Starting phenix.real_space_refine on Thu Mar 21 23:05:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/03_2024/8pdm_17614.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/03_2024/8pdm_17614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/03_2024/8pdm_17614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/03_2024/8pdm_17614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/03_2024/8pdm_17614.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/03_2024/8pdm_17614.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 77 5.49 5 S 121 5.16 5 C 19602 2.51 5 N 5445 2.21 5 O 6226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 128": "OD1" <-> "OD2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 128": "OD1" <-> "OD2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 287": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E GLU 287": "OE1" <-> "OE2" Residue "E GLU 294": "OE1" <-> "OE2" Residue "E GLU 298": "OE1" <-> "OE2" Residue "E TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 360": "OE1" <-> "OE2" Residue "G TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 128": "OD1" <-> "OD2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G GLU 241": "OE1" <-> "OE2" Residue "G GLU 287": "OE1" <-> "OE2" Residue "G GLU 294": "OE1" <-> "OE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "I TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 128": "OD1" <-> "OD2" Residue "I ASP 202": "OD1" <-> "OD2" Residue "I GLU 241": "OE1" <-> "OE2" Residue "I GLU 287": "OE1" <-> "OE2" Residue "I GLU 294": "OE1" <-> "OE2" Residue "I GLU 298": "OE1" <-> "OE2" Residue "I TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 360": "OE1" <-> "OE2" Residue "K TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 128": "OD1" <-> "OD2" Residue "K ASP 202": "OD1" <-> "OD2" Residue "K GLU 241": "OE1" <-> "OE2" Residue "K GLU 287": "OE1" <-> "OE2" Residue "K GLU 294": "OE1" <-> "OE2" Residue "K GLU 298": "OE1" <-> "OE2" Residue "K TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 360": "OE1" <-> "OE2" Residue "M TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 128": "OD1" <-> "OD2" Residue "M ASP 202": "OD1" <-> "OD2" Residue "M GLU 241": "OE1" <-> "OE2" Residue "M GLU 287": "OE1" <-> "OE2" Residue "M GLU 294": "OE1" <-> "OE2" Residue "M GLU 298": "OE1" <-> "OE2" Residue "M TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "O TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 128": "OD1" <-> "OD2" Residue "O ASP 202": "OD1" <-> "OD2" Residue "O GLU 241": "OE1" <-> "OE2" Residue "O GLU 287": "OE1" <-> "OE2" Residue "O GLU 294": "OE1" <-> "OE2" Residue "O GLU 298": "OE1" <-> "OE2" Residue "O TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 360": "OE1" <-> "OE2" Residue "Q TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 128": "OD1" <-> "OD2" Residue "Q ASP 202": "OD1" <-> "OD2" Residue "Q GLU 241": "OE1" <-> "OE2" Residue "Q GLU 287": "OE1" <-> "OE2" Residue "Q GLU 294": "OE1" <-> "OE2" Residue "Q GLU 298": "OE1" <-> "OE2" Residue "Q TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 360": "OE1" <-> "OE2" Residue "S TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 128": "OD1" <-> "OD2" Residue "S ASP 202": "OD1" <-> "OD2" Residue "S GLU 241": "OE1" <-> "OE2" Residue "S GLU 287": "OE1" <-> "OE2" Residue "S GLU 294": "OE1" <-> "OE2" Residue "S GLU 298": "OE1" <-> "OE2" Residue "S TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 360": "OE1" <-> "OE2" Residue "U TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 128": "OD1" <-> "OD2" Residue "U ASP 202": "OD1" <-> "OD2" Residue "U GLU 241": "OE1" <-> "OE2" Residue "U GLU 287": "OE1" <-> "OE2" Residue "U GLU 294": "OE1" <-> "OE2" Residue "U GLU 298": "OE1" <-> "OE2" Residue "U TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 360": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31471 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "E" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "G" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "I" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "K" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "L" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "M" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "N" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "O" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "P" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "Q" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "R" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "S" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "T" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "U" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain breaks: 1 Chain: "V" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 15.28, per 1000 atoms: 0.49 Number of scatterers: 31471 At special positions: 0 Unit cell: (199.5, 200.55, 82.95, 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 121 16.00 P 77 15.00 O 6226 8.00 N 5445 7.00 C 19602 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: 11.66 Conformation dependent library (CDL) restraints added in 5.2 seconds 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7172 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 22 sheets defined 68.4% alpha, 2.3% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 10.87 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 141 Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 141 Processing helix chain 'C' and resid 156 through 170 Processing helix chain 'C' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR E 13 " --> pdb=" O SER E 9 " (cutoff:3.500A) 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 51 removed outlier: 3.962A pdb=" N LEU E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) 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 141 Processing helix chain 'E' and resid 156 through 170 Processing helix chain 'E' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 344 through 361 Processing helix chain 'G' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU G 46 " --> pdb=" O GLN G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 141 Processing helix chain 'G' and resid 156 through 170 Processing helix chain 'G' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 251 Processing helix chain 'G' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'I' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR I 13 " --> pdb=" O SER I 9 " (cutoff:3.500A) 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 51 removed outlier: 3.962A pdb=" N LEU I 46 " --> pdb=" O GLN I 42 " (cutoff:3.500A) 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 141 Processing helix chain 'I' and resid 156 through 170 Processing helix chain 'I' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 251 Processing helix chain 'I' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG I 260 " --> pdb=" O GLN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 274 Processing helix chain 'I' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS I 283 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 297 through 300' Processing helix chain 'I' and resid 318 through 332 Processing helix chain 'I' and resid 344 through 361 Processing helix chain 'K' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR K 13 " --> pdb=" O SER K 9 " (cutoff:3.500A) 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 51 removed outlier: 3.963A pdb=" N LEU K 46 " --> pdb=" O GLN K 42 " (cutoff:3.500A) 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 141 Processing helix chain 'K' and resid 156 through 170 Processing helix chain 'K' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 198 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER K 222 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 251 Processing helix chain 'K' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS K 283 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY K 300 " --> pdb=" O PRO K 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 318 through 332 Processing helix chain 'K' and resid 344 through 361 Processing helix chain 'M' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR M 13 " --> pdb=" O SER M 9 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 40 through 51 removed outlier: 3.962A pdb=" N LEU M 46 " --> pdb=" O GLN M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 75 Processing helix chain 'M' and resid 75 through 86 Processing helix chain 'M' and resid 120 through 141 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 175 through 191 removed outlier: 4.032A pdb=" N ARG M 189 " --> pdb=" O ARG M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 198 Processing helix chain 'M' and resid 202 through 217 Processing helix chain 'M' and resid 218 through 233 removed outlier: 3.844A pdb=" N SER M 222 " --> pdb=" O VAL M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 238 through 251 Processing helix chain 'M' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG M 260 " --> pdb=" O GLN M 256 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 274 Processing helix chain 'M' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS M 283 " --> pdb=" O GLN M 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN M 284 " --> pdb=" O ALA M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'O' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR O 13 " --> pdb=" O SER O 9 " (cutoff:3.500A) 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 51 removed outlier: 3.963A pdb=" N LEU O 46 " --> pdb=" O GLN O 42 " (cutoff:3.500A) 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 141 Processing helix chain 'O' and resid 156 through 170 Processing helix chain 'O' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG O 189 " --> pdb=" O ARG O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 198 Processing helix chain 'O' and resid 202 through 217 Processing helix chain 'O' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER O 222 " --> pdb=" O VAL O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 251 Processing helix chain 'O' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG O 260 " --> pdb=" O GLN O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 274 Processing helix chain 'O' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS O 283 " --> pdb=" O GLN O 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN O 284 " --> pdb=" O ALA O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY O 300 " --> pdb=" O PRO O 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 297 through 300' Processing helix chain 'O' and resid 318 through 332 Processing helix chain 'O' and resid 344 through 361 Processing helix chain 'Q' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR Q 13 " --> pdb=" O SER Q 9 " (cutoff:3.500A) 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 51 removed outlier: 3.963A pdb=" N LEU Q 46 " --> pdb=" O GLN Q 42 " (cutoff:3.500A) 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 141 Processing helix chain 'Q' and resid 156 through 170 Processing helix chain 'Q' and resid 175 through 191 removed outlier: 4.034A pdb=" N ARG Q 189 " --> pdb=" O ARG Q 185 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 198 Processing helix chain 'Q' and resid 202 through 217 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER Q 222 " --> pdb=" O VAL Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 251 Processing helix chain 'Q' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG Q 260 " --> pdb=" O GLN Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 270 through 274 Processing helix chain 'Q' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS Q 283 " --> pdb=" O GLN Q 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN Q 284 " --> pdb=" O ALA Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY Q 300 " --> pdb=" O PRO Q 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 297 through 300' Processing helix chain 'Q' and resid 318 through 332 Processing helix chain 'Q' and resid 344 through 361 Processing helix chain 'S' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR S 13 " --> pdb=" O SER S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 39 No H-bonds generated for 'chain 'S' and resid 37 through 39' Processing helix chain 'S' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU S 46 " --> pdb=" O GLN S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 75 Processing helix chain 'S' and resid 75 through 86 Processing helix chain 'S' and resid 120 through 141 Processing helix chain 'S' and resid 156 through 170 Processing helix chain 'S' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG S 189 " --> pdb=" O ARG S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 198 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER S 222 " --> pdb=" O VAL S 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 238 through 251 Processing helix chain 'S' and resid 256 through 269 removed outlier: 3.574A pdb=" N ARG S 260 " --> pdb=" O GLN S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 270 through 274 Processing helix chain 'S' and resid 275 through 296 removed outlier: 4.526A pdb=" N LYS S 283 " --> pdb=" O GLN S 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN S 284 " --> pdb=" O ALA S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.910A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing helix chain 'U' and resid 9 through 20 removed outlier: 3.517A pdb=" N TYR U 13 " --> pdb=" O SER U 9 " (cutoff:3.500A) Processing helix chain 'U' and resid 37 through 39 No H-bonds generated for 'chain 'U' and resid 37 through 39' Processing helix chain 'U' and resid 40 through 51 removed outlier: 3.963A pdb=" N LEU U 46 " --> pdb=" O GLN U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 61 through 75 Processing helix chain 'U' and resid 75 through 86 Processing helix chain 'U' and resid 120 through 141 Processing helix chain 'U' and resid 156 through 170 Processing helix chain 'U' and resid 175 through 191 removed outlier: 4.033A pdb=" N ARG U 189 " --> pdb=" O ARG U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 198 Processing helix chain 'U' and resid 202 through 217 Processing helix chain 'U' and resid 218 through 233 removed outlier: 3.843A pdb=" N SER U 222 " --> pdb=" O VAL U 218 " (cutoff:3.500A) Processing helix chain 'U' and resid 238 through 251 Processing helix chain 'U' and resid 256 through 269 removed outlier: 3.575A pdb=" N ARG U 260 " --> pdb=" O GLN U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 270 through 274 Processing helix chain 'U' and resid 275 through 296 removed outlier: 4.527A pdb=" N LYS U 283 " --> pdb=" O GLN U 279 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN U 284 " --> pdb=" O ALA U 280 " (cutoff:3.500A) Processing helix chain 'U' and resid 297 through 300 removed outlier: 3.911A pdb=" N GLY U 300 " --> pdb=" O PRO U 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 297 through 300' Processing helix chain 'U' and resid 318 through 332 Processing helix chain 'U' and resid 344 through 361 Processing sheet with id= 1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR A 33 " --> pdb=" O VAL A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG A 96 " --> pdb=" O ASP A 115 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR C 33 " --> pdb=" O VAL C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 3 Processing sheet with id= 4, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG C 96 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'E' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR E 33 " --> pdb=" O VAL E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'E' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG E 96 " --> pdb=" O ASP E 115 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'G' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR G 33 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 7 Processing sheet with id= 8, first strand: chain 'G' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG G 96 " --> pdb=" O ASP G 115 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'I' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR I 33 " --> pdb=" O VAL I 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'I' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG I 96 " --> pdb=" O ASP I 115 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR K 33 " --> pdb=" O VAL K 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'K' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG K 96 " --> pdb=" O ASP K 115 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'M' and resid 32 through 34 removed outlier: 6.237A pdb=" N THR M 33 " --> pdb=" O VAL M 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'M' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG M 96 " --> pdb=" O ASP M 115 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'O' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR O 33 " --> pdb=" O VAL O 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 15 Processing sheet with id= 16, first strand: chain 'O' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG O 96 " --> pdb=" O ASP O 115 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'Q' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR Q 33 " --> pdb=" O VAL Q 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'Q' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG Q 96 " --> pdb=" O ASP Q 115 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'S' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR S 33 " --> pdb=" O VAL S 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'S' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG S 96 " --> pdb=" O ASP S 115 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'U' and resid 32 through 34 removed outlier: 6.236A pdb=" N THR U 33 " --> pdb=" O VAL U 93 " (cutoff:3.500A) No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'U' and resid 96 through 98 removed outlier: 3.668A pdb=" N ARG U 96 " --> pdb=" O ASP U 115 " (cutoff:3.500A) 1826 hydrogen bonds defined for protein. 5379 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 11.80 Time building geometry restraints manager: 12.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10136 1.34 - 1.45: 4379 1.45 - 1.57: 17209 1.57 - 1.69: 154 1.69 - 1.80: 209 Bond restraints: 32087 Sorted by residual: bond pdb=" CB VAL U 325 " pdb=" CG1 VAL U 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.54e+00 bond pdb=" CB VAL O 325 " pdb=" CG1 VAL O 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.53e+00 bond pdb=" CB VAL S 325 " pdb=" CG1 VAL S 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.52e+00 bond pdb=" CB VAL M 325 " pdb=" CG1 VAL M 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 bond pdb=" CB VAL I 325 " pdb=" CG1 VAL I 325 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 32082 not shown) Histogram of bond angle deviations from ideal: 97.25 - 104.58: 623 104.58 - 111.91: 15786 111.91 - 119.23: 10970 119.23 - 126.56: 15983 126.56 - 133.89: 275 Bond angle restraints: 43637 Sorted by residual: angle pdb=" CA TYR O 61 " pdb=" CB TYR O 61 " pdb=" CG TYR O 61 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.99e+00 angle pdb=" CA TYR K 61 " pdb=" CB TYR K 61 " pdb=" CG TYR K 61 " ideal model delta sigma weight residual 113.90 118.65 -4.75 1.80e+00 3.09e-01 6.96e+00 angle pdb=" CA TYR S 61 " pdb=" CB TYR S 61 " pdb=" CG TYR S 61 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.93e+00 angle pdb=" CA TYR I 61 " pdb=" CB TYR I 61 " pdb=" CG TYR I 61 " ideal model delta sigma weight residual 113.90 118.64 -4.74 1.80e+00 3.09e-01 6.92e+00 angle pdb=" CA TYR E 61 " pdb=" CB TYR E 61 " pdb=" CG TYR E 61 " ideal model delta sigma weight residual 113.90 118.63 -4.73 1.80e+00 3.09e-01 6.92e+00 ... (remaining 43632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 17412 16.60 - 33.20: 1806 33.20 - 49.80: 263 49.80 - 66.40: 143 66.40 - 83.00: 132 Dihedral angle restraints: 19756 sinusoidal: 8580 harmonic: 11176 Sorted by residual: dihedral pdb=" CA TYR I 59 " pdb=" C TYR I 59 " pdb=" N LYS I 60 " pdb=" CA LYS I 60 " ideal model delta harmonic sigma weight residual 180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR G 59 " pdb=" C TYR G 59 " pdb=" N LYS G 60 " pdb=" CA LYS G 60 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR Q 59 " pdb=" C TYR Q 59 " pdb=" N LYS Q 60 " pdb=" CA LYS Q 60 " ideal model delta harmonic sigma weight residual -180.00 -163.51 -16.49 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 19753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2885 0.034 - 0.068: 1518 0.068 - 0.102: 546 0.102 - 0.136: 177 0.136 - 0.171: 22 Chirality restraints: 5148 Sorted by residual: chirality pdb=" C1' C P 75 " pdb=" O4' C P 75 " pdb=" C2' C P 75 " pdb=" N1 C P 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" C1' C N 75 " pdb=" O4' C N 75 " pdb=" C2' C N 75 " pdb=" N1 C N 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.25e-01 chirality pdb=" C1' C D 75 " pdb=" O4' C D 75 " pdb=" C2' C D 75 " pdb=" N1 C D 75 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.22e-01 ... (remaining 5145 not shown) Planarity restraints: 5291 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY S 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C GLY S 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY S 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS S 229 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLY G 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY G 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS G 229 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Q 228 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.80e+00 pdb=" C GLY Q 228 " -0.054 2.00e-02 2.50e+03 pdb=" O GLY Q 228 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS Q 229 " 0.018 2.00e-02 2.50e+03 ... (remaining 5288 not shown) Histogram of nonbonded interaction distances: 0.28 - 1.20: 99 1.20 - 2.13: 319 2.13 - 3.05: 21721 3.05 - 3.98: 85850 3.98 - 4.90: 159663 Warning: very small nonbonded interaction distances. Nonbonded interactions: 267652 Sorted by model distance: nonbonded pdb=" NH2 ARG E 78 " pdb=" CE1 TYR G 23 " model vdw 0.279 3.420 nonbonded pdb=" NH2 ARG I 78 " pdb=" CE1 TYR K 23 " model vdw 0.279 3.420 nonbonded pdb=" NH2 ARG O 78 " pdb=" CE1 TYR Q 23 " model vdw 0.279 3.420 nonbonded pdb=" NH2 ARG K 78 " pdb=" CE1 TYR M 23 " model vdw 0.279 3.420 nonbonded pdb=" NH2 ARG A 78 " pdb=" CE1 TYR C 23 " model vdw 0.279 3.420 ... (remaining 267647 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.030 Extract box with map and model: 15.990 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 86.690 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.006 0.070 32087 Z= 0.394 Angle : 0.733 5.921 43637 Z= 0.417 Chirality : 0.047 0.171 5148 Planarity : 0.006 0.052 5291 Dihedral : 15.484 82.999 12584 Min Nonbonded Distance : 0.279 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % 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: 0.75 (0.13), residues: 3817 helix: 1.00 (0.10), residues: 2464 sheet: -1.19 (0.33), residues: 165 loop : -0.11 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 261 HIS 0.003 0.001 HIS U 275 PHE 0.013 0.003 PHE I 214 TYR 0.027 0.003 TYR E 61 ARG 0.007 0.001 ARG S 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7657 (ttp-110) cc_final: 0.7370 (ttp-110) REVERT: A 347 LEU cc_start: 0.8262 (mt) cc_final: 0.7951 (mt) REVERT: G 138 LEU cc_start: 0.8331 (mp) cc_final: 0.8064 (mp) REVERT: I 53 TYR cc_start: 0.6243 (p90) cc_final: 0.6002 (p90) REVERT: I 138 LEU cc_start: 0.8393 (mp) cc_final: 0.8159 (mp) REVERT: I 249 MET cc_start: 0.7609 (mmm) cc_final: 0.7024 (mmm) REVERT: K 138 LEU cc_start: 0.8610 (mp) cc_final: 0.8360 (mp) REVERT: M 39 SER cc_start: 0.8582 (m) cc_final: 0.8338 (p) REVERT: M 84 ARG cc_start: 0.7633 (ttp-110) cc_final: 0.7382 (ttp-110) REVERT: M 249 MET cc_start: 0.7274 (mmm) cc_final: 0.6836 (mmm) REVERT: O 7 HIS cc_start: 0.7683 (t70) cc_final: 0.7452 (t70) REVERT: Q 138 LEU cc_start: 0.8544 (mp) cc_final: 0.8304 (mp) REVERT: S 249 MET cc_start: 0.7545 (mmm) cc_final: 0.7133 (mmm) REVERT: U 39 SER cc_start: 0.8580 (m) cc_final: 0.8320 (p) REVERT: U 138 LEU cc_start: 0.8580 (mp) cc_final: 0.8334 (mp) outliers start: 0 outliers final: 0 residues processed: 544 average time/residue: 0.4706 time to fit residues: 390.5404 Evaluate side-chains 391 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 2.9990 chunk 291 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 196 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 301 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 349 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 148 GLN A 306 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 306 GLN E 80 GLN E 306 GLN ** E 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 306 GLN ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN I 306 GLN ** I 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 306 GLN ** K 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN M 148 GLN M 306 GLN ** M 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 148 GLN O 306 GLN ** O 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 80 GLN Q 306 GLN ** Q 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN S 306 GLN ** S 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN U 306 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32087 Z= 0.218 Angle : 0.574 12.509 43637 Z= 0.299 Chirality : 0.041 0.217 5148 Planarity : 0.005 0.049 5291 Dihedral : 11.742 73.889 5412 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.31 % Allowed : 6.96 % Favored : 91.73 % 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: 1.18 (0.14), residues: 3817 helix: 1.35 (0.11), residues: 2519 sheet: -0.61 (0.35), residues: 165 loop : -0.13 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 261 HIS 0.007 0.001 HIS O 117 PHE 0.027 0.002 PHE A 348 TYR 0.012 0.002 TYR C 227 ARG 0.004 0.000 ARG Q 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 507 time to evaluate : 3.184 Fit side-chains REVERT: A 80 GLN cc_start: 0.8352 (tp40) cc_final: 0.7648 (tt0) REVERT: A 81 GLN cc_start: 0.8205 (tm-30) cc_final: 0.7771 (mt0) REVERT: A 249 MET cc_start: 0.7326 (mmm) cc_final: 0.7087 (mmm) REVERT: A 347 LEU cc_start: 0.8243 (mt) cc_final: 0.7893 (mt) REVERT: C 80 GLN cc_start: 0.8348 (tp40) cc_final: 0.7687 (tt0) REVERT: C 249 MET cc_start: 0.7241 (mmm) cc_final: 0.7001 (mmm) REVERT: E 80 GLN cc_start: 0.8294 (tp40) cc_final: 0.7583 (tt0) REVERT: E 290 ASP cc_start: 0.7608 (m-30) cc_final: 0.7278 (m-30) REVERT: G 80 GLN cc_start: 0.8390 (tp40) cc_final: 0.7737 (tt0) REVERT: G 138 LEU cc_start: 0.8551 (mp) cc_final: 0.8260 (mp) REVERT: I 53 TYR cc_start: 0.6218 (p90) cc_final: 0.5713 (p90) REVERT: I 80 GLN cc_start: 0.8359 (tp40) cc_final: 0.7697 (tt0) REVERT: I 151 ARG cc_start: 0.7406 (ptp-170) cc_final: 0.7047 (ptp-170) REVERT: I 249 MET cc_start: 0.7325 (mmm) cc_final: 0.7064 (mmm) REVERT: K 80 GLN cc_start: 0.8330 (tp40) cc_final: 0.7668 (tt0) REVERT: K 81 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7741 (mt0) REVERT: K 347 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7789 (mt) REVERT: M 80 GLN cc_start: 0.8421 (tp40) cc_final: 0.7780 (tt0) REVERT: M 81 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7624 (mt0) REVERT: O 80 GLN cc_start: 0.8323 (tp40) cc_final: 0.7663 (tt0) REVERT: O 249 MET cc_start: 0.7254 (mmm) cc_final: 0.7006 (mmm) REVERT: Q 80 GLN cc_start: 0.8363 (tp40) cc_final: 0.7725 (tt0) REVERT: Q 81 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7735 (mt0) REVERT: S 80 GLN cc_start: 0.8352 (tp40) cc_final: 0.7735 (tt0) REVERT: S 81 GLN cc_start: 0.8168 (tm-30) cc_final: 0.7594 (mt0) REVERT: S 249 MET cc_start: 0.7184 (mmm) cc_final: 0.6907 (mmm) REVERT: U 80 GLN cc_start: 0.8301 (tp40) cc_final: 0.7666 (tt0) REVERT: U 81 GLN cc_start: 0.8120 (tm-30) cc_final: 0.7735 (mt0) REVERT: U 138 LEU cc_start: 0.8765 (mp) cc_final: 0.8549 (mp) outliers start: 43 outliers final: 13 residues processed: 515 average time/residue: 0.4952 time to fit residues: 394.5755 Evaluate side-chains 451 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 437 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 290 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 350 optimal weight: 6.9990 chunk 378 optimal weight: 0.1980 chunk 311 optimal weight: 2.9990 chunk 347 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 148 GLN M 148 GLN Q 148 GLN Q 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32087 Z= 0.227 Angle : 0.542 11.389 43637 Z= 0.279 Chirality : 0.040 0.184 5148 Planarity : 0.005 0.046 5291 Dihedral : 11.583 73.790 5412 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.56 % Allowed : 10.92 % Favored : 87.52 % 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: 1.30 (0.14), residues: 3817 helix: 1.47 (0.11), residues: 2508 sheet: -0.47 (0.35), residues: 165 loop : -0.15 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 261 HIS 0.007 0.001 HIS O 117 PHE 0.029 0.003 PHE Q 348 TYR 0.013 0.002 TYR U 53 ARG 0.009 0.000 ARG M 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 479 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8323 (tp40) cc_final: 0.7657 (tt0) REVERT: A 347 LEU cc_start: 0.8194 (mt) cc_final: 0.7811 (mt) REVERT: C 80 GLN cc_start: 0.8400 (tp40) cc_final: 0.7738 (tt0) REVERT: C 249 MET cc_start: 0.7325 (mmm) cc_final: 0.7037 (mmm) REVERT: C 346 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7445 (tt0) REVERT: E 80 GLN cc_start: 0.8340 (tp40) cc_final: 0.7682 (tt0) REVERT: E 290 ASP cc_start: 0.7602 (m-30) cc_final: 0.7105 (m-30) REVERT: G 138 LEU cc_start: 0.8386 (mp) cc_final: 0.8016 (mp) REVERT: I 53 TYR cc_start: 0.6193 (p90) cc_final: 0.5779 (p90) REVERT: I 128 ASP cc_start: 0.7427 (t70) cc_final: 0.7153 (t0) REVERT: I 249 MET cc_start: 0.7513 (mmm) cc_final: 0.6795 (mmm) REVERT: K 347 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7881 (mt) REVERT: M 80 GLN cc_start: 0.8399 (tp40) cc_final: 0.7747 (tt0) REVERT: O 80 GLN cc_start: 0.8260 (tp40) cc_final: 0.7693 (tt0) REVERT: O 81 GLN cc_start: 0.8630 (tm-30) cc_final: 0.7957 (mt0) REVERT: O 249 MET cc_start: 0.7327 (mmm) cc_final: 0.7012 (mmm) REVERT: Q 80 GLN cc_start: 0.8328 (tp40) cc_final: 0.7717 (tt0) REVERT: Q 346 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7464 (tt0) REVERT: S 249 MET cc_start: 0.7234 (mmm) cc_final: 0.6880 (mmm) REVERT: U 80 GLN cc_start: 0.8368 (tp40) cc_final: 0.7752 (tt0) REVERT: U 138 LEU cc_start: 0.8822 (mp) cc_final: 0.8614 (mp) REVERT: U 151 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6911 (ptp-170) outliers start: 51 outliers final: 17 residues processed: 491 average time/residue: 0.4925 time to fit residues: 363.8027 Evaluate side-chains 441 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 422 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 290 ASP Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 151 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 235 optimal weight: 7.9990 chunk 351 optimal weight: 0.6980 chunk 372 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 333 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN K 80 GLN M 148 GLN ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32087 Z= 0.194 Angle : 0.516 11.802 43637 Z= 0.263 Chirality : 0.038 0.177 5148 Planarity : 0.004 0.048 5291 Dihedral : 11.500 73.760 5412 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.86 % Allowed : 12.78 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 3817 helix: 1.58 (0.11), residues: 2519 sheet: -0.44 (0.36), residues: 165 loop : -0.15 (0.20), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Q 261 HIS 0.008 0.001 HIS S 117 PHE 0.028 0.002 PHE O 348 TYR 0.021 0.001 TYR S 61 ARG 0.005 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 454 time to evaluate : 3.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8326 (tp40) cc_final: 0.7713 (tt0) REVERT: A 249 MET cc_start: 0.7368 (mmm) cc_final: 0.7013 (mmm) REVERT: C 80 GLN cc_start: 0.8397 (tp40) cc_final: 0.7752 (tt0) REVERT: C 175 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.8018 (p) REVERT: C 249 MET cc_start: 0.7296 (mmm) cc_final: 0.7008 (mmm) REVERT: C 346 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7376 (tt0) REVERT: E 80 GLN cc_start: 0.8335 (tp40) cc_final: 0.7729 (tt0) REVERT: E 290 ASP cc_start: 0.7688 (m-30) cc_final: 0.7107 (m-30) REVERT: G 80 GLN cc_start: 0.8364 (tp40) cc_final: 0.7720 (tt0) REVERT: G 138 LEU cc_start: 0.8395 (mp) cc_final: 0.7999 (mp) REVERT: I 53 TYR cc_start: 0.6324 (p90) cc_final: 0.6119 (p90) REVERT: I 80 GLN cc_start: 0.8361 (tp40) cc_final: 0.7749 (tt0) REVERT: I 128 ASP cc_start: 0.7522 (t70) cc_final: 0.7216 (t0) REVERT: I 249 MET cc_start: 0.7485 (mmm) cc_final: 0.6847 (mmm) REVERT: K 80 GLN cc_start: 0.8346 (tp40) cc_final: 0.7714 (tt0) REVERT: K 347 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7849 (mt) REVERT: M 23 TYR cc_start: 0.6509 (m-10) cc_final: 0.6279 (m-80) REVERT: M 26 LYS cc_start: 0.7620 (mmtp) cc_final: 0.7402 (mmtm) REVERT: M 78 ARG cc_start: 0.7360 (tpp-160) cc_final: 0.6789 (tpp-160) REVERT: O 80 GLN cc_start: 0.8281 (tp40) cc_final: 0.7706 (tt0) REVERT: O 81 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8070 (mt0) REVERT: O 249 MET cc_start: 0.7284 (mmm) cc_final: 0.6995 (mmm) REVERT: O 346 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7318 (tt0) REVERT: Q 80 GLN cc_start: 0.8287 (tp40) cc_final: 0.7692 (tt0) REVERT: S 80 GLN cc_start: 0.8349 (tp40) cc_final: 0.7792 (tt0) REVERT: S 249 MET cc_start: 0.7198 (mmm) cc_final: 0.6863 (mmm) REVERT: S 346 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7467 (tt0) REVERT: U 80 GLN cc_start: 0.8338 (tp40) cc_final: 0.7768 (tt0) REVERT: U 138 LEU cc_start: 0.8752 (mp) cc_final: 0.8436 (mp) REVERT: U 151 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6814 (ptp-170) outliers start: 61 outliers final: 35 residues processed: 467 average time/residue: 0.4867 time to fit residues: 342.4482 Evaluate side-chains 459 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 421 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 113 MET Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain U residue 113 MET Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 277 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 317 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 HIS ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 32087 Z= 0.371 Angle : 0.624 12.245 43637 Z= 0.314 Chirality : 0.043 0.176 5148 Planarity : 0.005 0.051 5291 Dihedral : 11.459 73.942 5412 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.02 % Allowed : 14.55 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.14), residues: 3817 helix: 1.31 (0.11), residues: 2519 sheet: -0.22 (0.37), residues: 165 loop : -0.47 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 261 HIS 0.025 0.002 HIS C 275 PHE 0.031 0.004 PHE I 348 TYR 0.024 0.002 TYR K 338 ARG 0.009 0.001 ARG O 151 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 436 time to evaluate : 3.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8418 (tp40) cc_final: 0.7749 (tt0) REVERT: A 249 MET cc_start: 0.7511 (mmm) cc_final: 0.7238 (mmm) REVERT: C 175 THR cc_start: 0.8252 (OUTLIER) cc_final: 0.8010 (p) REVERT: C 249 MET cc_start: 0.7376 (mmm) cc_final: 0.7098 (mmm) REVERT: E 53 TYR cc_start: 0.6334 (p90) cc_final: 0.5660 (p90) REVERT: E 80 GLN cc_start: 0.8373 (tp40) cc_final: 0.7761 (tt0) REVERT: E 249 MET cc_start: 0.7540 (mmm) cc_final: 0.7180 (mmm) REVERT: G 46 LEU cc_start: 0.8613 (tp) cc_final: 0.8399 (tp) REVERT: G 138 LEU cc_start: 0.8428 (mp) cc_final: 0.8105 (mp) REVERT: I 53 TYR cc_start: 0.6449 (p90) cc_final: 0.6228 (p90) REVERT: I 128 ASP cc_start: 0.7520 (t70) cc_final: 0.7227 (t0) REVERT: I 249 MET cc_start: 0.7553 (mmm) cc_final: 0.7035 (mmm) REVERT: K 347 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7834 (mt) REVERT: M 23 TYR cc_start: 0.6686 (m-10) cc_final: 0.6395 (m-80) REVERT: M 80 GLN cc_start: 0.8466 (tp40) cc_final: 0.7793 (tt0) REVERT: O 80 GLN cc_start: 0.8344 (tp40) cc_final: 0.7664 (tt0) REVERT: O 249 MET cc_start: 0.7430 (mmm) cc_final: 0.7096 (mmm) REVERT: O 295 MET cc_start: 0.8637 (mtm) cc_final: 0.8274 (mtp) REVERT: O 347 LEU cc_start: 0.8219 (mm) cc_final: 0.7641 (mt) REVERT: Q 80 GLN cc_start: 0.8349 (tp40) cc_final: 0.7699 (tt0) REVERT: Q 249 MET cc_start: 0.7370 (mmm) cc_final: 0.7157 (mmm) REVERT: S 78 ARG cc_start: 0.7333 (tpp-160) cc_final: 0.6948 (tpp-160) REVERT: S 249 MET cc_start: 0.7365 (mmm) cc_final: 0.7013 (mmm) REVERT: U 138 LEU cc_start: 0.8588 (mp) cc_final: 0.8208 (mp) REVERT: U 151 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6851 (ptp-170) outliers start: 99 outliers final: 65 residues processed: 475 average time/residue: 0.5015 time to fit residues: 357.2771 Evaluate side-chains 473 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 405 time to evaluate : 3.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 113 MET Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 290 ASP Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 8 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 290 ASP Chi-restraints excluded: chain M residue 358 LEU Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain O residue 358 LEU Chi-restraints excluded: chain Q residue 113 MET Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 113 MET Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 10 ASP Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 113 MET Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 0.6980 chunk 335 optimal weight: 0.2980 chunk 73 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 372 optimal weight: 1.9990 chunk 309 optimal weight: 0.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 195 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 148 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN G 275 HIS ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 80 GLN U 275 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 32087 Z= 0.186 Angle : 0.520 12.668 43637 Z= 0.265 Chirality : 0.038 0.170 5148 Planarity : 0.004 0.052 5291 Dihedral : 11.378 73.805 5412 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.80 % Allowed : 16.60 % Favored : 81.60 % 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: 1.39 (0.14), residues: 3817 helix: 1.60 (0.11), residues: 2530 sheet: -0.32 (0.37), residues: 165 loop : -0.36 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 261 HIS 0.014 0.001 HIS G 275 PHE 0.032 0.003 PHE G 348 TYR 0.024 0.001 TYR C 23 ARG 0.004 0.000 ARG K 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 447 time to evaluate : 3.406 Fit side-chains REVERT: A 80 GLN cc_start: 0.8344 (tp40) cc_final: 0.7779 (tt0) REVERT: A 151 ARG cc_start: 0.6481 (mtt90) cc_final: 0.6249 (mtm-85) REVERT: C 80 GLN cc_start: 0.8383 (tp40) cc_final: 0.7636 (tt0) REVERT: C 175 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.8033 (p) REVERT: C 249 MET cc_start: 0.7322 (mmm) cc_final: 0.6976 (mmm) REVERT: E 53 TYR cc_start: 0.6452 (p90) cc_final: 0.5861 (p90) REVERT: E 80 GLN cc_start: 0.8324 (tp40) cc_final: 0.7760 (tt0) REVERT: G 46 LEU cc_start: 0.8431 (tp) cc_final: 0.8230 (tp) REVERT: G 50 GLU cc_start: 0.7306 (tp30) cc_final: 0.7093 (mm-30) REVERT: G 80 GLN cc_start: 0.8373 (tp40) cc_final: 0.7704 (tt0) REVERT: G 138 LEU cc_start: 0.8445 (mp) cc_final: 0.8130 (mp) REVERT: I 80 GLN cc_start: 0.8402 (tp40) cc_final: 0.7807 (tt0) REVERT: I 128 ASP cc_start: 0.7474 (t70) cc_final: 0.7182 (t0) REVERT: I 249 MET cc_start: 0.7469 (mmm) cc_final: 0.6876 (mmm) REVERT: K 80 GLN cc_start: 0.8397 (tp40) cc_final: 0.7719 (tt0) REVERT: K 347 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7754 (mt) REVERT: M 78 ARG cc_start: 0.7390 (tpp-160) cc_final: 0.6784 (tpp-160) REVERT: M 80 GLN cc_start: 0.8361 (tp40) cc_final: 0.7730 (tt0) REVERT: O 80 GLN cc_start: 0.8295 (tp40) cc_final: 0.7613 (tt0) REVERT: O 249 MET cc_start: 0.7284 (mmm) cc_final: 0.7026 (mmm) REVERT: O 344 ASN cc_start: 0.6468 (t0) cc_final: 0.6102 (t0) REVERT: Q 80 GLN cc_start: 0.8282 (tp40) cc_final: 0.7680 (tt0) REVERT: S 80 GLN cc_start: 0.8370 (tp-100) cc_final: 0.7726 (tt0) REVERT: S 151 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6480 (mtt90) REVERT: S 249 MET cc_start: 0.7206 (mmm) cc_final: 0.6890 (mmm) REVERT: U 80 GLN cc_start: 0.8433 (tp40) cc_final: 0.7799 (tt0) REVERT: U 138 LEU cc_start: 0.8508 (mp) cc_final: 0.8205 (mp) REVERT: U 151 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7066 (ptp-170) outliers start: 59 outliers final: 40 residues processed: 472 average time/residue: 0.4961 time to fit residues: 352.7037 Evaluate side-chains 471 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 427 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 275 HIS Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 215 GLU Chi-restraints excluded: chain S residue 290 ASP Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 113 MET Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 210 optimal weight: 4.9990 chunk 313 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 232 optimal weight: 3.9990 chunk 226 optimal weight: 0.0770 chunk 171 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 HIS ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 HIS ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN U 275 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32087 Z= 0.184 Angle : 0.524 12.927 43637 Z= 0.263 Chirality : 0.038 0.137 5148 Planarity : 0.004 0.050 5291 Dihedral : 11.423 73.765 5412 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.59 % Allowed : 17.05 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.14), residues: 3817 helix: 1.71 (0.11), residues: 2530 sheet: -0.44 (0.36), residues: 165 loop : -0.37 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP G 123 HIS 0.013 0.001 HIS G 275 PHE 0.033 0.002 PHE G 348 TYR 0.022 0.001 TYR C 23 ARG 0.005 0.000 ARG K 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 441 time to evaluate : 3.600 Fit side-chains REVERT: A 80 GLN cc_start: 0.8352 (tp40) cc_final: 0.7902 (tt0) REVERT: A 84 ARG cc_start: 0.7829 (ttp-110) cc_final: 0.7471 (ttp-110) REVERT: C 80 GLN cc_start: 0.8417 (tp40) cc_final: 0.7772 (tt0) REVERT: C 175 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8058 (p) REVERT: C 249 MET cc_start: 0.7291 (mmm) cc_final: 0.6960 (mmm) REVERT: E 53 TYR cc_start: 0.6406 (p90) cc_final: 0.5722 (p90) REVERT: E 78 ARG cc_start: 0.7483 (tpp-160) cc_final: 0.7026 (tpp-160) REVERT: E 80 GLN cc_start: 0.8312 (tp40) cc_final: 0.7779 (tt0) REVERT: E 249 MET cc_start: 0.7519 (mmm) cc_final: 0.7234 (mmm) REVERT: G 80 GLN cc_start: 0.8369 (tp40) cc_final: 0.7764 (tt0) REVERT: G 138 LEU cc_start: 0.8449 (mp) cc_final: 0.8148 (mp) REVERT: I 78 ARG cc_start: 0.7145 (tpp-160) cc_final: 0.6712 (tpp-160) REVERT: I 80 GLN cc_start: 0.8327 (tp40) cc_final: 0.7740 (tt0) REVERT: I 128 ASP cc_start: 0.7453 (t70) cc_final: 0.7184 (t0) REVERT: K 80 GLN cc_start: 0.8372 (tp40) cc_final: 0.7767 (tt0) REVERT: K 113 MET cc_start: 0.4416 (OUTLIER) cc_final: 0.3888 (mtm) REVERT: M 80 GLN cc_start: 0.8351 (tp40) cc_final: 0.7733 (tt0) REVERT: O 80 GLN cc_start: 0.8333 (tp40) cc_final: 0.7675 (tt0) REVERT: O 249 MET cc_start: 0.7285 (mmm) cc_final: 0.6992 (mmm) REVERT: O 347 LEU cc_start: 0.8248 (mm) cc_final: 0.7750 (mt) REVERT: Q 80 GLN cc_start: 0.8297 (tp40) cc_final: 0.7709 (tt0) REVERT: S 80 GLN cc_start: 0.8354 (tp40) cc_final: 0.7815 (tt0) REVERT: S 151 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7008 (ptp-170) REVERT: S 249 MET cc_start: 0.7213 (mmm) cc_final: 0.6879 (mmm) REVERT: U 80 GLN cc_start: 0.8382 (tp40) cc_final: 0.7814 (tt0) REVERT: U 138 LEU cc_start: 0.8433 (mp) cc_final: 0.8117 (mp) REVERT: U 151 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7075 (ptp-170) outliers start: 52 outliers final: 43 residues processed: 460 average time/residue: 0.4949 time to fit residues: 342.9427 Evaluate side-chains 480 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 433 time to evaluate : 3.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 275 HIS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 215 GLU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 113 MET Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 235 optimal weight: 0.8980 chunk 252 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 291 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 HIS ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 HIS I 275 HIS ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 32087 Z= 0.233 Angle : 0.554 14.930 43637 Z= 0.274 Chirality : 0.039 0.135 5148 Planarity : 0.004 0.051 5291 Dihedral : 11.524 73.845 5412 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.83 % Allowed : 17.45 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.14), residues: 3817 helix: 1.67 (0.11), residues: 2530 sheet: -0.42 (0.36), residues: 165 loop : -0.43 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 261 HIS 0.016 0.001 HIS G 275 PHE 0.033 0.003 PHE G 348 TYR 0.017 0.001 TYR E 23 ARG 0.006 0.000 ARG M 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 431 time to evaluate : 3.624 Fit side-chains REVERT: A 80 GLN cc_start: 0.8404 (tp40) cc_final: 0.7898 (tt0) REVERT: A 84 ARG cc_start: 0.7815 (ttp-110) cc_final: 0.7415 (ttp-110) REVERT: C 80 GLN cc_start: 0.8390 (tp40) cc_final: 0.7724 (tt0) REVERT: C 175 THR cc_start: 0.8287 (OUTLIER) cc_final: 0.8079 (p) REVERT: C 249 MET cc_start: 0.7334 (mmm) cc_final: 0.7001 (mmm) REVERT: E 53 TYR cc_start: 0.6338 (p90) cc_final: 0.5674 (p90) REVERT: E 80 GLN cc_start: 0.8335 (tp40) cc_final: 0.7792 (tt0) REVERT: E 249 MET cc_start: 0.7530 (mmm) cc_final: 0.7190 (mmm) REVERT: E 339 ARG cc_start: 0.7061 (tpp-160) cc_final: 0.6858 (mmt-90) REVERT: G 80 GLN cc_start: 0.8372 (tp40) cc_final: 0.7740 (tt0) REVERT: G 138 LEU cc_start: 0.8449 (mp) cc_final: 0.8142 (mp) REVERT: I 78 ARG cc_start: 0.7183 (tpp-160) cc_final: 0.6791 (tpp-160) REVERT: I 128 ASP cc_start: 0.7466 (t70) cc_final: 0.7203 (t0) REVERT: I 249 MET cc_start: 0.7430 (mmm) cc_final: 0.6990 (mmm) REVERT: K 113 MET cc_start: 0.4049 (mtp) cc_final: 0.3608 (mtm) REVERT: O 80 GLN cc_start: 0.8328 (tp40) cc_final: 0.7672 (tt0) REVERT: O 249 MET cc_start: 0.7319 (mmm) cc_final: 0.7014 (mmm) REVERT: Q 80 GLN cc_start: 0.8304 (tp40) cc_final: 0.7715 (tt0) REVERT: Q 151 ARG cc_start: 0.6877 (mtt90) cc_final: 0.6325 (mtm-85) REVERT: Q 339 ARG cc_start: 0.7212 (tpp-160) cc_final: 0.6982 (mmt-90) REVERT: S 80 GLN cc_start: 0.8371 (tp40) cc_final: 0.7833 (tt0) REVERT: S 151 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6984 (ptp-170) REVERT: S 249 MET cc_start: 0.7247 (mmm) cc_final: 0.6904 (mmm) REVERT: U 80 GLN cc_start: 0.8414 (tp40) cc_final: 0.7823 (tt0) REVERT: U 138 LEU cc_start: 0.8434 (mp) cc_final: 0.8117 (mp) REVERT: U 151 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7088 (ptp-170) outliers start: 60 outliers final: 47 residues processed: 455 average time/residue: 0.4986 time to fit residues: 340.3746 Evaluate side-chains 475 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 425 time to evaluate : 3.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 22 GLN Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 275 HIS Chi-restraints excluded: chain I residue 290 ASP Chi-restraints excluded: chain K residue 10 ASP Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 24 THR Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 215 GLU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 113 MET Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 3.9990 chunk 355 optimal weight: 1.9990 chunk 324 optimal weight: 0.9990 chunk 345 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 312 optimal weight: 0.0980 chunk 327 optimal weight: 1.9990 chunk 344 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 HIS ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN I 275 HIS ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 117 HIS ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 HIS U 275 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32087 Z= 0.179 Angle : 0.540 15.872 43637 Z= 0.265 Chirality : 0.038 0.127 5148 Planarity : 0.004 0.051 5291 Dihedral : 11.672 73.753 5412 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.46 % Allowed : 18.49 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.14), residues: 3817 helix: 1.77 (0.11), residues: 2530 sheet: -0.48 (0.35), residues: 165 loop : -0.40 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP O 261 HIS 0.012 0.001 HIS G 275 PHE 0.032 0.002 PHE M 348 TYR 0.019 0.001 TYR I 354 ARG 0.006 0.000 ARG O 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 447 time to evaluate : 2.886 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8380 (tp40) cc_final: 0.7914 (tt0) REVERT: A 84 ARG cc_start: 0.7772 (ttp-110) cc_final: 0.7376 (ttp-110) REVERT: A 151 ARG cc_start: 0.6761 (mtm-85) cc_final: 0.6545 (mtm-85) REVERT: C 80 GLN cc_start: 0.8388 (tp40) cc_final: 0.7755 (tt0) REVERT: C 175 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8099 (p) REVERT: C 249 MET cc_start: 0.7314 (mmm) cc_final: 0.6976 (mmm) REVERT: C 339 ARG cc_start: 0.7116 (tpp-160) cc_final: 0.6816 (mmt-90) REVERT: E 53 TYR cc_start: 0.6379 (p90) cc_final: 0.5689 (p90) REVERT: E 80 GLN cc_start: 0.8322 (tp40) cc_final: 0.7783 (tt0) REVERT: G 80 GLN cc_start: 0.8340 (tp40) cc_final: 0.7769 (tt0) REVERT: G 138 LEU cc_start: 0.8438 (mp) cc_final: 0.8108 (mp) REVERT: G 249 MET cc_start: 0.7685 (tpt) cc_final: 0.7331 (mmm) REVERT: I 80 GLN cc_start: 0.8350 (tp40) cc_final: 0.7759 (tt0) REVERT: I 128 ASP cc_start: 0.7451 (t70) cc_final: 0.7196 (t0) REVERT: I 249 MET cc_start: 0.7398 (mmm) cc_final: 0.6963 (mmm) REVERT: K 80 GLN cc_start: 0.8415 (tp40) cc_final: 0.7803 (tt0) REVERT: K 113 MET cc_start: 0.4125 (mtp) cc_final: 0.3660 (mtm) REVERT: M 80 GLN cc_start: 0.8367 (tp40) cc_final: 0.7687 (tt0) REVERT: M 339 ARG cc_start: 0.7372 (tpp-160) cc_final: 0.7039 (mmt-90) REVERT: O 80 GLN cc_start: 0.8333 (tp40) cc_final: 0.7667 (tt0) REVERT: O 249 MET cc_start: 0.7293 (mmm) cc_final: 0.7010 (mmm) REVERT: Q 80 GLN cc_start: 0.8281 (tp40) cc_final: 0.7722 (tt0) REVERT: Q 117 HIS cc_start: 0.7350 (t-90) cc_final: 0.7045 (t70) REVERT: Q 249 MET cc_start: 0.7158 (mmm) cc_final: 0.6713 (tpt) REVERT: Q 339 ARG cc_start: 0.7083 (tpp-160) cc_final: 0.6862 (mmt-90) REVERT: S 80 GLN cc_start: 0.8376 (tp40) cc_final: 0.7862 (tt0) REVERT: S 151 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7010 (ptp-170) REVERT: S 249 MET cc_start: 0.7206 (mmm) cc_final: 0.6876 (mmm) REVERT: U 80 GLN cc_start: 0.8345 (tp40) cc_final: 0.7779 (tt0) REVERT: U 138 LEU cc_start: 0.8417 (mp) cc_final: 0.8085 (mp) REVERT: U 151 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.7029 (ptp-170) REVERT: U 295 MET cc_start: 0.8532 (mtm) cc_final: 0.8256 (mtp) outliers start: 48 outliers final: 41 residues processed: 467 average time/residue: 0.4421 time to fit residues: 311.9093 Evaluate side-chains 479 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 435 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 275 HIS Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 275 HIS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 215 GLU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 2.9990 chunk 365 optimal weight: 0.0070 chunk 223 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 254 optimal weight: 0.9980 chunk 383 optimal weight: 2.9990 chunk 353 optimal weight: 0.6980 chunk 305 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 235 optimal weight: 0.8980 chunk 187 optimal weight: 5.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 HIS ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 275 HIS ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS O 275 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 HIS U 275 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32087 Z= 0.238 Angle : 0.572 16.735 43637 Z= 0.279 Chirality : 0.039 0.131 5148 Planarity : 0.004 0.058 5291 Dihedral : 11.475 73.848 5412 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.53 % Allowed : 18.46 % Favored : 80.02 % 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: 1.42 (0.14), residues: 3817 helix: 1.70 (0.11), residues: 2530 sheet: -1.21 (0.31), residues: 209 loop : -0.31 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 261 HIS 0.014 0.001 HIS G 275 PHE 0.033 0.003 PHE S 348 TYR 0.022 0.002 TYR S 23 ARG 0.005 0.000 ARG O 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7634 Ramachandran restraints generated. 3817 Oldfield, 0 Emsley, 3817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 429 time to evaluate : 3.360 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8400 (tp40) cc_final: 0.7949 (tt0) REVERT: A 84 ARG cc_start: 0.7783 (ttp-110) cc_final: 0.7389 (ttp-110) REVERT: A 151 ARG cc_start: 0.6796 (mtm-85) cc_final: 0.6531 (mtm-85) REVERT: C 80 GLN cc_start: 0.8399 (tp40) cc_final: 0.7747 (tt0) REVERT: C 175 THR cc_start: 0.8282 (OUTLIER) cc_final: 0.8058 (p) REVERT: C 249 MET cc_start: 0.7320 (mmm) cc_final: 0.7001 (mmm) REVERT: C 339 ARG cc_start: 0.7151 (tpp-160) cc_final: 0.6902 (mmt-90) REVERT: E 53 TYR cc_start: 0.6350 (p90) cc_final: 0.5687 (p90) REVERT: E 80 GLN cc_start: 0.8343 (tp40) cc_final: 0.7792 (tt0) REVERT: E 249 MET cc_start: 0.7527 (mmm) cc_final: 0.7292 (mmm) REVERT: G 80 GLN cc_start: 0.8338 (tp40) cc_final: 0.7766 (tt0) REVERT: G 138 LEU cc_start: 0.8405 (mp) cc_final: 0.8120 (mp) REVERT: G 249 MET cc_start: 0.7745 (tpt) cc_final: 0.7372 (mmm) REVERT: I 80 GLN cc_start: 0.8371 (tp40) cc_final: 0.7746 (tt0) REVERT: I 128 ASP cc_start: 0.7468 (t70) cc_final: 0.7210 (t0) REVERT: I 249 MET cc_start: 0.7433 (mmm) cc_final: 0.6986 (mmm) REVERT: K 80 GLN cc_start: 0.8447 (tp40) cc_final: 0.7789 (tt0) REVERT: K 113 MET cc_start: 0.4137 (mtp) cc_final: 0.3664 (mtm) REVERT: M 23 TYR cc_start: 0.6679 (m-10) cc_final: 0.6357 (m-80) REVERT: M 78 ARG cc_start: 0.7316 (tpp-160) cc_final: 0.6796 (tpp-160) REVERT: M 80 GLN cc_start: 0.8396 (tp40) cc_final: 0.7672 (tt0) REVERT: M 339 ARG cc_start: 0.7418 (tpp-160) cc_final: 0.7163 (mmt-90) REVERT: O 81 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8113 (mt0) REVERT: O 249 MET cc_start: 0.7316 (mmm) cc_final: 0.7014 (mmm) REVERT: Q 80 GLN cc_start: 0.8318 (tp40) cc_final: 0.7718 (tt0) REVERT: Q 117 HIS cc_start: 0.7384 (t-90) cc_final: 0.7031 (t70) REVERT: Q 339 ARG cc_start: 0.7137 (tpp-160) cc_final: 0.6918 (mmt-90) REVERT: S 80 GLN cc_start: 0.8396 (tp40) cc_final: 0.7873 (tt0) REVERT: S 151 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.7067 (ptp-170) REVERT: S 249 MET cc_start: 0.7244 (mmm) cc_final: 0.6925 (mmm) REVERT: S 347 LEU cc_start: 0.8509 (mt) cc_final: 0.8076 (mt) REVERT: U 80 GLN cc_start: 0.8367 (tp40) cc_final: 0.7785 (tt0) REVERT: U 138 LEU cc_start: 0.8389 (mp) cc_final: 0.8076 (mp) REVERT: U 151 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7057 (ptp-170) outliers start: 50 outliers final: 43 residues processed: 450 average time/residue: 0.5107 time to fit residues: 344.9026 Evaluate side-chains 469 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 423 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 337 MET Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 151 ARG Chi-restraints excluded: chain I residue 175 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 275 HIS Chi-restraints excluded: chain K residue 17 ILE Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain K residue 195 LEU Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 282 LEU Chi-restraints excluded: chain O residue 10 ASP Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 190 VAL Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain O residue 275 HIS Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain S residue 151 ARG Chi-restraints excluded: chain S residue 175 THR Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 190 VAL Chi-restraints excluded: chain S residue 215 GLU Chi-restraints excluded: chain U residue 3 LEU Chi-restraints excluded: chain U residue 24 THR Chi-restraints excluded: chain U residue 151 ARG Chi-restraints excluded: chain U residue 175 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 275 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 242 optimal weight: 0.0870 chunk 325 optimal weight: 0.1980 chunk 93 optimal weight: 1.9990 chunk 281 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 0.0970 chunk 305 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 314 optimal weight: 0.3980 chunk 38 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS C 117 HIS C 275 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 344 ASN G 275 HIS I 275 HIS ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN ** M 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** O 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 HIS O 275 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 117 HIS U 275 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.169298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141212 restraints weight = 42752.014| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.33 r_work: 0.3446 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 32087 Z= 0.152 Angle : 0.537 17.083 43637 Z= 0.261 Chirality : 0.037 0.159 5148 Planarity : 0.004 0.062 5291 Dihedral : 11.463 73.661 5412 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.56 % Allowed : 18.64 % Favored : 79.80 % 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: 1.63 (0.14), residues: 3817 helix: 1.86 (0.11), residues: 2530 sheet: -1.26 (0.30), residues: 209 loop : -0.24 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP K 261 HIS 0.026 0.001 HIS O 275 PHE 0.032 0.002 PHE G 348 TYR 0.020 0.001 TYR S 23 ARG 0.007 0.000 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7623.98 seconds wall clock time: 138 minutes 17.83 seconds (8297.83 seconds total)