Starting phenix.real_space_refine on Sat Apr 13 11:11:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/04_2024/8pdl_17613.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/04_2024/8pdl_17613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/04_2024/8pdl_17613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/04_2024/8pdl_17613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/04_2024/8pdl_17613.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/04_2024/8pdl_17613.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 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 70 5.49 5 S 110 5.16 5 C 17820 2.51 5 N 4950 2.21 5 O 5660 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 GLU 181": "OE1" <-> "OE2" Residue "A ASP 202": "OD1" <-> "OD2" Residue "A TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "C TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ASP 202": "OD1" <-> "OD2" Residue "C TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "E TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "E GLU 360": "OE1" <-> "OE2" Residue "G TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G ASP 202": "OD1" <-> "OD2" Residue "G TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "I TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 181": "OE1" <-> "OE2" Residue "I ASP 202": "OD1" <-> "OD2" Residue "I TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "I GLU 360": "OE1" <-> "OE2" Residue "K TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 181": "OE1" <-> "OE2" Residue "K ASP 202": "OD1" <-> "OD2" Residue "K TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "K GLU 360": "OE1" <-> "OE2" Residue "M TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 181": "OE1" <-> "OE2" Residue "M ASP 202": "OD1" <-> "OD2" Residue "M TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "M GLU 360": "OE1" <-> "OE2" Residue "O TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 181": "OE1" <-> "OE2" Residue "O ASP 202": "OD1" <-> "OD2" Residue "O TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "O GLU 360": "OE1" <-> "OE2" Residue "Q TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 181": "OE1" <-> "OE2" Residue "Q ASP 202": "OD1" <-> "OD2" Residue "Q TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "Q GLU 360": "OE1" <-> "OE2" Residue "S TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 181": "OE1" <-> "OE2" Residue "S ASP 202": "OD1" <-> "OD2" Residue "S TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 215": "OE1" <-> "OE2" 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 346": "OE1" <-> "OE2" Residue "S GLU 360": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28610 Number of models: 1 Model: "" Number of chains: 20 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} Time building chain proxies: 14.51, per 1000 atoms: 0.51 Number of scatterers: 28610 At special positions: 0 Unit cell: (192.15, 183.75, 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 110 16.00 P 70 15.00 O 5660 8.00 N 4950 7.00 C 17820 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.11 Conformation dependent library (CDL) restraints added in 5.0 seconds 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6520 Finding SS restraints... Secondary structure from input PDB file: 190 helices and 20 sheets defined 70.1% alpha, 2.3% beta 0 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 8.76 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 removed outlier: 3.645A 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: 3.990A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.871A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'C' and resid 9 through 20 removed outlier: 3.645A 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: 3.990A 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: 3.950A 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: 3.698A 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: 3.630A 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: 4.716A pdb=" N LYS C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN C 284 " --> pdb=" O ALA C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.871A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 301 through 306 Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 361 Processing helix chain 'E' and resid 9 through 20 removed outlier: 3.645A 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: 3.989A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN E 284 " --> pdb=" O ALA E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.872A 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 301 through 306 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: 3.645A 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: 3.989A 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: 3.950A 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: 3.698A 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: 3.630A 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: 4.715A pdb=" N LYS G 283 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.870A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 301 through 306 Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 361 Processing helix chain 'I' and resid 9 through 20 removed outlier: 3.645A 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: 3.990A 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: 3.950A 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: 3.698A 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: 3.631A 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: 4.716A pdb=" N LYS I 283 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN I 284 " --> pdb=" O ALA I 280 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.990A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS K 283 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN K 284 " --> pdb=" O ALA K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.990A 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: 3.949A 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: 3.698A 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: 3.630A 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: 4.716A pdb=" N LYS M 283 " --> pdb=" O GLN M 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN M 284 " --> pdb=" O ALA M 280 " (cutoff:3.500A) Processing helix chain 'M' and resid 297 through 300 removed outlier: 3.871A pdb=" N GLY M 300 " --> pdb=" O PRO M 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 297 through 300' Processing helix chain 'M' and resid 301 through 306 Processing helix chain 'M' and resid 318 through 332 Processing helix chain 'M' and resid 344 through 361 Processing helix chain 'O' and resid 9 through 20 removed outlier: 3.645A 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: 3.989A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.716A pdb=" N LYS O 283 " --> pdb=" O GLN O 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN O 284 " --> pdb=" O ALA O 280 " (cutoff:3.500A) Processing helix chain 'O' and resid 297 through 300 removed outlier: 3.871A 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 301 through 306 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: 3.645A 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: 3.989A 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: 3.950A 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: 3.698A 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: 3.630A 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: 4.715A pdb=" N LYS Q 283 " --> pdb=" O GLN Q 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN Q 284 " --> pdb=" O ALA Q 280 " (cutoff:3.500A) Processing helix chain 'Q' and resid 297 through 300 removed outlier: 3.870A 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 301 through 306 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: 3.645A 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: 3.990A 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: 3.950A 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: 3.699A 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: 3.630A 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: 4.715A pdb=" N LYS S 283 " --> pdb=" O GLN S 279 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN S 284 " --> pdb=" O ALA S 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 297 through 300 removed outlier: 3.871A pdb=" N GLY S 300 " --> pdb=" O PRO S 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 297 through 300' Processing helix chain 'S' and resid 301 through 306 Processing helix chain 'S' and resid 318 through 332 Processing helix chain 'S' and resid 344 through 361 Processing sheet with id= 1, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.715A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.714A 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: 6.218A 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: 3.715A 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: 6.218A 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: 3.713A pdb=" N ARG S 96 " --> pdb=" O ASP S 115 " (cutoff:3.500A) 1680 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 9.71 Time building geometry restraints manager: 12.13 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: 9127 1.34 - 1.45: 4088 1.45 - 1.57: 15635 1.57 - 1.69: 130 1.69 - 1.80: 190 Bond restraints: 29170 Sorted by residual: bond pdb=" CB VAL A 325 " pdb=" CG1 VAL A 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 bond pdb=" CB VAL K 325 " pdb=" CG1 VAL K 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.44e+00 bond pdb=" CB VAL G 325 " pdb=" CG1 VAL G 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB VAL Q 325 " pdb=" CG1 VAL Q 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.42e+00 bond pdb=" CB VAL S 325 " pdb=" CG1 VAL S 325 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.40e+00 ... (remaining 29165 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.35: 860 106.35 - 113.27: 16255 113.27 - 120.19: 11147 120.19 - 127.11: 11208 127.11 - 134.02: 200 Bond angle restraints: 39670 Sorted by residual: angle pdb=" CA PRO C 319 " pdb=" N PRO C 319 " pdb=" CD PRO C 319 " ideal model delta sigma weight residual 112.00 106.36 5.64 1.40e+00 5.10e-01 1.62e+01 angle pdb=" CA PRO M 319 " pdb=" N PRO M 319 " pdb=" CD PRO M 319 " ideal model delta sigma weight residual 112.00 106.36 5.64 1.40e+00 5.10e-01 1.62e+01 angle pdb=" CA PRO Q 319 " pdb=" N PRO Q 319 " pdb=" CD PRO Q 319 " ideal model delta sigma weight residual 112.00 106.38 5.62 1.40e+00 5.10e-01 1.61e+01 angle pdb=" CA PRO K 319 " pdb=" N PRO K 319 " pdb=" CD PRO K 319 " ideal model delta sigma weight residual 112.00 106.40 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" CA PRO A 319 " pdb=" N PRO A 319 " pdb=" CD PRO A 319 " ideal model delta sigma weight residual 112.00 106.40 5.60 1.40e+00 5.10e-01 1.60e+01 ... (remaining 39665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 15595 16.10 - 32.19: 1785 32.19 - 48.29: 320 48.29 - 64.39: 130 64.39 - 80.48: 130 Dihedral angle restraints: 17960 sinusoidal: 7800 harmonic: 10160 Sorted by residual: dihedral pdb=" CA TYR M 59 " pdb=" C TYR M 59 " pdb=" N LYS M 60 " pdb=" CA LYS M 60 " ideal model delta harmonic sigma weight residual 180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA TYR E 59 " pdb=" C TYR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR O 59 " pdb=" C TYR O 59 " pdb=" N LYS O 60 " pdb=" CA LYS O 60 " ideal model delta harmonic sigma weight residual -180.00 -163.46 -16.54 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 17957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3064 0.046 - 0.091: 1138 0.091 - 0.137: 376 0.137 - 0.183: 72 0.183 - 0.229: 30 Chirality restraints: 4680 Sorted by residual: chirality pdb=" CB VAL G 35 " pdb=" CA VAL G 35 " pdb=" CG1 VAL G 35 " pdb=" CG2 VAL G 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL Q 35 " pdb=" CA VAL Q 35 " pdb=" CG1 VAL Q 35 " pdb=" CG2 VAL Q 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 4677 not shown) Planarity restraints: 4810 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS I 318 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO I 319 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO I 319 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO I 319 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS S 318 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO S 319 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO S 319 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO S 319 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS K 318 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.79e+01 pdb=" N PRO K 319 " 0.228 5.00e-02 4.00e+02 pdb=" CA PRO K 319 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO K 319 " -0.070 5.00e-02 4.00e+02 ... (remaining 4807 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.72: 70 1.72 - 2.51: 280 2.51 - 3.31: 35123 3.31 - 4.10: 72943 4.10 - 4.90: 137795 Warning: very small nonbonded interaction distances. Nonbonded interactions: 246211 Sorted by model distance: nonbonded pdb=" P C B 71 " pdb=" O3' C T 77 " model vdw 0.922 3.400 nonbonded pdb=" O3' C J 77 " pdb=" P C L 71 " model vdw 0.922 3.400 nonbonded pdb=" O3' C H 77 " pdb=" P C J 71 " model vdw 0.922 3.400 nonbonded pdb=" O3' C R 77 " pdb=" P C T 71 " model vdw 0.922 3.400 nonbonded pdb=" O3' C B 77 " pdb=" P C D 71 " model vdw 0.922 3.400 ... (remaining 246206 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' } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.170 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: 14.800 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 79.380 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.009 0.062 29170 Z= 0.552 Angle : 0.831 6.076 39670 Z= 0.466 Chirality : 0.055 0.229 4680 Planarity : 0.009 0.132 4810 Dihedral : 15.938 80.482 11440 Min Nonbonded Distance : 0.922 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 0.63 (0.14), residues: 3470 helix: 0.97 (0.11), residues: 2240 sheet: -1.09 (0.35), residues: 150 loop : -0.33 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 261 HIS 0.008 0.002 HIS G 7 PHE 0.017 0.004 PHE M 244 TYR 0.036 0.003 TYR M 198 ARG 0.008 0.001 ARG O 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 TYR cc_start: 0.9080 (m-10) cc_final: 0.8865 (m-10) REVERT: I 208 ARG cc_start: 0.7930 (tpt90) cc_final: 0.7726 (tpt170) REVERT: Q 13 TYR cc_start: 0.9080 (m-10) cc_final: 0.8866 (m-10) REVERT: S 208 ARG cc_start: 0.7931 (tpt90) cc_final: 0.7718 (tpt170) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.4285 time to fit residues: 219.6120 Evaluate side-chains 264 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 0.9990 chunk 265 optimal weight: 0.5980 chunk 147 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 178 optimal weight: 0.6980 chunk 141 optimal weight: 0.4980 chunk 274 optimal weight: 0.5980 chunk 106 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 317 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN C 306 GLN E 306 GLN G 306 GLN I 306 GLN K 306 GLN M 306 GLN O 306 GLN Q 306 GLN S 306 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29170 Z= 0.186 Angle : 0.525 9.570 39670 Z= 0.278 Chirality : 0.039 0.128 4680 Planarity : 0.005 0.071 4810 Dihedral : 11.830 74.014 4920 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.07 % Allowed : 5.64 % Favored : 93.29 % 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: 1.27 (0.14), residues: 3470 helix: 1.52 (0.11), residues: 2300 sheet: -1.61 (0.28), residues: 190 loop : -0.09 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 261 HIS 0.003 0.001 HIS E 7 PHE 0.010 0.002 PHE I 224 TYR 0.019 0.002 TYR C 354 ARG 0.004 0.000 ARG Q 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 307 time to evaluate : 3.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 113 MET cc_start: 0.5033 (mmm) cc_final: 0.4620 (mmt) REVERT: I 26 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8111 (mtmm) REVERT: S 26 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8112 (mtmm) REVERT: S 216 GLN cc_start: 0.7648 (mt0) cc_final: 0.7402 (mt0) outliers start: 32 outliers final: 22 residues processed: 331 average time/residue: 0.4269 time to fit residues: 224.4407 Evaluate side-chains 256 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 234 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 88 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 88 SER Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 343 optimal weight: 0.7980 chunk 283 optimal weight: 4.9990 chunk 315 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 255 optimal weight: 0.0470 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 275 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29170 Z= 0.275 Angle : 0.550 10.467 39670 Z= 0.283 Chirality : 0.041 0.157 4680 Planarity : 0.005 0.055 4810 Dihedral : 11.593 74.395 4920 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.54 % Allowed : 8.19 % Favored : 90.27 % 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 (0.15), residues: 3470 helix: 1.46 (0.11), residues: 2300 sheet: -1.65 (0.27), residues: 190 loop : -0.13 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 261 HIS 0.004 0.001 HIS E 7 PHE 0.010 0.002 PHE M 169 TYR 0.017 0.002 TYR C 354 ARG 0.004 0.000 ARG O 208 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 274 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4729 (mmm) cc_final: 0.4471 (mmt) REVERT: A 341 ARG cc_start: 0.5966 (mpt-90) cc_final: 0.5727 (mpt90) REVERT: C 272 MET cc_start: 0.6661 (mmm) cc_final: 0.6423 (mmp) REVERT: E 341 ARG cc_start: 0.6217 (mpt-90) cc_final: 0.6000 (mpt90) REVERT: G 113 MET cc_start: 0.4841 (mmm) cc_final: 0.4477 (mmt) REVERT: G 272 MET cc_start: 0.6432 (mmm) cc_final: 0.6193 (mmm) REVERT: I 26 LYS cc_start: 0.8505 (mtmm) cc_final: 0.8258 (mtmm) REVERT: I 46 LEU cc_start: 0.8145 (tp) cc_final: 0.7925 (tp) REVERT: I 339 ARG cc_start: 0.7056 (ttm170) cc_final: 0.6794 (ttp-170) REVERT: K 113 MET cc_start: 0.4721 (mmm) cc_final: 0.4461 (mmt) REVERT: K 341 ARG cc_start: 0.5972 (mpt-90) cc_final: 0.5736 (mpt90) REVERT: M 272 MET cc_start: 0.6534 (mmm) cc_final: 0.6309 (mmp) REVERT: O 341 ARG cc_start: 0.6220 (mpt-90) cc_final: 0.6004 (mpt90) REVERT: Q 272 MET cc_start: 0.6425 (mmm) cc_final: 0.6186 (mmm) REVERT: S 26 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8257 (mtmm) REVERT: S 46 LEU cc_start: 0.8146 (tp) cc_final: 0.7924 (tp) REVERT: S 339 ARG cc_start: 0.7053 (ttm170) cc_final: 0.6793 (ttp-170) outliers start: 46 outliers final: 24 residues processed: 312 average time/residue: 0.4338 time to fit residues: 212.9302 Evaluate side-chains 271 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 247 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 0.9980 chunk 239 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 213 optimal weight: 0.8980 chunk 319 optimal weight: 0.9990 chunk 338 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29170 Z= 0.233 Angle : 0.516 10.317 39670 Z= 0.267 Chirality : 0.039 0.130 4680 Planarity : 0.005 0.049 4810 Dihedral : 11.522 74.203 4920 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.78 % Allowed : 9.66 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.15), residues: 3470 helix: 1.25 (0.11), residues: 2400 sheet: -1.79 (0.27), residues: 190 loop : -0.68 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 261 HIS 0.004 0.001 HIS O 7 PHE 0.011 0.002 PHE C 169 TYR 0.015 0.002 TYR M 354 ARG 0.003 0.000 ARG E 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 253 time to evaluate : 3.117 Fit side-chains REVERT: A 113 MET cc_start: 0.4760 (mmm) cc_final: 0.4517 (mmt) REVERT: A 341 ARG cc_start: 0.6092 (mpt-90) cc_final: 0.5875 (mpt90) REVERT: G 113 MET cc_start: 0.4862 (mmm) cc_final: 0.4491 (mmt) REVERT: I 26 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8301 (mtmm) REVERT: I 339 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6809 (ttm170) REVERT: K 113 MET cc_start: 0.4750 (mmm) cc_final: 0.4501 (mmt) REVERT: K 341 ARG cc_start: 0.6101 (mpt-90) cc_final: 0.5878 (mpt90) REVERT: S 26 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8285 (mtmm) REVERT: S 339 ARG cc_start: 0.7050 (ttm170) cc_final: 0.6805 (ttm170) outliers start: 53 outliers final: 22 residues processed: 301 average time/residue: 0.4010 time to fit residues: 194.2602 Evaluate side-chains 256 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 234 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 47 LEU Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 47 LEU Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Chi-restraints excluded: chain S residue 342 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 251 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 172 optimal weight: 0.0070 chunk 303 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN C 275 HIS E 275 HIS G 85 ASN K 344 ASN O 275 HIS Q 85 ASN S 275 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29170 Z= 0.182 Angle : 0.495 11.342 39670 Z= 0.256 Chirality : 0.038 0.126 4680 Planarity : 0.004 0.046 4810 Dihedral : 11.513 73.968 4920 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.51 % Allowed : 10.40 % Favored : 88.09 % 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: 1.13 (0.15), residues: 3470 helix: 1.46 (0.11), residues: 2380 sheet: -1.67 (0.28), residues: 190 loop : -0.48 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 123 HIS 0.003 0.001 HIS O 7 PHE 0.010 0.001 PHE C 169 TYR 0.018 0.001 TYR M 354 ARG 0.002 0.000 ARG K 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 267 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4787 (mmm) cc_final: 0.4566 (mmt) REVERT: C 181 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: G 113 MET cc_start: 0.4872 (mmm) cc_final: 0.4527 (mmt) REVERT: I 23 TYR cc_start: 0.8149 (m-80) cc_final: 0.7947 (m-80) REVERT: I 26 LYS cc_start: 0.8522 (mtmm) cc_final: 0.8271 (mtmm) REVERT: I 339 ARG cc_start: 0.7036 (ttm170) cc_final: 0.6788 (ttp-170) REVERT: K 113 MET cc_start: 0.4785 (mmm) cc_final: 0.4563 (mmt) REVERT: M 181 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: S 23 TYR cc_start: 0.8151 (m-80) cc_final: 0.7948 (m-80) REVERT: S 26 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8273 (mtmm) REVERT: S 339 ARG cc_start: 0.7033 (ttm170) cc_final: 0.6777 (ttp-170) outliers start: 45 outliers final: 17 residues processed: 302 average time/residue: 0.3997 time to fit residues: 196.3677 Evaluate side-chains 271 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 252 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 181 GLU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 92 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 176 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 1.9990 chunk 304 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 83 optimal weight: 9.9990 chunk 338 optimal weight: 1.9990 chunk 281 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN G 275 HIS I 275 HIS K 306 GLN ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 279 GLN Q 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29170 Z= 0.262 Angle : 0.540 11.898 39670 Z= 0.275 Chirality : 0.040 0.257 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.504 74.297 4920 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.24 % Allowed : 10.67 % Favored : 88.09 % 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: 0.86 (0.15), residues: 3470 helix: 1.31 (0.11), residues: 2400 sheet: -1.79 (0.29), residues: 190 loop : -0.80 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 261 HIS 0.004 0.001 HIS E 7 PHE 0.012 0.002 PHE E 169 TYR 0.015 0.002 TYR C 354 ARG 0.002 0.000 ARG K 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4788 (mmm) cc_final: 0.4544 (mmt) REVERT: C 181 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: G 113 MET cc_start: 0.4902 (mmm) cc_final: 0.4540 (mmt) REVERT: I 26 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8330 (mtmm) REVERT: I 337 MET cc_start: 0.6869 (mmm) cc_final: 0.6605 (tmm) REVERT: I 339 ARG cc_start: 0.7095 (ttm170) cc_final: 0.6842 (ttm170) REVERT: K 113 MET cc_start: 0.4786 (mmm) cc_final: 0.4540 (mmt) REVERT: M 181 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7315 (mp0) REVERT: S 26 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8334 (mtmm) REVERT: S 337 MET cc_start: 0.6877 (mmm) cc_final: 0.6615 (tmm) REVERT: S 339 ARG cc_start: 0.7092 (ttm170) cc_final: 0.6842 (ttm170) outliers start: 37 outliers final: 25 residues processed: 316 average time/residue: 0.4065 time to fit residues: 205.6359 Evaluate side-chains 298 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 271 time to evaluate : 3.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 181 GLU Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain S residue 176 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 chunk 285 optimal weight: 10.0000 chunk 189 optimal weight: 0.0970 chunk 337 optimal weight: 3.9990 chunk 211 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** G 41 GLN G 279 GLN G 306 GLN Q 41 GLN Q 279 GLN Q 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29170 Z= 0.200 Angle : 0.510 12.387 39670 Z= 0.261 Chirality : 0.039 0.242 4680 Planarity : 0.004 0.043 4810 Dihedral : 11.473 74.104 4920 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.58 % Allowed : 11.38 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3470 helix: 1.52 (0.11), residues: 2380 sheet: -1.73 (0.29), residues: 190 loop : -0.56 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 123 HIS 0.003 0.001 HIS O 7 PHE 0.010 0.001 PHE C 169 TYR 0.018 0.002 TYR S 354 ARG 0.002 0.000 ARG Q 341 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 275 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TYR cc_start: 0.8201 (m-80) cc_final: 0.7989 (m-80) REVERT: A 113 MET cc_start: 0.4721 (mmm) cc_final: 0.4463 (mmt) REVERT: E 17 ILE cc_start: 0.8186 (mt) cc_final: 0.7916 (mm) REVERT: E 80 GLN cc_start: 0.8373 (tp40) cc_final: 0.7724 (tp40) REVERT: E 81 GLN cc_start: 0.8133 (tt0) cc_final: 0.7722 (tt0) REVERT: G 113 MET cc_start: 0.4895 (mmm) cc_final: 0.4552 (mmt) REVERT: I 26 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8356 (mtmm) REVERT: I 258 MET cc_start: 0.8102 (mmm) cc_final: 0.6832 (mmm) REVERT: I 279 GLN cc_start: 0.7518 (mm110) cc_final: 0.7284 (mm-40) REVERT: I 337 MET cc_start: 0.6888 (mmm) cc_final: 0.6643 (tmm) REVERT: K 113 MET cc_start: 0.4703 (mmm) cc_final: 0.4446 (mmt) REVERT: O 80 GLN cc_start: 0.8373 (tp40) cc_final: 0.7722 (tp40) REVERT: O 81 GLN cc_start: 0.8134 (tt0) cc_final: 0.7720 (tt0) REVERT: S 26 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8356 (mtmm) REVERT: S 258 MET cc_start: 0.8102 (mmm) cc_final: 0.6828 (mmm) REVERT: S 279 GLN cc_start: 0.7527 (mm110) cc_final: 0.7287 (mm-40) REVERT: S 337 MET cc_start: 0.6895 (mmm) cc_final: 0.6633 (tmm) REVERT: S 339 ARG cc_start: 0.7098 (ttm170) cc_final: 0.6841 (ttm170) outliers start: 47 outliers final: 23 residues processed: 314 average time/residue: 0.3940 time to fit residues: 201.2364 Evaluate side-chains 285 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 262 time to evaluate : 3.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 201 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 65 optimal weight: 0.7980 chunk 214 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 150 GLN I 306 GLN K 275 HIS ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 150 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 29170 Z= 0.229 Angle : 0.536 12.786 39670 Z= 0.270 Chirality : 0.039 0.202 4680 Planarity : 0.004 0.043 4810 Dihedral : 11.479 74.221 4920 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.14 % Allowed : 12.18 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.15), residues: 3470 helix: 1.53 (0.11), residues: 2380 sheet: -1.63 (0.30), residues: 190 loop : -0.60 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 261 HIS 0.003 0.001 HIS E 7 PHE 0.011 0.002 PHE O 169 TYR 0.017 0.002 TYR M 354 ARG 0.002 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 276 time to evaluate : 3.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4846 (mmm) cc_final: 0.4570 (mmt) REVERT: C 258 MET cc_start: 0.7931 (mmm) cc_final: 0.7042 (mmm) REVERT: E 17 ILE cc_start: 0.8199 (mt) cc_final: 0.7918 (mm) REVERT: E 80 GLN cc_start: 0.8369 (tp40) cc_final: 0.7745 (tp40) REVERT: G 113 MET cc_start: 0.4975 (mmm) cc_final: 0.4612 (mmt) REVERT: I 26 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8367 (mtmm) REVERT: I 258 MET cc_start: 0.8175 (mmm) cc_final: 0.7538 (mmm) REVERT: K 113 MET cc_start: 0.4836 (mmm) cc_final: 0.4561 (mmt) REVERT: M 258 MET cc_start: 0.7927 (mmm) cc_final: 0.7036 (mmm) REVERT: O 80 GLN cc_start: 0.8366 (tp40) cc_final: 0.7743 (tp40) REVERT: S 26 LYS cc_start: 0.8599 (mtmm) cc_final: 0.8369 (mtmm) REVERT: S 258 MET cc_start: 0.8176 (mmm) cc_final: 0.7537 (mmm) REVERT: S 279 GLN cc_start: 0.7534 (mm110) cc_final: 0.7263 (mm-40) REVERT: S 339 ARG cc_start: 0.7072 (ttm170) cc_final: 0.6810 (ttm170) outliers start: 34 outliers final: 26 residues processed: 304 average time/residue: 0.3975 time to fit residues: 196.0937 Evaluate side-chains 292 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 266 time to evaluate : 3.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain K residue 332 LEU Chi-restraints excluded: chain K residue 342 VAL Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 0.9990 chunk 323 optimal weight: 0.1980 chunk 294 optimal weight: 0.0870 chunk 314 optimal weight: 6.9990 chunk 189 optimal weight: 0.0050 chunk 136 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 313 optimal weight: 0.9980 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 GLN C 306 GLN E 306 GLN I 85 ASN ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 GLN O 306 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29170 Z= 0.164 Angle : 0.524 14.047 39670 Z= 0.262 Chirality : 0.038 0.165 4680 Planarity : 0.004 0.042 4810 Dihedral : 11.474 73.899 4920 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.81 % Allowed : 12.45 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.15), residues: 3470 helix: 1.74 (0.11), residues: 2380 sheet: -1.49 (0.31), residues: 190 loop : -0.55 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP Q 123 HIS 0.003 0.001 HIS O 7 PHE 0.009 0.001 PHE M 169 TYR 0.021 0.001 TYR I 354 ARG 0.002 0.000 ARG S 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 278 time to evaluate : 3.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4557 (mmm) cc_final: 0.4330 (mmt) REVERT: C 55 LYS cc_start: 0.7992 (tttm) cc_final: 0.7699 (tppt) REVERT: C 258 MET cc_start: 0.7982 (mmm) cc_final: 0.7195 (mmm) REVERT: E 17 ILE cc_start: 0.8231 (mt) cc_final: 0.7980 (mm) REVERT: G 113 MET cc_start: 0.4897 (mmm) cc_final: 0.4596 (mmt) REVERT: I 26 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8344 (mtmm) REVERT: I 258 MET cc_start: 0.8025 (mmm) cc_final: 0.6978 (mmm) REVERT: K 81 GLN cc_start: 0.7953 (tt0) cc_final: 0.7747 (tt0) REVERT: K 113 MET cc_start: 0.4550 (mmm) cc_final: 0.4322 (mmt) REVERT: M 55 LYS cc_start: 0.7996 (tttm) cc_final: 0.7700 (tppt) REVERT: M 258 MET cc_start: 0.7984 (mmm) cc_final: 0.7191 (mmm) REVERT: S 26 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8349 (mtmm) REVERT: S 81 GLN cc_start: 0.8067 (tt0) cc_final: 0.7859 (tt0) REVERT: S 85 ASN cc_start: 0.7835 (m110) cc_final: 0.7591 (t0) REVERT: S 258 MET cc_start: 0.8022 (mmm) cc_final: 0.6972 (mmm) outliers start: 24 outliers final: 19 residues processed: 298 average time/residue: 0.3985 time to fit residues: 192.0668 Evaluate side-chains 279 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 175 THR Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 0.5980 chunk 332 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 231 optimal weight: 0.9990 chunk 348 optimal weight: 0.9980 chunk 320 optimal weight: 10.0000 chunk 277 optimal weight: 0.0470 chunk 28 optimal weight: 0.5980 chunk 214 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 GLN S 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29170 Z= 0.191 Angle : 0.524 13.956 39670 Z= 0.263 Chirality : 0.038 0.195 4680 Planarity : 0.004 0.042 4810 Dihedral : 11.495 74.017 4920 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.84 % Allowed : 12.82 % Favored : 86.34 % 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: 1.41 (0.15), residues: 3470 helix: 1.73 (0.11), residues: 2380 sheet: -1.41 (0.31), residues: 190 loop : -0.60 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP S 123 HIS 0.004 0.001 HIS C 117 PHE 0.010 0.001 PHE C 169 TYR 0.020 0.001 TYR G 354 ARG 0.001 0.000 ARG E 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6940 Ramachandran restraints generated. 3470 Oldfield, 0 Emsley, 3470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 294 time to evaluate : 2.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.4558 (mmm) cc_final: 0.4326 (mmt) REVERT: C 55 LYS cc_start: 0.7978 (tttm) cc_final: 0.7678 (tppt) REVERT: C 80 GLN cc_start: 0.7933 (tp40) cc_final: 0.7666 (tp-100) REVERT: C 81 GLN cc_start: 0.7996 (tt0) cc_final: 0.7724 (tt0) REVERT: C 258 MET cc_start: 0.8126 (mmm) cc_final: 0.7309 (mmm) REVERT: E 17 ILE cc_start: 0.8171 (mt) cc_final: 0.7892 (mm) REVERT: E 258 MET cc_start: 0.8132 (mmm) cc_final: 0.7403 (mmm) REVERT: G 113 MET cc_start: 0.4837 (mmm) cc_final: 0.4572 (mmt) REVERT: G 258 MET cc_start: 0.8267 (mmm) cc_final: 0.7469 (mmm) REVERT: I 26 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8363 (mtmm) REVERT: I 55 LYS cc_start: 0.7823 (tttm) cc_final: 0.7546 (tppt) REVERT: I 85 ASN cc_start: 0.7887 (m-40) cc_final: 0.7685 (m110) REVERT: I 258 MET cc_start: 0.8067 (mmm) cc_final: 0.7560 (mmm) REVERT: K 113 MET cc_start: 0.4547 (mmm) cc_final: 0.4310 (mmt) REVERT: M 55 LYS cc_start: 0.7982 (tttm) cc_final: 0.7679 (tppt) REVERT: M 258 MET cc_start: 0.8125 (mmm) cc_final: 0.7304 (mmm) REVERT: O 258 MET cc_start: 0.8137 (mmm) cc_final: 0.7407 (mmm) REVERT: Q 258 MET cc_start: 0.8268 (mmm) cc_final: 0.7471 (mmm) REVERT: S 26 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8363 (mtmm) REVERT: S 55 LYS cc_start: 0.7820 (tttm) cc_final: 0.7542 (tppt) REVERT: S 81 GLN cc_start: 0.8064 (tt0) cc_final: 0.7858 (tt0) REVERT: S 85 ASN cc_start: 0.7797 (m110) cc_final: 0.7558 (t0) REVERT: S 258 MET cc_start: 0.8063 (mmm) cc_final: 0.7558 (mmm) outliers start: 25 outliers final: 19 residues processed: 317 average time/residue: 0.4379 time to fit residues: 226.8505 Evaluate side-chains 289 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 270 time to evaluate : 3.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain E residue 175 THR Chi-restraints excluded: chain E residue 342 VAL Chi-restraints excluded: chain G residue 176 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 176 ILE Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 342 VAL Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 90 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 342 VAL Chi-restraints excluded: chain S residue 176 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 256 optimal weight: 0.6980 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 278 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.194067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.164996 restraints weight = 33226.348| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 1.61 r_work: 0.3558 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29170 Z= 0.262 Angle : 0.568 13.889 39670 Z= 0.284 Chirality : 0.040 0.206 4680 Planarity : 0.004 0.043 4810 Dihedral : 11.432 74.365 4920 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.94 % Allowed : 13.02 % Favored : 86.04 % 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: 1.25 (0.15), residues: 3470 helix: 1.59 (0.11), residues: 2380 sheet: -1.38 (0.32), residues: 190 loop : -0.65 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 261 HIS 0.004 0.001 HIS E 7 PHE 0.012 0.002 PHE K 169 TYR 0.018 0.002 TYR S 354 ARG 0.002 0.000 ARG A 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5753.31 seconds wall clock time: 106 minutes 58.16 seconds (6418.16 seconds total)