Starting phenix.real_space_refine on Fri Jul 26 02:25:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/07_2024/8pdm_17614.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/07_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_17614/07_2024/8pdm_17614.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/07_2024/8pdm_17614.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/07_2024/8pdm_17614.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdm_17614/07_2024/8pdm_17614.cif" } 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-5388/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: 17.45, per 1000 atoms: 0.55 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: 14.15 Conformation dependent library (CDL) restraints added in 5.6 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: 10.30 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: 11.37 Time building geometry restraints manager: 15.37 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: 4378 1.45 - 1.57: 17210 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: 15788 111.91 - 119.23: 10972 119.23 - 126.56: 15979 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: 2884 0.034 - 0.068: 1519 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: 159665 Warning: very small nonbonded interaction distances. Nonbonded interactions: 267654 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 267649 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: 5.980 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: 1.350 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 92.170 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.230 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.850 ------------------------------------------------------------------------------- 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 U 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 : 3.614 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: 0.6244 (p90) cc_final: 0.6003 (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: 0.8545 (mp) cc_final: 0.8304 (mp) REVERT: S 249 MET cc_start: 0.7544 (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: 0.4783 time to fit residues: 396.6262 Evaluate side-chains 391 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 3.297 ------------------------------------------------------------------------------- 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: 3.9990 chunk 291 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 196 optimal weight: 0.6980 chunk 155 optimal weight: 0.5980 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: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7580 moved from start: 0.1652 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= 0.208 Angle : 0.571 12.524 43637 Z= 0.298 Chirality : 0.041 0.225 5148 Planarity : 0.005 0.049 5291 Dihedral : 11.721 73.866 5412 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.34 % Allowed : 6.86 % Favored : 91.79 % 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: 1.20 (0.14), residues: 3817 helix: 1.36 (0.11), residues: 2519 sheet: -0.61 (0.35), residues: 165 loop : -0.12 (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 0.026 0.002 PHE A 348 TYR 0.012 0.002 TYR C 227 ARG 0.003 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 552 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 508 time to evaluate : 3.443 Fit side-chains REVERT: A 80 GLN cc_start: 0.8347 (tp40) cc_final: 0.7647 (tt0) REVERT: A 81 GLN cc_start: 0.8200 (tm-30) cc_final: 0.7784 (mt0) REVERT: A 249 MET cc_start: 0.7325 (mmm) cc_final: 0.7098 (mmm) REVERT: A 347 LEU cc_start: 0.8256 (mt) cc_final: 0.7913 (mt) REVERT: C 80 GLN cc_start: 0.8346 (tp40) cc_final: 0.7693 (tt0) REVERT: C 249 MET cc_start: 0.7222 (mmm) cc_final: 0.6992 (mmm) REVERT: E 53 TYR cc_start: 0.6428 (p90) cc_final: 0.6150 (p90) REVERT: E 80 GLN cc_start: 0.8294 (tp40) cc_final: 0.7590 (tt0) REVERT: E 290 ASP cc_start: 0.7605 (m-30) cc_final: 0.7277 (m-30) REVERT: G 80 GLN cc_start: 0.8311 (tp40) cc_final: 0.7696 (tt0) REVERT: G 138 LEU cc_start: 0.8540 (mp) cc_final: 0.8248 (mp) REVERT: I 53 TYR cc_start: 0.6200 (p90) cc_final: 0.5709 (p90) REVERT: I 80 GLN cc_start: 0.8359 (tp40) cc_final: 0.7705 (tt0) REVERT: I 151 ARG cc_start: 0.7394 (ptp-170) cc_final: 0.7000 (ptp-170) REVERT: I 249 MET cc_start: 0.7321 (mmm) cc_final: 0.7086 (mmm) REVERT: K 80 GLN cc_start: 0.8331 (tp40) cc_final: 0.7677 (tt0) REVERT: K 81 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7738 (mt0) REVERT: K 347 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7782 (mt) REVERT: M 80 GLN cc_start: 0.8417 (tp40) cc_final: 0.7783 (tt0) REVERT: M 81 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7630 (mt0) REVERT: O 80 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: O 249 MET cc_start: 0.7249 (mmm) cc_final: 0.7012 (mmm) REVERT: Q 80 GLN cc_start: 0.8343 (tp40) cc_final: 0.7719 (tt0) REVERT: Q 81 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7738 (mt0) REVERT: S 80 GLN cc_start: 0.8351 (tp40) cc_final: 0.7736 (tt0) REVERT: S 81 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7600 (mt0) REVERT: S 249 MET cc_start: 0.7174 (mmm) cc_final: 0.6901 (mmm) REVERT: U 80 GLN cc_start: 0.8300 (tp40) cc_final: 0.7671 (tt0) REVERT: U 81 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7736 (mt0) REVERT: U 138 LEU cc_start: 0.8765 (mp) cc_final: 0.8550 (mp) outliers start: 44 outliers final: 12 residues processed: 515 average time/residue: 0.4635 time to fit residues: 367.0456 Evaluate side-chains 453 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 439 time to evaluate : 3.743 ------------------------------------------------------------------------------- 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 O residue 80 GLN 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: 2.9990 chunk 108 optimal weight: 0.7980 chunk 290 optimal weight: 0.4980 chunk 238 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 350 optimal weight: 0.0970 chunk 378 optimal weight: 0.0000 chunk 311 optimal weight: 1.9990 chunk 347 optimal weight: 0.0170 chunk 119 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 overall best weight: 0.2820 ------------------------------------------------------------------------------- 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** K 148 GLN M 148 GLN ** O 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 148 GLN Q 284 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 32087 Z= 0.152 Angle : 0.507 11.649 43637 Z= 0.263 Chirality : 0.038 0.183 5148 Planarity : 0.004 0.045 5291 Dihedral : 11.624 73.692 5412 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.22 % Allowed : 10.62 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.14), residues: 3817 helix: 1.59 (0.11), residues: 2519 sheet: -0.50 (0.35), residues: 165 loop : 0.04 (0.20), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP E 261 HIS 0.008 0.001 HIS O 275 PHE 0.029 0.002 PHE Q 348 TYR 0.010 0.001 TYR U 53 ARG 0.004 0.000 ARG O 132 *********************** 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 519 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 479 time to evaluate : 3.341 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8237 (tp40) cc_final: 0.7610 (tt0) REVERT: A 347 LEU cc_start: 0.8059 (mt) cc_final: 0.7608 (mt) REVERT: C 80 GLN cc_start: 0.8340 (tp40) cc_final: 0.7722 (tt0) REVERT: C 249 MET cc_start: 0.7234 (mmm) cc_final: 0.6875 (mmm) REVERT: C 346 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7403 (tt0) REVERT: E 80 GLN cc_start: 0.8285 (tp40) cc_final: 0.7653 (tt0) REVERT: E 290 ASP cc_start: 0.7581 (m-30) cc_final: 0.7084 (m-30) REVERT: G 80 GLN cc_start: 0.8277 (tp40) cc_final: 0.7702 (tt0) REVERT: G 138 LEU cc_start: 0.8363 (mp) cc_final: 0.7992 (mp) REVERT: G 249 MET cc_start: 0.7408 (mmm) cc_final: 0.7136 (mmm) REVERT: I 50 GLU cc_start: 0.7201 (tp30) cc_final: 0.6995 (tp30) REVERT: I 53 TYR cc_start: 0.6173 (p90) cc_final: 0.5753 (p90) REVERT: I 80 GLN cc_start: 0.8293 (tp40) cc_final: 0.7715 (tt0) REVERT: I 128 ASP cc_start: 0.7355 (t70) cc_final: 0.7086 (t0) REVERT: K 80 GLN cc_start: 0.8302 (tp40) cc_final: 0.7676 (tt0) REVERT: K 175 THR cc_start: 0.8154 (m) cc_final: 0.7923 (p) REVERT: K 347 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7846 (mt) REVERT: M 80 GLN cc_start: 0.8341 (tp40) cc_final: 0.7745 (tt0) REVERT: O 80 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7695 (tt0) REVERT: O 81 GLN cc_start: 0.8365 (tm-30) cc_final: 0.7707 (mt0) REVERT: O 128 ASP cc_start: 0.7456 (t70) cc_final: 0.7251 (t0) REVERT: Q 80 GLN cc_start: 0.8278 (tp40) cc_final: 0.7702 (tt0) REVERT: Q 346 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7490 (tt0) REVERT: S 80 GLN cc_start: 0.8336 (tp40) cc_final: 0.7787 (tt0) REVERT: S 249 MET cc_start: 0.7151 (mmm) cc_final: 0.6772 (mmm) REVERT: U 80 GLN cc_start: 0.8253 (tp40) cc_final: 0.7658 (tt0) REVERT: U 138 LEU cc_start: 0.8801 (mp) cc_final: 0.8505 (mp) REVERT: U 151 ARG cc_start: 0.7228 (OUTLIER) cc_final: 0.6927 (ptp-170) REVERT: U 249 MET cc_start: 0.7181 (mmm) cc_final: 0.6763 (mmm) outliers start: 40 outliers final: 5 residues processed: 487 average time/residue: 0.4783 time to fit residues: 355.5797 Evaluate side-chains 440 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 432 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain K residue 347 LEU Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain O residue 215 GLU Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 176 ILE 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: 1.9990 chunk 263 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 235 optimal weight: 6.9990 chunk 351 optimal weight: 0.4980 chunk 372 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- 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** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 148 GLN ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN O 275 HIS ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32087 Z= 0.298 Angle : 0.573 11.502 43637 Z= 0.292 Chirality : 0.041 0.183 5148 Planarity : 0.005 0.048 5291 Dihedral : 11.494 73.840 5412 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.20 % Allowed : 11.90 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 3817 helix: 1.46 (0.11), residues: 2519 sheet: -0.39 (0.36), residues: 165 loop : -0.17 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.008 0.002 HIS Q 117 PHE 0.029 0.003 PHE O 348 TYR 0.017 0.002 TYR E 338 ARG 0.004 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 520 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 448 time to evaluate : 3.480 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8367 (tp40) cc_final: 0.7677 (tt0) REVERT: A 249 MET cc_start: 0.7352 (mmm) cc_final: 0.7097 (mmm) REVERT: C 175 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.8000 (p) REVERT: C 249 MET cc_start: 0.7344 (mmm) cc_final: 0.7015 (mmm) REVERT: C 346 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7373 (tt0) REVERT: E 80 GLN cc_start: 0.8364 (tp40) cc_final: 0.7691 (tt0) REVERT: E 128 ASP cc_start: 0.7678 (t70) cc_final: 0.7441 (t0) REVERT: G 138 LEU cc_start: 0.8404 (mp) cc_final: 0.8113 (mp) REVERT: I 53 TYR cc_start: 0.6431 (p90) cc_final: 0.6044 (p90) REVERT: I 128 ASP cc_start: 0.7536 (t70) cc_final: 0.7246 (t0) REVERT: K 347 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7844 (mt) REVERT: M 346 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7384 (tt0) REVERT: O 80 GLN cc_start: 0.8423 (tp40) cc_final: 0.7685 (tt0) REVERT: Q 80 GLN cc_start: 0.8310 (tp40) cc_final: 0.7680 (tt0) REVERT: S 249 MET cc_start: 0.7272 (mmm) cc_final: 0.6917 (mmm) REVERT: U 80 GLN cc_start: 0.8356 (tp40) cc_final: 0.7768 (tt0) REVERT: U 138 LEU cc_start: 0.8765 (mp) cc_final: 0.8512 (mp) REVERT: U 151 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6970 (ptp-170) outliers start: 72 outliers final: 45 residues processed: 459 average time/residue: 0.5047 time to fit residues: 349.4402 Evaluate side-chains 463 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 415 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 275 HIS Chi-restraints excluded: chain A residue 290 ASP 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 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 24 THR Chi-restraints excluded: chain G residue 175 THR Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 113 MET 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 290 ASP Chi-restraints excluded: chain K residue 10 ASP 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 19 LYS Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 175 THR Chi-restraints excluded: chain O residue 10 ASP 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 O residue 290 ASP 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 Q residue 290 ASP Chi-restraints excluded: chain Q residue 358 LEU 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 309 optimal weight: 0.9980 chunk 211 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 277 optimal weight: 0.0270 chunk 153 optimal weight: 7.9990 chunk 317 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 80 GLN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 HIS ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 80 GLN ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS ** U 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2571 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= 0.205 Angle : 0.520 12.540 43637 Z= 0.265 Chirality : 0.039 0.168 5148 Planarity : 0.004 0.051 5291 Dihedral : 11.433 73.786 5412 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.17 % Allowed : 13.94 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 3817 helix: 1.57 (0.11), residues: 2530 sheet: -0.34 (0.36), residues: 165 loop : -0.17 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 261 HIS 0.019 0.001 HIS O 275 PHE 0.031 0.002 PHE I 348 TYR 0.015 0.001 TYR M 61 ARG 0.003 0.000 ARG C 132 *********************** 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 507 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 436 time to evaluate : 3.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.6654 (m-10) cc_final: 0.6309 (m-80) REVERT: A 80 GLN cc_start: 0.8327 (tp40) cc_final: 0.7628 (tt0) REVERT: A 249 MET cc_start: 0.7421 (mmm) cc_final: 0.7167 (mmm) REVERT: C 80 GLN cc_start: 0.8378 (tp40) cc_final: 0.7699 (tt0) REVERT: C 175 THR cc_start: 0.8230 (OUTLIER) cc_final: 0.8019 (p) REVERT: C 249 MET cc_start: 0.7319 (mmm) cc_final: 0.6990 (mmm) REVERT: C 346 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7293 (tt0) REVERT: E 80 GLN cc_start: 0.8333 (tp40) cc_final: 0.7752 (tt0) REVERT: G 80 GLN cc_start: 0.8348 (tp40) cc_final: 0.7764 (tt0) REVERT: G 138 LEU cc_start: 0.8401 (mp) cc_final: 0.8104 (mp) REVERT: I 53 TYR cc_start: 0.6342 (p90) cc_final: 0.6097 (p90) REVERT: I 80 GLN cc_start: 0.8346 (tp40) cc_final: 0.7744 (tt0) REVERT: I 128 ASP cc_start: 0.7505 (t70) cc_final: 0.7210 (t0) REVERT: K 80 GLN cc_start: 0.8412 (tp40) cc_final: 0.7767 (tt0) REVERT: K 347 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7786 (mt) REVERT: M 26 LYS cc_start: 0.7638 (mmtp) cc_final: 0.7436 (mmtm) REVERT: M 80 GLN cc_start: 0.8434 (tp40) cc_final: 0.7825 (tt0) REVERT: O 23 TYR cc_start: 0.6641 (m-80) cc_final: 0.6419 (m-80) REVERT: O 80 GLN cc_start: 0.8273 (tp40) cc_final: 0.7719 (tt0) REVERT: O 346 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7246 (tm-30) REVERT: Q 80 GLN cc_start: 0.8288 (tp40) cc_final: 0.7691 (tt0) REVERT: S 80 GLN cc_start: 0.8341 (tp40) cc_final: 0.7823 (tt0) REVERT: S 249 MET cc_start: 0.7211 (mmm) cc_final: 0.6888 (mmm) REVERT: U 80 GLN cc_start: 0.8360 (tp40) cc_final: 0.7797 (tt0) REVERT: U 138 LEU cc_start: 0.8743 (mp) cc_final: 0.8402 (mp) REVERT: U 151 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.7021 (ptp-170) outliers start: 71 outliers final: 43 residues processed: 466 average time/residue: 0.4979 time to fit residues: 349.3947 Evaluate side-chains 451 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 405 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 275 HIS 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 275 HIS 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 G residue 332 LEU Chi-restraints excluded: chain I residue 17 ILE 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 K residue 24 THR 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 215 GLU Chi-restraints excluded: chain M residue 290 ASP 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 Q residue 19 LYS 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 290 ASP Chi-restraints excluded: chain S residue 24 THR 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 U residue 3 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 125 optimal weight: 0.5980 chunk 335 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 218 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 372 optimal weight: 3.9990 chunk 309 optimal weight: 0.7980 chunk 172 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 148 GLN ** S 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2749 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= 0.178 Angle : 0.512 12.734 43637 Z= 0.258 Chirality : 0.037 0.135 5148 Planarity : 0.004 0.050 5291 Dihedral : 11.429 73.730 5412 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.92 % Allowed : 14.89 % Favored : 83.19 % 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: 1.53 (0.14), residues: 3817 helix: 1.72 (0.11), residues: 2530 sheet: -1.22 (0.31), residues: 209 loop : -0.09 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 261 HIS 0.013 0.001 HIS O 275 PHE 0.030 0.002 PHE S 348 TYR 0.015 0.001 TYR K 338 ARG 0.005 0.000 ARG O 151 *********************** 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 503 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 440 time to evaluate : 3.471 Fit side-chains REVERT: A 78 ARG cc_start: 0.7206 (tpp-160) cc_final: 0.6686 (tpp-160) REVERT: A 80 GLN cc_start: 0.8334 (tp40) cc_final: 0.7721 (tt0) REVERT: C 80 GLN cc_start: 0.8382 (tp40) cc_final: 0.7753 (tt0) REVERT: C 175 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8054 (p) REVERT: C 249 MET cc_start: 0.7292 (mmm) cc_final: 0.6960 (mmm) REVERT: E 80 GLN cc_start: 0.8319 (tp40) cc_final: 0.7771 (tt0) REVERT: E 249 MET cc_start: 0.7524 (mmm) cc_final: 0.7192 (mmm) REVERT: G 80 GLN cc_start: 0.8311 (tp40) cc_final: 0.7815 (tt0) REVERT: G 138 LEU cc_start: 0.8426 (mp) cc_final: 0.8113 (mp) REVERT: I 50 GLU cc_start: 0.7354 (tp30) cc_final: 0.7143 (mm-30) REVERT: I 80 GLN cc_start: 0.8312 (tp40) cc_final: 0.7762 (tt0) REVERT: I 128 ASP cc_start: 0.7499 (t70) cc_final: 0.7207 (t0) REVERT: K 80 GLN cc_start: 0.8411 (tp40) cc_final: 0.7832 (tt0) REVERT: M 80 GLN cc_start: 0.8347 (tp40) cc_final: 0.7713 (tt0) REVERT: O 80 GLN cc_start: 0.8260 (tp40) cc_final: 0.7710 (tt0) REVERT: O 249 MET cc_start: 0.7329 (mmm) cc_final: 0.7084 (mmm) REVERT: Q 80 GLN cc_start: 0.8293 (tp40) cc_final: 0.7705 (tt0) REVERT: S 80 GLN cc_start: 0.8280 (tp40) cc_final: 0.7802 (tt0) REVERT: S 249 MET cc_start: 0.7227 (mmm) cc_final: 0.6934 (mmm) REVERT: U 80 GLN cc_start: 0.8321 (tp40) cc_final: 0.7765 (tt0) REVERT: U 138 LEU cc_start: 0.8432 (mp) cc_final: 0.8137 (mp) REVERT: U 151 ARG cc_start: 0.7288 (OUTLIER) cc_final: 0.7028 (ptp-170) outliers start: 63 outliers final: 46 residues processed: 459 average time/residue: 0.4926 time to fit residues: 341.2300 Evaluate side-chains 464 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 416 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 275 HIS 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 C residue 275 HIS 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 G residue 275 HIS Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 113 MET 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 K residue 113 MET Chi-restraints excluded: chain K residue 175 THR Chi-restraints excluded: chain M residue 19 LYS Chi-restraints excluded: chain M residue 215 GLU Chi-restraints excluded: chain M residue 290 ASP 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 215 GLU Chi-restraints excluded: chain O residue 275 HIS 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 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 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 275 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 359 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 272 optimal weight: 4.9990 chunk 210 optimal weight: 0.7980 chunk 313 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 232 optimal weight: 0.6980 chunk 226 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 148 GLN E 148 GLN ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 275 HIS ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 275 HIS ** Q 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32087 Z= 0.255 Angle : 0.557 12.976 43637 Z= 0.278 Chirality : 0.039 0.137 5148 Planarity : 0.004 0.049 5291 Dihedral : 11.375 73.849 5412 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.59 % Allowed : 14.92 % Favored : 82.49 % 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: 1.61 (0.11), residues: 2541 sheet: -0.30 (0.36), residues: 165 loop : -0.29 (0.20), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 261 HIS 0.020 0.001 HIS O 275 PHE 0.032 0.003 PHE G 348 TYR 0.021 0.002 TYR K 338 ARG 0.003 0.000 ARG Q 151 *********************** 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 508 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 423 time to evaluate : 3.532 Fit side-chains REVERT: A 78 ARG cc_start: 0.7243 (tpp-160) cc_final: 0.6717 (tpp-160) REVERT: A 80 GLN cc_start: 0.8355 (tp40) cc_final: 0.7698 (tt0) REVERT: C 80 GLN cc_start: 0.8421 (tp40) cc_final: 0.7751 (tt0) REVERT: C 175 THR cc_start: 0.8283 (OUTLIER) cc_final: 0.8073 (p) REVERT: C 249 MET cc_start: 0.7329 (mmm) cc_final: 0.6992 (mmm) REVERT: E 80 GLN cc_start: 0.8344 (tp40) cc_final: 0.7763 (tt0) REVERT: G 80 GLN cc_start: 0.8358 (tp40) cc_final: 0.7814 (tt0) REVERT: G 138 LEU cc_start: 0.8461 (mp) cc_final: 0.8151 (mp) REVERT: I 128 ASP cc_start: 0.7488 (t70) cc_final: 0.7206 (t0) REVERT: I 249 MET cc_start: 0.7321 (mmm) cc_final: 0.6939 (mmm) REVERT: K 113 MET cc_start: 0.4401 (OUTLIER) cc_final: 0.3833 (mtm) REVERT: M 80 GLN cc_start: 0.8378 (tp40) cc_final: 0.7748 (tt0) REVERT: O 80 GLN cc_start: 0.8286 (tp40) cc_final: 0.7708 (tt0) REVERT: O 249 MET cc_start: 0.7345 (mmm) cc_final: 0.7080 (mmm) REVERT: Q 80 GLN cc_start: 0.8314 (tp40) cc_final: 0.7693 (tt0) REVERT: S 80 GLN cc_start: 0.8298 (tp40) cc_final: 0.7748 (tt0) REVERT: S 249 MET cc_start: 0.7253 (mmm) cc_final: 0.6908 (mmm) REVERT: U 80 GLN cc_start: 0.8365 (tp40) cc_final: 0.7805 (tt0) REVERT: U 138 LEU cc_start: 0.8443 (mp) cc_final: 0.8129 (mp) REVERT: U 151 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6951 (ptp-170) outliers start: 85 outliers final: 71 residues processed: 450 average time/residue: 0.5529 time to fit residues: 377.2833 Evaluate side-chains 482 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 408 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR 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 275 HIS 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 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 E residue 190 VAL Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 10 ASP Chi-restraints excluded: chain G residue 24 THR 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 G residue 332 LEU Chi-restraints excluded: chain I residue 3 LEU Chi-restraints excluded: chain I residue 17 ILE Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 113 MET 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 290 ASP Chi-restraints excluded: chain K residue 10 ASP 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 K residue 195 LEU Chi-restraints excluded: chain K residue 290 ASP 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 290 ASP 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 Q residue 19 LYS Chi-restraints excluded: chain Q residue 24 THR 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 Q residue 275 HIS Chi-restraints excluded: chain Q residue 290 ASP Chi-restraints excluded: chain S residue 24 THR 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 3 LEU 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 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: 3.9990 chunk 148 optimal weight: 1.9990 chunk 221 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 235 optimal weight: 0.5980 chunk 252 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 291 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 80 GLN I 117 HIS ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 275 HIS U 275 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2891 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= 0.201 Angle : 0.534 13.413 43637 Z= 0.267 Chirality : 0.038 0.132 5148 Planarity : 0.004 0.050 5291 Dihedral : 11.374 73.777 5412 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.29 % Allowed : 15.99 % Favored : 81.73 % 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: 1.49 (0.14), residues: 3817 helix: 1.70 (0.11), residues: 2541 sheet: -1.17 (0.31), residues: 209 loop : -0.19 (0.21), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 261 HIS 0.017 0.001 HIS O 275 PHE 0.032 0.002 PHE C 348 TYR 0.020 0.001 TYR I 354 ARG 0.004 0.000 ARG O 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 508 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 433 time to evaluate : 3.768 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8333 (tp40) cc_final: 0.7734 (tt0) REVERT: A 151 ARG cc_start: 0.6509 (mtt90) cc_final: 0.6178 (mtm-85) REVERT: A 200 ARG cc_start: 0.6984 (ptp90) cc_final: 0.6780 (mtm-85) REVERT: A 249 MET cc_start: 0.7378 (tpp) cc_final: 0.7171 (mmm) REVERT: C 80 GLN cc_start: 0.8406 (tp40) cc_final: 0.7738 (tt0) REVERT: C 175 THR cc_start: 0.8295 (OUTLIER) cc_final: 0.8081 (p) REVERT: C 249 MET cc_start: 0.7326 (mmm) cc_final: 0.6997 (mmm) REVERT: E 80 GLN cc_start: 0.8316 (tp40) cc_final: 0.7768 (tt0) REVERT: E 249 MET cc_start: 0.7528 (mmm) cc_final: 0.7261 (mmm) REVERT: G 80 GLN cc_start: 0.8324 (tp40) cc_final: 0.7813 (tt0) REVERT: G 138 LEU cc_start: 0.8452 (mp) cc_final: 0.8145 (mp) REVERT: I 80 GLN cc_start: 0.8360 (tp40) cc_final: 0.7754 (tt0) REVERT: I 128 ASP cc_start: 0.7470 (t70) cc_final: 0.7209 (t0) REVERT: K 80 GLN cc_start: 0.8410 (tp40) cc_final: 0.7755 (tt0) REVERT: K 113 MET cc_start: 0.3969 (mtp) cc_final: 0.3513 (mtm) REVERT: M 80 GLN cc_start: 0.8368 (tp40) cc_final: 0.7723 (tt0) REVERT: O 80 GLN cc_start: 0.8303 (tp40) cc_final: 0.7729 (tt0) REVERT: O 249 MET cc_start: 0.7315 (mmm) cc_final: 0.7052 (mmm) REVERT: Q 80 GLN cc_start: 0.8311 (tp40) cc_final: 0.7692 (tt0) REVERT: Q 151 ARG cc_start: 0.6893 (mtt90) cc_final: 0.6389 (mtm-85) REVERT: S 80 GLN cc_start: 0.8262 (tp40) cc_final: 0.7759 (tt0) REVERT: S 249 MET cc_start: 0.7209 (mmm) cc_final: 0.6889 (mmm) REVERT: U 80 GLN cc_start: 0.8314 (tp40) cc_final: 0.7763 (tt0) REVERT: U 138 LEU cc_start: 0.8430 (mp) cc_final: 0.8105 (mp) REVERT: U 151 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6986 (ptp-170) outliers start: 75 outliers final: 58 residues processed: 457 average time/residue: 0.5028 time to fit residues: 345.5638 Evaluate side-chains 479 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 419 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 24 THR 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 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU 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 C residue 275 HIS Chi-restraints excluded: chain E residue 94 LEU 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 24 THR 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 G residue 332 LEU Chi-restraints excluded: chain I residue 3 LEU 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 K residue 175 THR Chi-restraints excluded: chain K residue 195 LEU 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 290 ASP 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 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 Q residue 275 HIS Chi-restraints excluded: chain S residue 22 GLN Chi-restraints excluded: chain S residue 24 THR 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 337 optimal weight: 0.4980 chunk 355 optimal weight: 9.9990 chunk 324 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 208 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 271 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 312 optimal weight: 0.8980 chunk 327 optimal weight: 0.9990 chunk 344 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32087 Z= 0.176 Angle : 0.532 15.492 43637 Z= 0.262 Chirality : 0.037 0.134 5148 Planarity : 0.004 0.050 5291 Dihedral : 11.428 73.729 5412 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.71 % Allowed : 16.93 % 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: 1.58 (0.14), residues: 3817 helix: 1.78 (0.11), residues: 2541 sheet: -1.16 (0.31), residues: 209 loop : -0.16 (0.21), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 123 HIS 0.008 0.001 HIS O 117 PHE 0.032 0.002 PHE G 348 TYR 0.019 0.001 TYR S 23 ARG 0.005 0.000 ARG M 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 500 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 444 time to evaluate : 4.083 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8342 (tp40) cc_final: 0.7767 (tt0) REVERT: A 200 ARG cc_start: 0.6973 (ptp90) cc_final: 0.6756 (mtm-85) REVERT: A 249 MET cc_start: 0.7412 (tpp) cc_final: 0.7203 (mmm) REVERT: C 80 GLN cc_start: 0.8393 (tp40) cc_final: 0.7744 (tt0) REVERT: C 117 HIS cc_start: 0.7675 (t-90) cc_final: 0.7376 (t70) REVERT: C 175 THR cc_start: 0.8288 (OUTLIER) cc_final: 0.8087 (p) REVERT: C 249 MET cc_start: 0.7309 (mmm) cc_final: 0.6980 (mmm) REVERT: C 295 MET cc_start: 0.8451 (mtm) cc_final: 0.8177 (mtp) REVERT: E 80 GLN cc_start: 0.8309 (tp40) cc_final: 0.7780 (tt0) REVERT: E 249 MET cc_start: 0.7517 (mmm) cc_final: 0.7214 (mmm) REVERT: G 80 GLN cc_start: 0.8292 (tp40) cc_final: 0.7781 (tt0) REVERT: G 138 LEU cc_start: 0.8446 (mp) cc_final: 0.8147 (mp) REVERT: I 80 GLN cc_start: 0.8345 (tp40) cc_final: 0.7757 (tt0) REVERT: I 128 ASP cc_start: 0.7446 (t70) cc_final: 0.7192 (t0) REVERT: I 249 MET cc_start: 0.7380 (mmm) cc_final: 0.7081 (mmm) REVERT: K 80 GLN cc_start: 0.8430 (tp40) cc_final: 0.7811 (tt0) REVERT: K 113 MET cc_start: 0.3695 (mtp) cc_final: 0.3269 (mtm) REVERT: M 80 GLN cc_start: 0.8355 (tp40) cc_final: 0.7784 (tt0) REVERT: M 84 ARG cc_start: 0.7617 (ttp-110) cc_final: 0.7335 (ttp-110) REVERT: O 26 LYS cc_start: 0.7602 (mmtp) cc_final: 0.7308 (mmtm) REVERT: O 80 GLN cc_start: 0.8267 (tp40) cc_final: 0.7706 (tt0) REVERT: O 249 MET cc_start: 0.7286 (mmm) cc_final: 0.7052 (mmm) REVERT: Q 80 GLN cc_start: 0.8296 (tp40) cc_final: 0.7709 (tt0) REVERT: Q 151 ARG cc_start: 0.6954 (mtt90) cc_final: 0.6426 (mtm-85) REVERT: Q 249 MET cc_start: 0.7116 (mmm) cc_final: 0.6904 (tpt) REVERT: S 80 GLN cc_start: 0.8240 (tp40) cc_final: 0.7768 (tt0) REVERT: S 249 MET cc_start: 0.7196 (mmm) cc_final: 0.6866 (mmm) REVERT: U 78 ARG cc_start: 0.7130 (tpp-160) cc_final: 0.6606 (tpp-160) REVERT: U 80 GLN cc_start: 0.8274 (tp40) cc_final: 0.7770 (tt0) REVERT: U 138 LEU cc_start: 0.8383 (mp) cc_final: 0.8079 (mp) outliers start: 56 outliers final: 48 residues processed: 464 average time/residue: 0.5396 time to fit residues: 383.9408 Evaluate side-chains 479 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 430 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE 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 275 HIS Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 275 HIS Chi-restraints excluded: chain E residue 94 LEU 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 G residue 332 LEU Chi-restraints excluded: chain I residue 3 LEU 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 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 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 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 22 GLN Chi-restraints excluded: chain S residue 24 THR 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 U residue 3 LEU Chi-restraints excluded: chain U residue 113 MET 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: 0.7980 chunk 223 optimal weight: 8.9990 chunk 173 optimal weight: 0.7980 chunk 254 optimal weight: 6.9990 chunk 383 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 275 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32087 Z= 0.237 Angle : 0.567 17.124 43637 Z= 0.278 Chirality : 0.039 0.130 5148 Planarity : 0.004 0.055 5291 Dihedral : 11.552 73.820 5412 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.68 % Allowed : 17.24 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.14), residues: 3817 helix: 1.69 (0.11), residues: 2541 sheet: -1.16 (0.31), residues: 209 loop : -0.22 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 261 HIS 0.017 0.001 HIS U 275 PHE 0.034 0.003 PHE S 348 TYR 0.027 0.002 TYR U 23 ARG 0.006 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: 55 poor density : 424 time to evaluate : 3.176 Fit side-chains revert: symmetry clash REVERT: A 80 GLN cc_start: 0.8350 (tp40) cc_final: 0.7752 (tt0) REVERT: A 200 ARG cc_start: 0.6982 (ptp90) cc_final: 0.6775 (mtm-85) REVERT: A 249 MET cc_start: 0.7489 (tpp) cc_final: 0.7261 (mmm) REVERT: C 80 GLN cc_start: 0.8414 (tp40) cc_final: 0.7749 (tt0) REVERT: C 175 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.8062 (p) REVERT: C 249 MET cc_start: 0.7328 (mmm) cc_final: 0.7008 (mmm) REVERT: E 78 ARG cc_start: 0.7450 (tpp-160) cc_final: 0.7027 (tpp-160) REVERT: E 80 GLN cc_start: 0.8332 (tp40) cc_final: 0.7791 (tt0) REVERT: E 249 MET cc_start: 0.7547 (mmm) cc_final: 0.7248 (mmm) REVERT: G 138 LEU cc_start: 0.8447 (mp) cc_final: 0.8126 (mp) REVERT: I 128 ASP cc_start: 0.7433 (t70) cc_final: 0.7194 (t0) REVERT: I 249 MET cc_start: 0.7386 (mmm) cc_final: 0.7050 (mmm) REVERT: K 80 GLN cc_start: 0.8420 (tp40) cc_final: 0.7802 (tt0) REVERT: K 113 MET cc_start: 0.3855 (mtp) cc_final: 0.3402 (mtm) REVERT: M 84 ARG cc_start: 0.7629 (ttp-110) cc_final: 0.7340 (ttp-110) REVERT: O 26 LYS cc_start: 0.7642 (mmtp) cc_final: 0.7348 (mmtm) REVERT: O 80 GLN cc_start: 0.8332 (tp40) cc_final: 0.7751 (tt0) REVERT: O 113 MET cc_start: 0.4411 (OUTLIER) cc_final: 0.4143 (mtm) REVERT: O 249 MET cc_start: 0.7327 (mmm) cc_final: 0.7080 (mmm) REVERT: Q 80 GLN cc_start: 0.8306 (tp40) cc_final: 0.7686 (tt0) REVERT: S 80 GLN cc_start: 0.8332 (tp40) cc_final: 0.7805 (tt0) REVERT: S 249 MET cc_start: 0.7237 (mmm) cc_final: 0.6905 (mmm) REVERT: U 80 GLN cc_start: 0.8322 (tp40) cc_final: 0.7797 (tt0) REVERT: U 138 LEU cc_start: 0.8382 (mp) cc_final: 0.8079 (mp) outliers start: 55 outliers final: 47 residues processed: 445 average time/residue: 0.5004 time to fit residues: 332.6808 Evaluate side-chains 468 residues out of total 3278 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 419 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 24 THR 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 275 HIS Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 10 ASP 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 275 HIS Chi-restraints excluded: chain E residue 94 LEU 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 G residue 332 LEU Chi-restraints excluded: chain I residue 3 LEU 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 190 VAL 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 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 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 22 GLN Chi-restraints excluded: chain S residue 24 THR 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 U residue 3 LEU 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: 0.9980 chunk 325 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 281 optimal weight: 0.4980 chunk 45 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 305 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 314 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 80 GLN G 117 HIS G 275 HIS I 80 GLN ** I 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 GLN ** M 275 HIS ** 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 ** U 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.166728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139279 restraints weight = 42700.559| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.32 r_work: 0.3409 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32087 Z= 0.195 Angle : 0.555 17.229 43637 Z= 0.271 Chirality : 0.038 0.251 5148 Planarity : 0.004 0.061 5291 Dihedral : 11.649 73.759 5412 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.43 % Allowed : 17.72 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.14), residues: 3817 helix: 1.75 (0.11), residues: 2541 sheet: -1.19 (0.31), residues: 209 loop : -0.19 (0.21), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP O 261 HIS 0.011 0.001 HIS G 275 PHE 0.034 0.002 PHE S 348 TYR 0.030 0.001 TYR K 23 ARG 0.006 0.000 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7680.62 seconds wall clock time: 137 minutes 41.56 seconds (8261.56 seconds total)