 0.156 9820 Planarity : 0.004 0.036 10520 Dihedral : 11.376 79.540 10462 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.78 % Allowed : 8.35 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.10), residues: 7540 helix: 1.41 (0.07), residues: 4720 sheet: 0.72 (0.25), residues: 300 loop : 0.20 (0.13), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 260 HIS 0.004 0.001 HIS D 225 PHE 0.010 0.002 PHE L 219 TYR 0.010 0.001 TYR F 337 ARG 0.009 0.001 ARG O 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1004 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 828 time to evaluate : 5.456 Fit side-chains REVERT: A 193 GLU cc_start: 0.7697 (mp0) cc_final: 0.7338 (mp0) REVERT: A 366 SER cc_start: 0.8433 (m) cc_final: 0.8174 (p) REVERT: B 71 MET cc_start: 0.9201 (mtm) cc_final: 0.8816 (mtp) REVERT: B 192 ASN cc_start: 0.8437 (m110) cc_final: 0.8158 (m-40) REVERT: B 248 MET cc_start: 0.7727 (mmp) cc_final: 0.7390 (mmp) REVERT: B 271 MET cc_start: 0.8411 (mmm) cc_final: 0.7887 (mmm) REVERT: B 366 SER cc_start: 0.8339 (m) cc_final: 0.8006 (p) REVERT: C 64 LEU cc_start: 0.8980 (tt) cc_final: 0.8678 (tm) REVERT: C 336 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7194 (pt0) REVERT: C 342 ARG cc_start: 0.7559 (ptp-110) cc_final: 0.7202 (ptm160) REVERT: D 342 ARG cc_start: 0.7529 (ptp-110) cc_final: 0.7312 (ptm160) REVERT: E 71 MET cc_start: 0.9291 (mtm) cc_final: 0.8981 (mtp) REVERT: E 96 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7514 (p0) REVERT: E 342 ARG cc_start: 0.7319 (ptp-110) cc_final: 0.7034 (ptp-170) REVERT: F 193 GLU cc_start: 0.7696 (mp0) cc_final: 0.7338 (mp0) REVERT: F 366 SER cc_start: 0.8437 (m) cc_final: 0.8172 (p) REVERT: G 71 MET cc_start: 0.9205 (mtm) cc_final: 0.8818 (mtp) REVERT: G 192 ASN cc_start: 0.8429 (m110) cc_final: 0.8149 (m-40) REVERT: G 248 MET cc_start: 0.7723 (mmp) cc_final: 0.7387 (mmp) REVERT: G 271 MET cc_start: 0.8409 (mmm) cc_final: 0.7888 (mmm) REVERT: G 366 SER cc_start: 0.8344 (m) cc_final: 0.8008 (p) REVERT: H 64 LEU cc_start: 0.8984 (tt) cc_final: 0.8679 (tm) REVERT: H 336 GLU cc_start: 0.7424 (mt-10) cc_final: 0.7192 (pt0) REVERT: H 342 ARG cc_start: 0.7557 (ptp-110) cc_final: 0.7202 (ptm160) REVERT: I 342 ARG cc_start: 0.7528 (ptp-110) cc_final: 0.7308 (ptm160) REVERT: J 71 MET cc_start: 0.9292 (mtm) cc_final: 0.8981 (mtp) REVERT: J 96 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7514 (p0) REVERT: J 342 ARG cc_start: 0.7322 (ptp-110) cc_final: 0.7032 (ptp-170) REVERT: K 193 GLU cc_start: 0.7696 (mp0) cc_final: 0.7336 (mp0) REVERT: K 366 SER cc_start: 0.8435 (m) cc_final: 0.8174 (p) REVERT: L 71 MET cc_start: 0.9206 (mtm) cc_final: 0.8822 (mtp) REVERT: L 192 ASN cc_start: 0.8438 (m110) cc_final: 0.8158 (m-40) REVERT: L 248 MET cc_start: 0.7721 (mmp) cc_final: 0.7387 (mmp) REVERT: L 271 MET cc_start: 0.8409 (mmm) cc_final: 0.7888 (mmm) REVERT: L 366 SER cc_start: 0.8344 (m) cc_final: 0.8008 (p) REVERT: M 64 LEU cc_start: 0.8983 (tt) cc_final: 0.8675 (tm) REVERT: M 336 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7193 (pt0) REVERT: M 342 ARG cc_start: 0.7555 (ptp-110) cc_final: 0.7203 (ptm160) REVERT: N 342 ARG cc_start: 0.7525 (ptp-110) cc_final: 0.7308 (ptm160) REVERT: O 71 MET cc_start: 0.9289 (mtm) cc_final: 0.8984 (mtp) REVERT: O 96 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7516 (p0) REVERT: O 342 ARG cc_start: 0.7318 (ptp-110) cc_final: 0.7026 (ptp-170) REVERT: P 193 GLU cc_start: 0.7705 (mp0) cc_final: 0.7348 (mp0) REVERT: P 366 SER cc_start: 0.8436 (m) cc_final: 0.8171 (p) REVERT: Q 71 MET cc_start: 0.9205 (mtm) cc_final: 0.8825 (mtp) REVERT: Q 192 ASN cc_start: 0.8431 (m110) cc_final: 0.8152 (m-40) REVERT: Q 248 MET cc_start: 0.7720 (mmp) cc_final: 0.7385 (mmp) REVERT: Q 271 MET cc_start: 0.8406 (mmm) cc_final: 0.7883 (mmm) REVERT: Q 366 SER cc_start: 0.8348 (m) cc_final: 0.8011 (p) REVERT: R 64 LEU cc_start: 0.8985 (tt) cc_final: 0.8682 (tm) REVERT: R 336 GLU cc_start: 0.7429 (mt-10) cc_final: 0.7192 (pt0) REVERT: R 342 ARG cc_start: 0.7560 (ptp-110) cc_final: 0.7205 (ptm160) REVERT: S 342 ARG cc_start: 0.7526 (ptp-110) cc_final: 0.7309 (ptm160) REVERT: T 71 MET cc_start: 0.9293 (mtm) cc_final: 0.8983 (mtp) REVERT: T 96 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7510 (p0) REVERT: T 342 ARG cc_start: 0.7318 (ptp-110) cc_final: 0.7032 (ptp-170) outliers start: 176 outliers final: 72 residues processed: 920 average time/residue: 1.8003 time to fit residues: 2021.3308 Evaluate side-chains 833 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 757 time to evaluate : 5.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 64 LEU Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 248 MET Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 64 LEU Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 248 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 380 optimal weight: 2.9990 chunk 212 optimal weight: 0.6980 chunk 569 optimal weight: 4.9990 chunk 466 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 685 optimal weight: 0.0030 chunk 741 optimal weight: 1.9990 chunk 610 optimal weight: 0.5980 chunk 680 optimal weight: 0.8980 chunk 233 optimal weight: 0.5980 chunk 550 optimal weight: 0.6980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 HIS A 216 HIS B 26 GLN ** C 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 89 HIS D 356 GLN E 89 HIS F 89 HIS F 216 HIS G 26 GLN ** H 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 GLN I 89 HIS I 356 GLN J 89 HIS K 89 HIS K 216 HIS L 26 GLN ** M 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN N 89 HIS N 356 GLN O 89 HIS P 89 HIS P 216 HIS Q 26 GLN ** R 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 26 GLN S 89 HIS S 356 GLN T 89 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 63078 Z= 0.155 Angle : 0.474 6.040 85612 Z= 0.253 Chirality : 0.039 0.143 9820 Planarity : 0.003 0.037 10520 Dihedral : 11.127 73.727 10454 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.78 % Allowed : 10.65 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.10), residues: 7540 helix: 1.63 (0.07), residues: 4720 sheet: 0.72 (0.26), residues: 300 loop : 0.34 (0.13), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 260 HIS 0.004 0.001 HIS B 225 PHE 0.008 0.002 PHE M 226 TYR 0.010 0.001 TYR J 337 ARG 0.009 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 816 time to evaluate : 5.224 Fit side-chains REVERT: A 67 MET cc_start: 0.8711 (mmm) cc_final: 0.8370 (mmm) REVERT: A 77 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7338 (mm-30) REVERT: A 193 GLU cc_start: 0.7650 (mp0) cc_final: 0.7286 (mp0) REVERT: B 71 MET cc_start: 0.9189 (mtm) cc_final: 0.8820 (mtp) REVERT: B 175 ASP cc_start: 0.7782 (p0) cc_final: 0.7565 (p0) REVERT: B 192 ASN cc_start: 0.8418 (m110) cc_final: 0.8152 (m-40) REVERT: B 194 MET cc_start: 0.8553 (mtm) cc_final: 0.7918 (mtm) REVERT: B 271 MET cc_start: 0.8379 (mmm) cc_final: 0.7864 (mmm) REVERT: B 292 GLN cc_start: 0.8124 (pt0) cc_final: 0.7847 (mt0) REVERT: B 366 SER cc_start: 0.8328 (m) cc_final: 0.8009 (p) REVERT: C 64 LEU cc_start: 0.8970 (tt) cc_final: 0.8656 (tm) REVERT: C 130 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7228 (mp0) REVERT: D 194 MET cc_start: 0.8624 (mtm) cc_final: 0.7954 (mtm) REVERT: D 342 ARG cc_start: 0.7520 (ptp-110) cc_final: 0.7270 (pmm-80) REVERT: E 71 MET cc_start: 0.9258 (mtm) cc_final: 0.8938 (mtp) REVERT: E 96 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7522 (p0) REVERT: E 122 GLU cc_start: 0.7807 (mp0) cc_final: 0.7505 (mp0) REVERT: E 283 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7325 (mt0) REVERT: E 338 ARG cc_start: 0.6916 (ptt-90) cc_final: 0.6538 (ptt-90) REVERT: E 342 ARG cc_start: 0.7344 (ptp-110) cc_final: 0.7064 (ptp-170) REVERT: F 67 MET cc_start: 0.8708 (mmm) cc_final: 0.8368 (mmm) REVERT: F 77 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7341 (mm-30) REVERT: F 193 GLU cc_start: 0.7649 (mp0) cc_final: 0.7283 (mp0) REVERT: G 71 MET cc_start: 0.9193 (mtm) cc_final: 0.8820 (mtp) REVERT: G 175 ASP cc_start: 0.7784 (p0) cc_final: 0.7564 (p0) REVERT: G 192 ASN cc_start: 0.8409 (m110) cc_final: 0.8136 (m-40) REVERT: G 194 MET cc_start: 0.8547 (mtm) cc_final: 0.7923 (mtm) REVERT: G 271 MET cc_start: 0.8378 (mmm) cc_final: 0.7862 (mmm) REVERT: G 292 GLN cc_start: 0.8134 (pt0) cc_final: 0.7853 (mt0) REVERT: G 366 SER cc_start: 0.8326 (m) cc_final: 0.8006 (p) REVERT: H 64 LEU cc_start: 0.8970 (tt) cc_final: 0.8655 (tm) REVERT: H 130 GLU cc_start: 0.7540 (mm-30) cc_final: 0.7231 (mp0) REVERT: I 194 MET cc_start: 0.8628 (mtm) cc_final: 0.7959 (mtm) REVERT: I 342 ARG cc_start: 0.7523 (ptp-110) cc_final: 0.7279 (pmm-80) REVERT: J 71 MET cc_start: 0.9259 (mtm) cc_final: 0.8941 (mtp) REVERT: J 96 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7522 (p0) REVERT: J 122 GLU cc_start: 0.7816 (mp0) cc_final: 0.7513 (mp0) REVERT: J 283 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: J 338 ARG cc_start: 0.6917 (ptt-90) cc_final: 0.6538 (ptt-90) REVERT: J 342 ARG cc_start: 0.7345 (ptp-110) cc_final: 0.7064 (ptp-170) REVERT: K 67 MET cc_start: 0.8715 (mmm) cc_final: 0.8368 (mmm) REVERT: K 77 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7338 (mm-30) REVERT: K 193 GLU cc_start: 0.7644 (mp0) cc_final: 0.7280 (mp0) REVERT: L 71 MET cc_start: 0.9194 (mtm) cc_final: 0.8826 (mtp) REVERT: L 175 ASP cc_start: 0.7790 (p0) cc_final: 0.7570 (p0) REVERT: L 192 ASN cc_start: 0.8418 (m110) cc_final: 0.8152 (m-40) REVERT: L 194 MET cc_start: 0.8550 (mtm) cc_final: 0.7914 (mtm) REVERT: L 271 MET cc_start: 0.8379 (mmm) cc_final: 0.7866 (mmm) REVERT: L 292 GLN cc_start: 0.8120 (pt0) cc_final: 0.7845 (mt0) REVERT: L 366 SER cc_start: 0.8330 (m) cc_final: 0.8010 (p) REVERT: M 64 LEU cc_start: 0.8973 (tt) cc_final: 0.8655 (tm) REVERT: M 130 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7228 (mp0) REVERT: N 194 MET cc_start: 0.8627 (mtm) cc_final: 0.7957 (mtm) REVERT: N 342 ARG cc_start: 0.7521 (ptp-110) cc_final: 0.7275 (pmm-80) REVERT: O 71 MET cc_start: 0.9256 (mtm) cc_final: 0.8942 (mtp) REVERT: O 96 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7519 (p0) REVERT: O 122 GLU cc_start: 0.7810 (mp0) cc_final: 0.7511 (mp0) REVERT: O 283 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: O 338 ARG cc_start: 0.6919 (ptt-90) cc_final: 0.6541 (ptt-90) REVERT: O 342 ARG cc_start: 0.7345 (ptp-110) cc_final: 0.7062 (ptp-170) REVERT: P 67 MET cc_start: 0.8702 (mmm) cc_final: 0.8363 (mmm) REVERT: P 77 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7335 (mm-30) REVERT: P 193 GLU cc_start: 0.7658 (mp0) cc_final: 0.7294 (mp0) REVERT: Q 71 MET cc_start: 0.9194 (mtm) cc_final: 0.8828 (mtp) REVERT: Q 175 ASP cc_start: 0.7787 (p0) cc_final: 0.7569 (p0) REVERT: Q 192 ASN cc_start: 0.8410 (m110) cc_final: 0.8140 (m-40) REVERT: Q 194 MET cc_start: 0.8549 (mtm) cc_final: 0.7926 (mtm) REVERT: Q 271 MET cc_start: 0.8376 (mmm) cc_final: 0.7860 (mmm) REVERT: Q 292 GLN cc_start: 0.8137 (pt0) cc_final: 0.7856 (mt0) REVERT: Q 366 SER cc_start: 0.8334 (m) cc_final: 0.8013 (p) REVERT: R 64 LEU cc_start: 0.8974 (tt) cc_final: 0.8659 (tm) REVERT: R 130 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7232 (mp0) REVERT: S 194 MET cc_start: 0.8628 (mtm) cc_final: 0.7955 (mtm) REVERT: S 342 ARG cc_start: 0.7525 (ptp-110) cc_final: 0.7276 (pmm-80) REVERT: T 71 MET cc_start: 0.9259 (mtm) cc_final: 0.8940 (mtp) REVERT: T 96 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7517 (p0) REVERT: T 122 GLU cc_start: 0.7813 (mp0) cc_final: 0.7514 (mp0) REVERT: T 283 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.7324 (mt0) REVERT: T 338 ARG cc_start: 0.6916 (ptt-90) cc_final: 0.6535 (ptt-90) REVERT: T 342 ARG cc_start: 0.7344 (ptp-110) cc_final: 0.7061 (ptp-170) outliers start: 176 outliers final: 100 residues processed: 908 average time/residue: 1.7360 time to fit residues: 1935.2091 Evaluate side-chains 860 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 752 time to evaluate : 5.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 155 ASP Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain M residue 345 ASP Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 155 ASP Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 248 MET Chi-restraints excluded: chain R residue 345 ASP Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 155 ASP Chi-restraints excluded: chain T residue 248 MET Chi-restraints excluded: chain T residue 283 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 677 optimal weight: 3.9990 chunk 515 optimal weight: 3.9990 chunk 355 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 327 optimal weight: 1.9990 chunk 460 optimal weight: 0.0570 chunk 688 optimal weight: 2.9990 chunk 728 optimal weight: 0.7980 chunk 359 optimal weight: 0.5980 chunk 652 optimal weight: 9.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN D 356 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** H 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN ** J 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 364 ASN ** M 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 GLN N 356 GLN ** O 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 364 ASN ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 63078 Z= 0.206 Angle : 0.507 7.528 85612 Z= 0.269 Chirality : 0.040 0.145 9820 Planarity : 0.004 0.039 10520 Dihedral : 11.065 73.868 10454 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.41 % Allowed : 12.56 % Favored : 85.03 % 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: 1.56 (0.09), residues: 7540 helix: 1.58 (0.07), residues: 4720 sheet: 0.52 (0.26), residues: 260 loop : 0.20 (0.13), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.006 0.001 HIS G 225 PHE 0.010 0.002 PHE R 226 TYR 0.011 0.001 TYR E 337 ARG 0.009 0.001 ARG L 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 912 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 760 time to evaluate : 5.035 Fit side-chains REVERT: A 67 MET cc_start: 0.8719 (mmm) cc_final: 0.8378 (mmm) REVERT: A 77 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 193 GLU cc_start: 0.7642 (mp0) cc_final: 0.7306 (mp0) REVERT: A 366 SER cc_start: 0.8441 (m) cc_final: 0.8201 (p) REVERT: B 71 MET cc_start: 0.9158 (mtm) cc_final: 0.8806 (mtp) REVERT: B 192 ASN cc_start: 0.8398 (m110) cc_final: 0.8145 (m-40) REVERT: B 271 MET cc_start: 0.8388 (mmm) cc_final: 0.7913 (mmm) REVERT: B 366 SER cc_start: 0.8359 (m) cc_final: 0.8039 (p) REVERT: C 64 LEU cc_start: 0.8957 (tt) cc_final: 0.8637 (tm) REVERT: C 130 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7226 (mp0) REVERT: D 342 ARG cc_start: 0.7554 (ptp-110) cc_final: 0.7348 (ptp-170) REVERT: E 71 MET cc_start: 0.9252 (mtm) cc_final: 0.8923 (mtp) REVERT: E 96 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7447 (p0) REVERT: E 122 GLU cc_start: 0.7853 (mp0) cc_final: 0.7579 (mp0) REVERT: E 283 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: E 338 ARG cc_start: 0.6902 (ptt-90) cc_final: 0.6597 (ptt-90) REVERT: E 342 ARG cc_start: 0.7455 (ptp-110) cc_final: 0.7234 (ptp-110) REVERT: F 67 MET cc_start: 0.8713 (mmm) cc_final: 0.8376 (mmm) REVERT: F 77 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7316 (mm-30) REVERT: F 193 GLU cc_start: 0.7643 (mp0) cc_final: 0.7303 (mp0) REVERT: F 366 SER cc_start: 0.8444 (m) cc_final: 0.8203 (p) REVERT: G 71 MET cc_start: 0.9163 (mtm) cc_final: 0.8807 (mtp) REVERT: G 192 ASN cc_start: 0.8391 (m110) cc_final: 0.8131 (m-40) REVERT: G 271 MET cc_start: 0.8387 (mmm) cc_final: 0.7911 (mmm) REVERT: G 366 SER cc_start: 0.8354 (m) cc_final: 0.8034 (p) REVERT: H 64 LEU cc_start: 0.8960 (tt) cc_final: 0.8637 (tm) REVERT: H 130 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7232 (mp0) REVERT: I 89 HIS cc_start: 0.6625 (m-70) cc_final: 0.6262 (m170) REVERT: I 342 ARG cc_start: 0.7555 (ptp-110) cc_final: 0.7350 (ptp-170) REVERT: J 71 MET cc_start: 0.9252 (mtm) cc_final: 0.8927 (mtp) REVERT: J 96 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7445 (p0) REVERT: J 122 GLU cc_start: 0.7855 (mp0) cc_final: 0.7583 (mp0) REVERT: J 283 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: J 338 ARG cc_start: 0.6901 (ptt-90) cc_final: 0.6596 (ptt-90) REVERT: J 342 ARG cc_start: 0.7455 (ptp-110) cc_final: 0.7232 (ptp-110) REVERT: K 67 MET cc_start: 0.8720 (mmm) cc_final: 0.8378 (mmm) REVERT: K 77 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7314 (mm-30) REVERT: K 193 GLU cc_start: 0.7637 (mp0) cc_final: 0.7298 (mp0) REVERT: K 366 SER cc_start: 0.8446 (m) cc_final: 0.8207 (p) REVERT: L 71 MET cc_start: 0.9166 (mtm) cc_final: 0.8813 (mtp) REVERT: L 192 ASN cc_start: 0.8399 (m110) cc_final: 0.8146 (m-40) REVERT: L 271 MET cc_start: 0.8388 (mmm) cc_final: 0.7914 (mmm) REVERT: L 366 SER cc_start: 0.8360 (m) cc_final: 0.8038 (p) REVERT: M 64 LEU cc_start: 0.8960 (tt) cc_final: 0.8634 (tm) REVERT: M 130 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7224 (mp0) REVERT: N 342 ARG cc_start: 0.7553 (ptp-110) cc_final: 0.7347 (ptp-170) REVERT: O 71 MET cc_start: 0.9250 (mtm) cc_final: 0.8928 (mtp) REVERT: O 96 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7445 (p0) REVERT: O 122 GLU cc_start: 0.7853 (mp0) cc_final: 0.7579 (mp0) REVERT: O 283 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: O 338 ARG cc_start: 0.6905 (ptt-90) cc_final: 0.6599 (ptt-90) REVERT: O 342 ARG cc_start: 0.7455 (ptp-110) cc_final: 0.7232 (ptp-110) REVERT: P 67 MET cc_start: 0.8710 (mmm) cc_final: 0.8370 (mmm) REVERT: P 77 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7313 (mm-30) REVERT: P 193 GLU cc_start: 0.7649 (mp0) cc_final: 0.7313 (mp0) REVERT: P 366 SER cc_start: 0.8442 (m) cc_final: 0.8199 (p) REVERT: Q 71 MET cc_start: 0.9164 (mtm) cc_final: 0.8816 (mtp) REVERT: Q 192 ASN cc_start: 0.8392 (m110) cc_final: 0.8134 (m-40) REVERT: Q 271 MET cc_start: 0.8385 (mmm) cc_final: 0.7911 (mmm) REVERT: Q 366 SER cc_start: 0.8360 (m) cc_final: 0.8038 (p) REVERT: R 64 LEU cc_start: 0.8962 (tt) cc_final: 0.8640 (tm) REVERT: R 130 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7230 (mp0) REVERT: S 89 HIS cc_start: 0.6627 (m-70) cc_final: 0.6266 (m170) REVERT: S 342 ARG cc_start: 0.7555 (ptp-110) cc_final: 0.7349 (ptp-170) REVERT: T 71 MET cc_start: 0.9254 (mtm) cc_final: 0.8925 (mtp) REVERT: T 96 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7445 (p0) REVERT: T 122 GLU cc_start: 0.7853 (mp0) cc_final: 0.7584 (mp0) REVERT: T 283 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7394 (mt0) REVERT: T 338 ARG cc_start: 0.6903 (ptt-90) cc_final: 0.6596 (ptt-90) REVERT: T 342 ARG cc_start: 0.7453 (ptp-110) cc_final: 0.7231 (ptp-110) outliers start: 152 outliers final: 100 residues processed: 840 average time/residue: 1.7678 time to fit residues: 1818.9434 Evaluate side-chains 840 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 732 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 76 ARG Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 248 MET Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 248 MET Chi-restraints excluded: chain T residue 283 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 606 optimal weight: 4.9990 chunk 413 optimal weight: 0.0770 chunk 10 optimal weight: 0.6980 chunk 542 optimal weight: 4.9990 chunk 300 optimal weight: 3.9990 chunk 621 optimal weight: 3.9990 chunk 503 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 372 optimal weight: 4.9990 chunk 654 optimal weight: 0.8980 chunk 183 optimal weight: 0.9980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 GLN C 102 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 GLN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN I 356 GLN J 292 GLN ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 356 GLN M 102 GLN ** O 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 292 GLN ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 102 GLN S 356 GLN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 292 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 63078 Z= 0.255 Angle : 0.528 8.613 85612 Z= 0.278 Chirality : 0.041 0.168 9820 Planarity : 0.004 0.041 10520 Dihedral : 11.079 74.017 10454 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.85 % Allowed : 13.69 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.09), residues: 7540 helix: 1.40 (0.07), residues: 4720 sheet: 0.68 (0.26), residues: 260 loop : 0.17 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 260 HIS 0.006 0.001 HIS N 225 PHE 0.010 0.002 PHE G 223 TYR 0.012 0.001 TYR F 337 ARG 0.009 0.001 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 747 time to evaluate : 5.249 Fit side-chains REVERT: A 67 MET cc_start: 0.8715 (mmm) cc_final: 0.8384 (mmm) REVERT: A 193 GLU cc_start: 0.7647 (mp0) cc_final: 0.7308 (mp0) REVERT: A 364 ASN cc_start: 0.7822 (t0) cc_final: 0.7560 (t0) REVERT: B 71 MET cc_start: 0.9150 (mtm) cc_final: 0.8808 (mtp) REVERT: B 192 ASN cc_start: 0.8461 (m110) cc_final: 0.8212 (m-40) REVERT: B 271 MET cc_start: 0.8387 (mmm) cc_final: 0.7911 (mmm) REVERT: B 342 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6991 (mtt90) REVERT: B 366 SER cc_start: 0.8351 (m) cc_final: 0.8047 (p) REVERT: C 64 LEU cc_start: 0.9002 (tt) cc_final: 0.8702 (tm) REVERT: C 130 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7302 (mp0) REVERT: E 71 MET cc_start: 0.9231 (mtm) cc_final: 0.8882 (mtp) REVERT: E 96 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7285 (p0) REVERT: E 122 GLU cc_start: 0.7833 (mp0) cc_final: 0.7512 (mp0) REVERT: E 283 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7399 (mt0) REVERT: E 338 ARG cc_start: 0.7107 (ptt-90) cc_final: 0.6834 (ptt-90) REVERT: F 67 MET cc_start: 0.8711 (mmm) cc_final: 0.8381 (mmm) REVERT: F 193 GLU cc_start: 0.7648 (mp0) cc_final: 0.7312 (mp0) REVERT: F 364 ASN cc_start: 0.7819 (t0) cc_final: 0.7559 (t0) REVERT: G 71 MET cc_start: 0.9152 (mtm) cc_final: 0.8808 (mtp) REVERT: G 192 ASN cc_start: 0.8456 (m110) cc_final: 0.8208 (m-40) REVERT: G 271 MET cc_start: 0.8385 (mmm) cc_final: 0.7909 (mmm) REVERT: G 342 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.6993 (mtt90) REVERT: G 366 SER cc_start: 0.8349 (m) cc_final: 0.8043 (p) REVERT: H 64 LEU cc_start: 0.9004 (tt) cc_final: 0.8702 (tm) REVERT: H 130 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7306 (mp0) REVERT: I 89 HIS cc_start: 0.6841 (m-70) cc_final: 0.6481 (m170) REVERT: J 71 MET cc_start: 0.9232 (mtm) cc_final: 0.8885 (mtp) REVERT: J 96 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7286 (p0) REVERT: J 122 GLU cc_start: 0.7834 (mp0) cc_final: 0.7517 (mp0) REVERT: J 283 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7403 (mt0) REVERT: J 338 ARG cc_start: 0.7106 (ptt-90) cc_final: 0.6834 (ptt-90) REVERT: K 67 MET cc_start: 0.8718 (mmm) cc_final: 0.8380 (mmm) REVERT: K 193 GLU cc_start: 0.7643 (mp0) cc_final: 0.7305 (mp0) REVERT: K 364 ASN cc_start: 0.7820 (t0) cc_final: 0.7562 (t0) REVERT: L 71 MET cc_start: 0.9155 (mtm) cc_final: 0.8818 (mtp) REVERT: L 192 ASN cc_start: 0.8461 (m110) cc_final: 0.8213 (m-40) REVERT: L 271 MET cc_start: 0.8388 (mmm) cc_final: 0.7912 (mmm) REVERT: L 366 SER cc_start: 0.8352 (m) cc_final: 0.8044 (p) REVERT: M 64 LEU cc_start: 0.9004 (tt) cc_final: 0.8699 (tm) REVERT: M 130 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7305 (mp0) REVERT: O 71 MET cc_start: 0.9233 (mtm) cc_final: 0.8889 (mtp) REVERT: O 96 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7287 (p0) REVERT: O 122 GLU cc_start: 0.7830 (mp0) cc_final: 0.7511 (mp0) REVERT: O 283 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: O 338 ARG cc_start: 0.7099 (ptt-90) cc_final: 0.6828 (ptt-90) REVERT: P 67 MET cc_start: 0.8707 (mmm) cc_final: 0.8376 (mmm) REVERT: P 193 GLU cc_start: 0.7654 (mp0) cc_final: 0.7315 (mp0) REVERT: P 364 ASN cc_start: 0.7817 (t0) cc_final: 0.7556 (t0) REVERT: Q 71 MET cc_start: 0.9155 (mtm) cc_final: 0.8818 (mtp) REVERT: Q 192 ASN cc_start: 0.8454 (m110) cc_final: 0.8207 (m-40) REVERT: Q 271 MET cc_start: 0.8385 (mmm) cc_final: 0.7908 (mmm) REVERT: Q 366 SER cc_start: 0.8351 (m) cc_final: 0.8045 (p) REVERT: R 64 LEU cc_start: 0.9006 (tt) cc_final: 0.8705 (tm) REVERT: R 130 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7306 (mp0) REVERT: S 89 HIS cc_start: 0.6835 (m-70) cc_final: 0.6478 (m170) REVERT: T 71 MET cc_start: 0.9234 (mtm) cc_final: 0.8886 (mtp) REVERT: T 96 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7285 (p0) REVERT: T 122 GLU cc_start: 0.7837 (mp0) cc_final: 0.7517 (mp0) REVERT: T 283 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7397 (mt0) REVERT: T 338 ARG cc_start: 0.7106 (ptt-90) cc_final: 0.6831 (ptt-90) outliers start: 180 outliers final: 120 residues processed: 823 average time/residue: 1.7753 time to fit residues: 1787.5327 Evaluate side-chains 857 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 727 time to evaluate : 5.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 GLU Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 55 GLU Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 76 ARG Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 55 GLU Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 248 MET Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 239 VAL Chi-restraints excluded: chain T residue 248 MET Chi-restraints excluded: chain T residue 283 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 245 optimal weight: 1.9990 chunk 656 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 427 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 729 optimal weight: 0.9980 chunk 605 optimal weight: 1.9990 chunk 337 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 382 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 89 HIS ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** E 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 GLN G 89 HIS I 356 GLN L 26 GLN L 89 HIS ** M 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN ** O 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 GLN Q 89 HIS ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 63078 Z= 0.211 Angle : 0.506 8.794 85612 Z= 0.267 Chirality : 0.040 0.146 9820 Planarity : 0.004 0.054 10520 Dihedral : 11.044 73.910 10454 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.48 % Allowed : 14.94 % Favored : 82.58 % 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: 1.47 (0.09), residues: 7540 helix: 1.51 (0.07), residues: 4700 sheet: 1.30 (0.27), residues: 220 loop : 0.09 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 260 HIS 0.005 0.001 HIS Q 225 PHE 0.010 0.002 PHE G 223 TYR 0.010 0.001 TYR T 353 ARG 0.014 0.001 ARG E 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 740 time to evaluate : 5.092 Fit side-chains REVERT: A 67 MET cc_start: 0.8666 (mmm) cc_final: 0.8398 (mmm) REVERT: A 77 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7292 (mm-30) REVERT: A 193 GLU cc_start: 0.7687 (mp0) cc_final: 0.7326 (mp0) REVERT: A 364 ASN cc_start: 0.7803 (t0) cc_final: 0.7517 (t0) REVERT: B 71 MET cc_start: 0.9140 (mtm) cc_final: 0.8813 (mtp) REVERT: B 192 ASN cc_start: 0.8386 (m110) cc_final: 0.8146 (m-40) REVERT: B 271 MET cc_start: 0.8369 (mmm) cc_final: 0.7893 (mmm) REVERT: B 342 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7047 (mtt90) REVERT: B 366 SER cc_start: 0.8318 (m) cc_final: 0.8005 (p) REVERT: C 64 LEU cc_start: 0.9002 (tt) cc_final: 0.8698 (tm) REVERT: C 130 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7282 (mp0) REVERT: C 342 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7510 (ptp-110) REVERT: D 342 ARG cc_start: 0.7630 (ptp-170) cc_final: 0.7226 (mtt180) REVERT: E 71 MET cc_start: 0.9226 (mtm) cc_final: 0.8875 (mtp) REVERT: E 96 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7267 (p0) REVERT: E 122 GLU cc_start: 0.7845 (mp0) cc_final: 0.7522 (mp0) REVERT: E 283 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: E 338 ARG cc_start: 0.7071 (ptt-90) cc_final: 0.6784 (ptt-90) REVERT: F 67 MET cc_start: 0.8661 (mmm) cc_final: 0.8398 (mmm) REVERT: F 77 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7296 (mm-30) REVERT: F 193 GLU cc_start: 0.7686 (mp0) cc_final: 0.7327 (mp0) REVERT: F 364 ASN cc_start: 0.7800 (t0) cc_final: 0.7515 (t0) REVERT: G 71 MET cc_start: 0.9145 (mtm) cc_final: 0.8811 (mtp) REVERT: G 192 ASN cc_start: 0.8384 (m110) cc_final: 0.8141 (m-40) REVERT: G 271 MET cc_start: 0.8366 (mmm) cc_final: 0.7892 (mmm) REVERT: G 342 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.7051 (mtt90) REVERT: G 366 SER cc_start: 0.8313 (m) cc_final: 0.8000 (p) REVERT: H 64 LEU cc_start: 0.9006 (tt) cc_final: 0.8699 (tm) REVERT: H 130 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7287 (mp0) REVERT: H 342 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7509 (ptp-110) REVERT: I 342 ARG cc_start: 0.7632 (ptp-170) cc_final: 0.7229 (mtt180) REVERT: J 71 MET cc_start: 0.9226 (mtm) cc_final: 0.8880 (mtp) REVERT: J 96 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7268 (p0) REVERT: J 122 GLU cc_start: 0.7845 (mp0) cc_final: 0.7528 (mp0) REVERT: J 283 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: J 338 ARG cc_start: 0.7069 (ptt-90) cc_final: 0.6783 (ptt-90) REVERT: K 67 MET cc_start: 0.8668 (mmm) cc_final: 0.8394 (mmm) REVERT: K 77 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7294 (mm-30) REVERT: K 193 GLU cc_start: 0.7678 (mp0) cc_final: 0.7321 (mp0) REVERT: K 364 ASN cc_start: 0.7800 (t0) cc_final: 0.7519 (t0) REVERT: L 71 MET cc_start: 0.9149 (mtm) cc_final: 0.8821 (mtp) REVERT: L 192 ASN cc_start: 0.8389 (m110) cc_final: 0.8147 (m-40) REVERT: L 271 MET cc_start: 0.8369 (mmm) cc_final: 0.7893 (mmm) REVERT: L 342 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7134 (mtt90) REVERT: L 366 SER cc_start: 0.8319 (m) cc_final: 0.8003 (p) REVERT: M 64 LEU cc_start: 0.9005 (tt) cc_final: 0.8696 (tm) REVERT: M 130 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7284 (mp0) REVERT: M 342 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7513 (ptp-110) REVERT: N 342 ARG cc_start: 0.7629 (ptp-170) cc_final: 0.7225 (mtt180) REVERT: O 71 MET cc_start: 0.9223 (mtm) cc_final: 0.8879 (mtp) REVERT: O 96 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7264 (p0) REVERT: O 122 GLU cc_start: 0.7844 (mp0) cc_final: 0.7524 (mp0) REVERT: O 283 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7376 (mt0) REVERT: O 338 ARG cc_start: 0.7064 (ptt-90) cc_final: 0.6780 (ptt-90) REVERT: P 67 MET cc_start: 0.8656 (mmm) cc_final: 0.8390 (mmm) REVERT: P 77 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7294 (mm-30) REVERT: P 193 GLU cc_start: 0.7696 (mp0) cc_final: 0.7335 (mp0) REVERT: P 364 ASN cc_start: 0.7799 (t0) cc_final: 0.7516 (t0) REVERT: Q 71 MET cc_start: 0.9148 (mtm) cc_final: 0.8822 (mtp) REVERT: Q 192 ASN cc_start: 0.8382 (m110) cc_final: 0.8142 (m-40) REVERT: Q 271 MET cc_start: 0.8367 (mmm) cc_final: 0.7892 (mmm) REVERT: Q 342 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7138 (mtt90) REVERT: Q 366 SER cc_start: 0.8321 (m) cc_final: 0.8006 (p) REVERT: R 64 LEU cc_start: 0.9008 (tt) cc_final: 0.8702 (tm) REVERT: R 130 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7286 (mp0) REVERT: R 342 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7513 (ptp-110) REVERT: S 342 ARG cc_start: 0.7632 (ptp-170) cc_final: 0.7227 (mtt180) REVERT: T 71 MET cc_start: 0.9227 (mtm) cc_final: 0.8879 (mtp) REVERT: T 96 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7268 (p0) REVERT: T 122 GLU cc_start: 0.7849 (mp0) cc_final: 0.7530 (mp0) REVERT: T 283 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7373 (mt0) REVERT: T 338 ARG cc_start: 0.7071 (ptt-90) cc_final: 0.6780 (ptt-90) outliers start: 157 outliers final: 100 residues processed: 804 average time/residue: 1.7958 time to fit residues: 1763.8836 Evaluate side-chains 836 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 720 time to evaluate : 5.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 248 MET Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 248 MET Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 248 MET Chi-restraints excluded: chain H residue 342 ARG Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 248 MET Chi-restraints excluded: chain J residue 283 GLN Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 96 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 201 LEU Chi-restraints excluded: chain M residue 248 MET Chi-restraints excluded: chain M residue 342 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 248 MET Chi-restraints excluded: chain O residue 283 GLN Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 96 ASP Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 201 LEU Chi-restraints excluded: chain R residue 248 MET Chi-restraints excluded: chain R residue 342 ARG Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 248 MET Chi-restraints excluded: chain T residue 283 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 703 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 415 optimal weight: 4.9990 chunk 532 optimal weight: 4.9990 chunk 412 optimal weight: 2.9990 chunk 614 optimal weight: 3.9990 chunk 407 optimal weight: 0.9980 chunk 726 optimal weight: 2.9990 chunk 454 optimal weight: 0.3980 chunk 443 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** I 356 GLN ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 192 ASN N 356 GLN ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** S 356 GLN ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 63078 Z= 0.420 Angle : 0.626 9.285 85612 Z= 0.328 Chirality : 0.047 0.243 9820 Planarity : 0.005 0.047 10520 Dihedral : 11.226 74.216 10454 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.74 % Allowed : 15.49 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.09), residues: 7540 helix: 1.00 (0.07), residues: 4720 sheet: 1.56 (0.29), residues: 220 loop : -0.05 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP I 260 HIS 0.010 0.002 HIS Q 225 PHE 0.014 0.003 PHE L 243 TYR 0.015 0.002 TYR A 337 ARG 0.008 0.001 ARG L 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 722 time to evaluate : 5.141 Fit side-chains REVERT: A 193 GLU cc_start: 0.7760 (mp0) cc_final: 0.7404 (mp0) REVERT: A 366 SER cc_start: 0.8536 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 71 MET cc_start: 0.9154 (mtm) cc_final: 0.8793 (mtp) REVERT: B 271 MET cc_start: 0.8383 (mmm) cc_final: 0.7962 (mmm) REVERT: B 342 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7132 (mtt90) REVERT: B 366 SER cc_start: 0.8391 (m) cc_final: 0.8097 (p) REVERT: C 64 LEU cc_start: 0.9000 (tt) cc_final: 0.8734 (tm) REVERT: C 130 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7308 (mp0) REVERT: C 342 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7604 (ptp-110) REVERT: D 342 ARG cc_start: 0.7701 (ptp-170) cc_final: 0.7253 (mtt180) REVERT: E 71 MET cc_start: 0.9229 (mtm) cc_final: 0.8871 (mtp) REVERT: E 96 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7305 (p0) REVERT: E 122 GLU cc_start: 0.7856 (mp0) cc_final: 0.7522 (mp0) REVERT: E 338 ARG cc_start: 0.7238 (ptt-90) cc_final: 0.7000 (ptt-90) REVERT: F 193 GLU cc_start: 0.7763 (mp0) cc_final: 0.7409 (mp0) REVERT: F 366 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8302 (p) REVERT: G 71 MET cc_start: 0.9156 (mtm) cc_final: 0.8792 (mtp) REVERT: G 271 MET cc_start: 0.8381 (mmm) cc_final: 0.7958 (mmm) REVERT: G 336 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: G 342 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7134 (mtt90) REVERT: G 366 SER cc_start: 0.8386 (m) cc_final: 0.8091 (p) REVERT: H 64 LEU cc_start: 0.9005 (tt) cc_final: 0.8735 (tm) REVERT: H 130 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7316 (mp0) REVERT: H 342 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7602 (ptp-110) REVERT: I 89 HIS cc_start: 0.7849 (m-70) cc_final: 0.7581 (m170) REVERT: I 342 ARG cc_start: 0.7702 (ptp-170) cc_final: 0.7258 (mtt180) REVERT: J 71 MET cc_start: 0.9232 (mtm) cc_final: 0.8870 (mtp) REVERT: J 96 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7304 (p0) REVERT: J 122 GLU cc_start: 0.7861 (mp0) cc_final: 0.7531 (mp0) REVERT: J 338 ARG cc_start: 0.7238 (ptt-90) cc_final: 0.7004 (ptt-90) REVERT: K 193 GLU cc_start: 0.7760 (mp0) cc_final: 0.7407 (mp0) REVERT: K 366 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8303 (p) REVERT: L 71 MET cc_start: 0.9160 (mtm) cc_final: 0.8802 (mtp) REVERT: L 271 MET cc_start: 0.8381 (mmm) cc_final: 0.7962 (mmm) REVERT: L 342 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7238 (mtt90) REVERT: L 366 SER cc_start: 0.8392 (m) cc_final: 0.8094 (p) REVERT: M 64 LEU cc_start: 0.9042 (tt) cc_final: 0.8781 (tm) REVERT: M 130 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7316 (mp0) REVERT: M 342 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7604 (ptp-110) REVERT: N 342 ARG cc_start: 0.7696 (ptp-170) cc_final: 0.7253 (mtt180) REVERT: O 71 MET cc_start: 0.9228 (mtm) cc_final: 0.8871 (mtp) REVERT: O 96 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7308 (p0) REVERT: O 122 GLU cc_start: 0.7855 (mp0) cc_final: 0.7523 (mp0) REVERT: O 338 ARG cc_start: 0.7229 (ptt-90) cc_final: 0.6994 (ptt-90) REVERT: P 193 GLU cc_start: 0.7762 (mp0) cc_final: 0.7409 (mp0) REVERT: P 366 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8299 (p) REVERT: Q 71 MET cc_start: 0.9157 (mtm) cc_final: 0.8800 (mtp) REVERT: Q 271 MET cc_start: 0.8380 (mmm) cc_final: 0.7957 (mmm) REVERT: Q 336 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: Q 342 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7237 (mtt90) REVERT: Q 366 SER cc_start: 0.8392 (m) cc_final: 0.8095 (p) REVERT: R 64 LEU cc_start: 0.9004 (tt) cc_final: 0.8736 (tm) REVERT: R 130 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7315 (mp0) REVERT: R 342 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7605 (ptp-110) REVERT: S 89 HIS cc_start: 0.7847 (m-70) cc_final: 0.7583 (m170) REVERT: S 342 ARG cc_start: 0.7698 (ptp-170) cc_final: 0.7252 (mtt180) REVERT: T 71 MET cc_start: 0.9231 (mtm) cc_final: 0.8867 (mtp) REVERT: T 96 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7303 (p0) REVERT: T 122 GLU cc_start: 0.7862 (mp0) cc_final: 0.7529 (mp0) REVERT: T 338 ARG cc_start: 0.7237 (ptt-90) cc_final: 0.7002 (ptt-90) outliers start: 173 outliers final: 88 residues processed: 803 average time/residue: 1.7893 time to fit residues: 1759.5301 Evaluate side-chains 822 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 716 time to evaluate : 5.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 9 ASN Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 9 ASN Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 342 ARG Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain L residue 9 ASN Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 342 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain O residue 158 MET Chi-restraints excluded: chain O residue 239 VAL Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 76 ARG Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain Q residue 9 ASN Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 336 GLU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 342 ARG Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 97 VAL Chi-restraints excluded: chain T residue 158 MET Chi-restraints excluded: chain T residue 239 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 449 optimal weight: 0.9990 chunk 290 optimal weight: 0.5980 chunk 434 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 462 optimal weight: 1.9990 chunk 495 optimal weight: 3.9990 chunk 359 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 571 optimal weight: 0.4980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN B 89 HIS ** C 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 GLN G 26 GLN G 89 HIS I 356 GLN K 356 GLN L 26 GLN L 89 HIS ** M 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 356 GLN Q 26 GLN Q 89 HIS S 356 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 63078 Z= 0.200 Angle : 0.520 9.908 85612 Z= 0.274 Chirality : 0.040 0.147 9820 Planarity : 0.004 0.073 10520 Dihedral : 11.084 73.839 10454 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.01 % Allowed : 16.36 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.09), residues: 7540 helix: 1.38 (0.07), residues: 4700 sheet: 1.32 (0.28), residues: 220 loop : -0.04 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 260 HIS 0.004 0.001 HIS L 225 PHE 0.009 0.002 PHE H 226 TYR 0.010 0.001 TYR O 337 ARG 0.015 0.001 ARG E 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 744 time to evaluate : 5.136 Fit side-chains REVERT: A 67 MET cc_start: 0.8699 (mmm) cc_final: 0.8363 (mmm) REVERT: A 77 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7296 (mm-30) REVERT: A 193 GLU cc_start: 0.7682 (mp0) cc_final: 0.7398 (mp0) REVERT: A 364 ASN cc_start: 0.7822 (t0) cc_final: 0.7522 (t0) REVERT: B 130 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 271 MET cc_start: 0.8366 (mmm) cc_final: 0.7868 (mmm) REVERT: B 342 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7089 (mtt90) REVERT: B 366 SER cc_start: 0.8318 (m) cc_final: 0.7995 (p) REVERT: C 64 LEU cc_start: 0.8993 (tt) cc_final: 0.8678 (tm) REVERT: C 130 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7284 (mp0) REVERT: C 342 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7520 (ptp-110) REVERT: D 194 MET cc_start: 0.8470 (mtm) cc_final: 0.7773 (mtm) REVERT: D 342 ARG cc_start: 0.7686 (ptp-170) cc_final: 0.7330 (mtt180) REVERT: E 71 MET cc_start: 0.9246 (mtm) cc_final: 0.8919 (mtp) REVERT: E 96 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7171 (p0) REVERT: E 122 GLU cc_start: 0.7842 (mp0) cc_final: 0.7509 (mp0) REVERT: E 338 ARG cc_start: 0.7084 (ptt-90) cc_final: 0.6830 (ptt-90) REVERT: E 342 ARG cc_start: 0.7489 (ptp-110) cc_final: 0.7247 (ptp-170) REVERT: F 67 MET cc_start: 0.8696 (mmm) cc_final: 0.8364 (mmm) REVERT: F 77 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7296 (mm-30) REVERT: F 193 GLU cc_start: 0.7681 (mp0) cc_final: 0.7398 (mp0) REVERT: F 364 ASN cc_start: 0.7823 (t0) cc_final: 0.7524 (t0) REVERT: G 271 MET cc_start: 0.8368 (mmm) cc_final: 0.7867 (mmm) REVERT: G 342 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7094 (mtt90) REVERT: G 366 SER cc_start: 0.8310 (m) cc_final: 0.7991 (p) REVERT: H 64 LEU cc_start: 0.8995 (tt) cc_final: 0.8677 (tm) REVERT: H 130 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7286 (mp0) REVERT: H 342 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7517 (ptp-110) REVERT: I 89 HIS cc_start: 0.7770 (m-70) cc_final: 0.7525 (m170) REVERT: I 194 MET cc_start: 0.8473 (mtm) cc_final: 0.7776 (mtm) REVERT: I 342 ARG cc_start: 0.7689 (ptp-170) cc_final: 0.7335 (mtt180) REVERT: J 71 MET cc_start: 0.9248 (mtm) cc_final: 0.8922 (mtp) REVERT: J 96 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7169 (p0) REVERT: J 122 GLU cc_start: 0.7841 (mp0) cc_final: 0.7516 (mp0) REVERT: J 338 ARG cc_start: 0.7079 (ptt-90) cc_final: 0.6830 (ptt-90) REVERT: J 342 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.7247 (ptp-170) REVERT: K 67 MET cc_start: 0.8699 (mmm) cc_final: 0.8362 (mmm) REVERT: K 77 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7300 (mm-30) REVERT: K 193 GLU cc_start: 0.7675 (mp0) cc_final: 0.7395 (mp0) REVERT: K 364 ASN cc_start: 0.7822 (t0) cc_final: 0.7525 (t0) REVERT: L 130 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7503 (mm-30) REVERT: L 192 ASN cc_start: 0.8312 (m110) cc_final: 0.8093 (m-40) REVERT: L 271 MET cc_start: 0.8368 (mmm) cc_final: 0.7867 (mmm) REVERT: L 342 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7137 (mtt90) REVERT: L 366 SER cc_start: 0.8318 (m) cc_final: 0.7992 (p) REVERT: M 64 LEU cc_start: 0.8995 (tt) cc_final: 0.8675 (tm) REVERT: M 130 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7286 (mp0) REVERT: M 342 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7523 (ptp-110) REVERT: N 194 MET cc_start: 0.8473 (mtm) cc_final: 0.7777 (mtm) REVERT: N 342 ARG cc_start: 0.7682 (ptp-170) cc_final: 0.7329 (mtt180) REVERT: O 71 MET cc_start: 0.9244 (mtm) cc_final: 0.8924 (mtp) REVERT: O 96 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7166 (p0) REVERT: O 122 GLU cc_start: 0.7838 (mp0) cc_final: 0.7508 (mp0) REVERT: O 338 ARG cc_start: 0.7080 (ptt-90) cc_final: 0.6830 (ptt-90) REVERT: O 342 ARG cc_start: 0.7487 (ptp-110) cc_final: 0.7243 (ptp-170) REVERT: P 67 MET cc_start: 0.8690 (mmm) cc_final: 0.8357 (mmm) REVERT: P 77 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7299 (mm-30) REVERT: P 193 GLU cc_start: 0.7689 (mp0) cc_final: 0.7405 (mp0) REVERT: P 364 ASN cc_start: 0.7820 (t0) cc_final: 0.7520 (t0) REVERT: Q 271 MET cc_start: 0.8361 (mmm) cc_final: 0.7864 (mmm) REVERT: Q 342 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7141 (mtt90) REVERT: Q 366 SER cc_start: 0.8315 (m) cc_final: 0.7995 (p) REVERT: R 64 LEU cc_start: 0.8997 (tt) cc_final: 0.8681 (tm) REVERT: R 130 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7288 (mp0) REVERT: R 342 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7525 (ptp-110) REVERT: S 89 HIS cc_start: 0.7766 (m-70) cc_final: 0.7528 (m170) REVERT: S 194 MET cc_start: 0.8472 (mtm) cc_final: 0.7773 (mtm) REVERT: S 342 ARG cc_start: 0.7685 (ptp-170) cc_final: 0.7329 (mtt180) REVERT: T 71 MET cc_start: 0.9249 (mtm) cc_final: 0.8921 (mtp) REVERT: T 96 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7160 (p0) REVERT: T 122 GLU cc_start: 0.7845 (mp0) cc_final: 0.7516 (mp0) REVERT: T 338 ARG cc_start: 0.7080 (ptt-90) cc_final: 0.6829 (ptt-90) REVERT: T 342 ARG cc_start: 0.7488 (ptp-110) cc_final: 0.7247 (ptp-170) outliers start: 127 outliers final: 91 residues processed: 795 average time/residue: 1.8112 time to fit residues: 1758.5947 Evaluate side-chains 831 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 728 time to evaluate : 5.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 342 ARG Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 342 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 76 ARG Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 342 ARG Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 661 optimal weight: 0.8980 chunk 696 optimal weight: 0.9990 chunk 635 optimal weight: 0.0870 chunk 677 optimal weight: 2.9990 chunk 407 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 chunk 531 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 611 optimal weight: 0.9990 chunk 640 optimal weight: 0.3980 chunk 674 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN C 89 HIS ** C 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 HIS ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 ASN M 89 HIS ** M 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** R 151 HIS ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 63078 Z= 0.177 Angle : 0.507 11.107 85612 Z= 0.264 Chirality : 0.039 0.146 9820 Planarity : 0.004 0.059 10520 Dihedral : 11.041 73.835 10454 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.85 % Allowed : 16.58 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 7540 helix: 1.58 (0.07), residues: 4700 sheet: 1.32 (0.28), residues: 220 loop : -0.01 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 260 HIS 0.004 0.001 HIS Q 225 PHE 0.010 0.002 PHE G 223 TYR 0.011 0.001 TYR M 88 ARG 0.014 0.001 ARG T 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 760 time to evaluate : 5.168 Fit side-chains REVERT: A 67 MET cc_start: 0.8739 (mmm) cc_final: 0.8535 (mmm) REVERT: A 77 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7258 (mm-30) REVERT: A 193 GLU cc_start: 0.7648 (mp0) cc_final: 0.7362 (mp0) REVERT: A 364 ASN cc_start: 0.7813 (t0) cc_final: 0.7520 (t0) REVERT: B 89 HIS cc_start: 0.6840 (m-70) cc_final: 0.6399 (m170) REVERT: B 192 ASN cc_start: 0.8294 (m110) cc_final: 0.8087 (m-40) REVERT: B 271 MET cc_start: 0.8361 (mmm) cc_final: 0.7868 (mmm) REVERT: B 292 GLN cc_start: 0.8124 (pt0) cc_final: 0.7860 (mt0) REVERT: B 342 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7112 (mtt90) REVERT: B 366 SER cc_start: 0.8311 (m) cc_final: 0.7986 (p) REVERT: C 64 LEU cc_start: 0.8981 (tt) cc_final: 0.8648 (tm) REVERT: C 130 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7296 (mp0) REVERT: C 342 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7528 (ptp-110) REVERT: D 342 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7243 (mtt180) REVERT: E 71 MET cc_start: 0.9237 (mtm) cc_final: 0.8911 (mtp) REVERT: E 96 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7183 (p0) REVERT: E 122 GLU cc_start: 0.7842 (mp0) cc_final: 0.7532 (mp0) REVERT: E 342 ARG cc_start: 0.7442 (ptp-110) cc_final: 0.7112 (ptp-170) REVERT: F 67 MET cc_start: 0.8745 (mmm) cc_final: 0.8538 (mmm) REVERT: F 77 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7257 (mm-30) REVERT: F 193 GLU cc_start: 0.7653 (mp0) cc_final: 0.7365 (mp0) REVERT: F 364 ASN cc_start: 0.7810 (t0) cc_final: 0.7519 (t0) REVERT: G 89 HIS cc_start: 0.6847 (m-70) cc_final: 0.6397 (m170) REVERT: G 192 ASN cc_start: 0.8290 (m110) cc_final: 0.8080 (m-40) REVERT: G 271 MET cc_start: 0.8357 (mmm) cc_final: 0.7865 (mmm) REVERT: G 292 GLN cc_start: 0.8136 (pt0) cc_final: 0.7866 (mt0) REVERT: G 342 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7120 (mtt90) REVERT: G 366 SER cc_start: 0.8304 (m) cc_final: 0.7978 (p) REVERT: H 64 LEU cc_start: 0.8982 (tt) cc_final: 0.8647 (tm) REVERT: H 89 HIS cc_start: 0.7381 (m-70) cc_final: 0.7143 (m-70) REVERT: H 130 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7299 (mp0) REVERT: H 342 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7526 (ptp-110) REVERT: I 89 HIS cc_start: 0.7737 (m-70) cc_final: 0.7505 (m170) REVERT: I 342 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7243 (mtt180) REVERT: J 71 MET cc_start: 0.9239 (mtm) cc_final: 0.8915 (mtp) REVERT: J 96 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7179 (p0) REVERT: J 122 GLU cc_start: 0.7846 (mp0) cc_final: 0.7541 (mp0) REVERT: J 342 ARG cc_start: 0.7443 (ptp-110) cc_final: 0.7114 (ptp-170) REVERT: K 67 MET cc_start: 0.8744 (mmm) cc_final: 0.8534 (mmm) REVERT: K 77 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7258 (mm-30) REVERT: K 193 GLU cc_start: 0.7646 (mp0) cc_final: 0.7361 (mp0) REVERT: K 364 ASN cc_start: 0.7812 (t0) cc_final: 0.7523 (t0) REVERT: L 89 HIS cc_start: 0.6839 (m-70) cc_final: 0.6393 (m170) REVERT: L 192 ASN cc_start: 0.8300 (m110) cc_final: 0.8095 (m-40) REVERT: L 271 MET cc_start: 0.8360 (mmm) cc_final: 0.7868 (mmm) REVERT: L 292 GLN cc_start: 0.8122 (pt0) cc_final: 0.7857 (mt0) REVERT: L 342 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7167 (mtt90) REVERT: L 366 SER cc_start: 0.8313 (m) cc_final: 0.7985 (p) REVERT: M 64 LEU cc_start: 0.8984 (tt) cc_final: 0.8648 (tm) REVERT: M 130 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7299 (mp0) REVERT: M 342 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7529 (ptp-110) REVERT: N 342 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7242 (mtt180) REVERT: O 71 MET cc_start: 0.9234 (mtm) cc_final: 0.8916 (mtp) REVERT: O 96 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7180 (p0) REVERT: O 122 GLU cc_start: 0.7843 (mp0) cc_final: 0.7534 (mp0) REVERT: O 342 ARG cc_start: 0.7440 (ptp-110) cc_final: 0.7110 (ptp-170) REVERT: P 67 MET cc_start: 0.8736 (mmm) cc_final: 0.8531 (mmm) REVERT: P 77 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7257 (mm-30) REVERT: P 193 GLU cc_start: 0.7660 (mp0) cc_final: 0.7370 (mp0) REVERT: P 364 ASN cc_start: 0.7808 (t0) cc_final: 0.7516 (t0) REVERT: Q 89 HIS cc_start: 0.6838 (m-70) cc_final: 0.6391 (m170) REVERT: Q 192 ASN cc_start: 0.8291 (m110) cc_final: 0.8083 (m-40) REVERT: Q 271 MET cc_start: 0.8358 (mmm) cc_final: 0.7865 (mmm) REVERT: Q 292 GLN cc_start: 0.8140 (pt0) cc_final: 0.7870 (mt0) REVERT: Q 342 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7172 (mtt90) REVERT: Q 366 SER cc_start: 0.8311 (m) cc_final: 0.7984 (p) REVERT: R 64 LEU cc_start: 0.8985 (tt) cc_final: 0.8651 (tm) REVERT: R 130 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7301 (mp0) REVERT: R 342 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7531 (ptp-110) REVERT: S 89 HIS cc_start: 0.7719 (m-70) cc_final: 0.7492 (m170) REVERT: S 342 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7244 (mtt180) REVERT: T 71 MET cc_start: 0.9240 (mtm) cc_final: 0.8915 (mtp) REVERT: T 96 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7140 (p0) REVERT: T 122 GLU cc_start: 0.7848 (mp0) cc_final: 0.7537 (mp0) REVERT: T 342 ARG cc_start: 0.7443 (ptp-110) cc_final: 0.7116 (ptp-170) outliers start: 117 outliers final: 89 residues processed: 811 average time/residue: 1.8382 time to fit residues: 1822.7317 Evaluate side-chains 852 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 747 time to evaluate : 5.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 342 ARG Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 369 ASP Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 342 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 342 ARG Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 369 ASP Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 342 ARG Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 342 ARG Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 444 optimal weight: 0.0980 chunk 716 optimal weight: 0.9990 chunk 437 optimal weight: 0.9980 chunk 339 optimal weight: 0.0470 chunk 497 optimal weight: 0.9980 chunk 751 optimal weight: 0.7980 chunk 691 optimal weight: 2.9990 chunk 598 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 462 optimal weight: 2.9990 chunk 366 optimal weight: 0.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 ASN ** F 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 26 GLN H 45 ASN H 89 HIS ** H 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** I 364 ASN ** K 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 364 ASN ** P 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 ASN ** R 100 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** S 151 HIS S 364 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 63078 Z= 0.173 Angle : 0.514 11.111 85612 Z= 0.268 Chirality : 0.039 0.147 9820 Planarity : 0.004 0.057 10520 Dihedral : 11.025 73.807 10454 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.77 % Allowed : 17.26 % Favored : 80.97 % 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: 1.58 (0.09), residues: 7540 helix: 1.65 (0.07), residues: 4700 sheet: 1.34 (0.28), residues: 220 loop : 0.02 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 260 HIS 0.007 0.001 HIS A 89 PHE 0.009 0.002 PHE B 223 TYR 0.013 0.001 TYR E 337 ARG 0.014 0.001 ARG J 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15080 Ramachandran restraints generated. 7540 Oldfield, 0 Emsley, 7540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 754 time to evaluate : 5.177 Fit side-chains REVERT: A 67 MET cc_start: 0.8768 (mmm) cc_final: 0.8481 (mmm) REVERT: A 77 GLU cc_start: 0.7523 (mm-30) cc_final: 0.7320 (mm-30) REVERT: A 193 GLU cc_start: 0.7643 (mp0) cc_final: 0.7358 (mp0) REVERT: A 364 ASN cc_start: 0.7800 (t0) cc_final: 0.7524 (t0) REVERT: B 89 HIS cc_start: 0.6827 (m-70) cc_final: 0.6383 (m170) REVERT: B 271 MET cc_start: 0.8359 (mmm) cc_final: 0.7868 (mmm) REVERT: B 292 GLN cc_start: 0.8119 (pt0) cc_final: 0.7854 (mt0) REVERT: B 342 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7094 (mtt90) REVERT: B 366 SER cc_start: 0.8307 (m) cc_final: 0.7980 (p) REVERT: C 64 LEU cc_start: 0.8974 (tt) cc_final: 0.8654 (tm) REVERT: C 126 ASN cc_start: 0.8675 (m-40) cc_final: 0.8342 (m-40) REVERT: C 130 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7295 (mp0) REVERT: C 342 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7514 (ptp-110) REVERT: D 342 ARG cc_start: 0.7650 (OUTLIER) cc_final: 0.7242 (mtt180) REVERT: E 71 MET cc_start: 0.9235 (mtm) cc_final: 0.8903 (mtp) REVERT: E 96 ASP cc_start: 0.7767 (OUTLIER) cc_final: 0.7184 (p0) REVERT: E 122 GLU cc_start: 0.7864 (mp0) cc_final: 0.7559 (mp0) REVERT: E 342 ARG cc_start: 0.7412 (ptp-110) cc_final: 0.7078 (ptp-170) REVERT: F 67 MET cc_start: 0.8768 (mmm) cc_final: 0.8480 (mmm) REVERT: F 77 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7318 (mm-30) REVERT: F 193 GLU cc_start: 0.7646 (mp0) cc_final: 0.7359 (mp0) REVERT: F 364 ASN cc_start: 0.7797 (t0) cc_final: 0.7525 (t0) REVERT: G 89 HIS cc_start: 0.6834 (m-70) cc_final: 0.6350 (m170) REVERT: G 271 MET cc_start: 0.8356 (mmm) cc_final: 0.7868 (mmm) REVERT: G 292 GLN cc_start: 0.8131 (pt0) cc_final: 0.7860 (mt0) REVERT: G 342 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7101 (mtt90) REVERT: G 366 SER cc_start: 0.8298 (m) cc_final: 0.7970 (p) REVERT: H 64 LEU cc_start: 0.8978 (tt) cc_final: 0.8657 (tm) REVERT: H 126 ASN cc_start: 0.8678 (m-40) cc_final: 0.8342 (m-40) REVERT: H 130 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7299 (mp0) REVERT: H 342 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7509 (ptp-110) REVERT: I 89 HIS cc_start: 0.7685 (m-70) cc_final: 0.7481 (m170) REVERT: I 342 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7241 (mtt180) REVERT: J 71 MET cc_start: 0.9238 (mtm) cc_final: 0.8909 (mtp) REVERT: J 96 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7307 (p0) REVERT: J 122 GLU cc_start: 0.7864 (mp0) cc_final: 0.7568 (mp0) REVERT: J 342 ARG cc_start: 0.7411 (ptp-110) cc_final: 0.7079 (ptp-170) REVERT: K 67 MET cc_start: 0.8769 (mmm) cc_final: 0.8475 (mmm) REVERT: K 77 GLU cc_start: 0.7524 (mm-30) cc_final: 0.7321 (mm-30) REVERT: K 193 GLU cc_start: 0.7641 (mp0) cc_final: 0.7358 (mp0) REVERT: K 364 ASN cc_start: 0.7802 (t0) cc_final: 0.7529 (t0) REVERT: L 89 HIS cc_start: 0.6827 (m-70) cc_final: 0.6381 (m170) REVERT: L 271 MET cc_start: 0.8356 (mmm) cc_final: 0.7869 (mmm) REVERT: L 292 GLN cc_start: 0.8117 (pt0) cc_final: 0.7850 (mt0) REVERT: L 342 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7184 (mtt90) REVERT: L 366 SER cc_start: 0.8307 (m) cc_final: 0.7977 (p) REVERT: M 64 LEU cc_start: 0.8978 (tt) cc_final: 0.8652 (tm) REVERT: M 126 ASN cc_start: 0.8674 (m-40) cc_final: 0.8343 (m-40) REVERT: M 130 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7298 (mp0) REVERT: M 342 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7515 (ptp-110) REVERT: N 342 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7240 (mtt180) REVERT: O 71 MET cc_start: 0.9232 (mtm) cc_final: 0.8908 (mtp) REVERT: O 96 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7181 (p0) REVERT: O 122 GLU cc_start: 0.7863 (mp0) cc_final: 0.7564 (mp0) REVERT: O 342 ARG cc_start: 0.7412 (ptp-110) cc_final: 0.7079 (ptp-170) REVERT: P 67 MET cc_start: 0.8761 (mmm) cc_final: 0.8474 (mmm) REVERT: P 77 GLU cc_start: 0.7526 (mm-30) cc_final: 0.7318 (mm-30) REVERT: P 193 GLU cc_start: 0.7654 (mp0) cc_final: 0.7367 (mp0) REVERT: P 364 ASN cc_start: 0.7797 (t0) cc_final: 0.7521 (t0) REVERT: Q 89 HIS cc_start: 0.6829 (m-70) cc_final: 0.6353 (m170) REVERT: Q 271 MET cc_start: 0.8358 (mmm) cc_final: 0.7868 (mmm) REVERT: Q 292 GLN cc_start: 0.8134 (pt0) cc_final: 0.7863 (mt0) REVERT: Q 342 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7177 (mtt90) REVERT: Q 366 SER cc_start: 0.8306 (m) cc_final: 0.7973 (p) REVERT: R 64 LEU cc_start: 0.8981 (tt) cc_final: 0.8657 (tm) REVERT: R 126 ASN cc_start: 0.8673 (m-40) cc_final: 0.8344 (m-40) REVERT: R 130 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7302 (mp0) REVERT: R 342 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7518 (ptp-110) REVERT: S 342 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.7243 (mtt180) REVERT: T 71 MET cc_start: 0.9239 (mtm) cc_final: 0.8908 (mtp) REVERT: T 96 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7168 (p0) REVERT: T 122 GLU cc_start: 0.7869 (mp0) cc_final: 0.7496 (mp0) REVERT: T 342 ARG cc_start: 0.7413 (ptp-110) cc_final: 0.7081 (ptp-170) outliers start: 112 outliers final: 93 residues processed: 803 average time/residue: 1.8048 time to fit residues: 1774.6654 Evaluate side-chains 846 residues out of total 6280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 737 time to evaluate : 5.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 248 MET Chi-restraints excluded: chain A residue 342 ARG Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 76 ARG Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 342 ARG Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 109 MET Chi-restraints excluded: chain C residue 342 ARG Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 342 ARG Chi-restraints excluded: chain E residue 39 ASP Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 109 MET Chi-restraints excluded: chain F residue 248 MET Chi-restraints excluded: chain F residue 342 ARG Chi-restraints excluded: chain F residue 366 SER Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 155 ASP Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 76 ARG Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 342 ARG Chi-restraints excluded: chain I residue 39 ASP Chi-restraints excluded: chain I residue 97 VAL Chi-restraints excluded: chain I residue 201 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain J residue 39 ASP Chi-restraints excluded: chain J residue 96 ASP Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 39 ASP Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 109 MET Chi-restraints excluded: chain K residue 248 MET Chi-restraints excluded: chain K residue 342 ARG Chi-restraints excluded: chain K residue 366 SER Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 96 ASP Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 342 ARG Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain M residue 76 ARG Chi-restraints excluded: chain M residue 96 ASP Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain M residue 109 MET Chi-restraints excluded: chain M residue 342 ARG Chi-restraints excluded: chain N residue 39 ASP Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 201 LEU Chi-restraints excluded: chain N residue 342 ARG Chi-restraints excluded: chain O residue 39 ASP Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 97 VAL Chi-restraints excluded: chain P residue 39 ASP Chi-restraints excluded: chain P residue 64 LEU Chi-restraints excluded: chain P residue 97 VAL Chi-restraints excluded: chain P residue 109 MET Chi-restraints excluded: chain P residue 248 MET Chi-restraints excluded: chain P residue 342 ARG Chi-restraints excluded: chain P residue 366 SER Chi-restraints excluded: chain Q residue 39 ASP Chi-restraints excluded: chain Q residue 76 ARG Chi-restraints excluded: chain Q residue 96 ASP Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 155 ASP Chi-restraints excluded: chain Q residue 201 LEU Chi-restraints excluded: chain Q residue 342 ARG Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 ARG Chi-restraints excluded: chain R residue 96 ASP Chi-restraints excluded: chain R residue 97 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 342 ARG Chi-restraints excluded: chain S residue 39 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 LEU Chi-restraints excluded: chain S residue 342 ARG Chi-restraints excluded: chain T residue 39 ASP Chi-restraints excluded: chain T residue 96 ASP Chi-restraints excluded: chain T residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 754 random chunks: chunk 475 optimal weight: 6.9990 chunk 637 optimal weight: 0.7980 chunk 183 optimal weight: 0.0970 chunk 551 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 599 optimal weight: 0.2980 chunk 250 optimal weight: 0.2980 chunk 615 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 ASN ** E 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 ASN ** F 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 364 ASN ** K 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 ASN ** O 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 364 ASN ** P 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 364 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.113888 restraints weight = 130452.963| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 2.75 r_work: 0.2901 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2877 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 63078 Z= 0.160 Angle : 0.506 11.087 85612 Z= 0.264 Chirality : 0.038 0.151 9820 Planarity : 0.003 0.057 10520 Dihedral : 10.996 73.789 10454 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.53 % Allowed : 17.53 % Favored : 80.93 % 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: 1.68 (0.10), residues: 7540 helix: 1.74 (0.07), residues: 4700 sheet: 1.34 (0.28), residues: 220 loop : 0.05 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP N 260 HIS 0.004 0.001 HIS E 89 PHE 0.009 0.001 PHE B 223 TYR 0.012 0.001 TYR T 337 ARG 0.014 0.001 ARG E 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24485.05 seconds wall clock time: 423 minutes 30.15 seconds (25410.15 seconds total)