Starting phenix.real_space_refine on Thu Jul 25 05:01:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/07_2024/8pdl_17613.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/07_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_17613/07_2024/8pdl_17613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/07_2024/8pdl_17613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/07_2024/8pdl_17613.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdl_17613/07_2024/8pdl_17613.cif" } 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-5388/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: 15.42, per 1000 atoms: 0.54 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: 11.80 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: 8.87 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: 4.716A 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: 9.17 Time building geometry restraints manager: 12.83 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: 9128 1.34 - 1.45: 4086 1.45 - 1.57: 15636 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: 16254 113.27 - 120.19: 11149 120.19 - 127.11: 11207 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 -163.43 -16.57 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: 35121 3.31 - 4.10: 72945 4.10 - 4.90: 137796 Warning: very small nonbonded interaction distances. Nonbonded interactions: 246212 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 246207 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.000 Check model and map are aligned: 0.170 Set scattering table: 0.260 Process input model: 79.760 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.160 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.440 ------------------------------------------------------------------------------- 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 6.086 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 C 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 : 3.070 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: 0.4132 time to fit residues: 212.6551 Evaluate side-chains 264 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.051 ------------------------------------------------------------------------------- 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: 0.6980 chunk 265 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 178 optimal weight: 0.6980 chunk 141 optimal weight: 0.4980 chunk 274 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 317 optimal weight: 0.0270 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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: 0.7553 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29170 Z= 0.186 Angle : 0.525 9.570 39670 Z= 0.278 Chirality : 0.039 0.126 4680 Planarity : 0.005 0.070 4810 Dihedral : 11.818 74.001 4920 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.07 % Allowed : 5.60 % Favored : 93.32 % 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: 1.51 (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 S 261 HIS 0.004 0.001 HIS G 275 PHE 0.010 0.002 PHE I 224 TYR 0.019 0.002 TYR C 354 ARG 0.003 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 342 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 310 time to evaluate : 3.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 208 ARG cc_start: 0.7913 (tpt90) cc_final: 0.7709 (tpt90) REVERT: G 113 MET cc_start: 0.5105 (mmm) cc_final: 0.4702 (mmt) REVERT: I 26 LYS cc_start: 0.8400 (mtmm) cc_final: 0.8115 (mtmm) REVERT: O 208 ARG cc_start: 0.7914 (tpt90) cc_final: 0.7710 (tpt90) REVERT: S 26 LYS cc_start: 0.8401 (mtmm) cc_final: 0.8115 (mtmm) REVERT: S 216 GLN cc_start: 0.7645 (mt0) cc_final: 0.7404 (mt0) outliers start: 32 outliers final: 22 residues processed: 334 average time/residue: 0.4100 time to fit residues: 216.9853 Evaluate side-chains 261 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 239 time to evaluate : 3.083 ------------------------------------------------------------------------------- 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: 0.6980 chunk 98 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 318 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 315 optimal weight: 0.0060 chunk 108 optimal weight: 2.9990 chunk 255 optimal weight: 7.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- 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: 0.7657 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29170 Z= 0.293 Angle : 0.562 10.356 39670 Z= 0.289 Chirality : 0.041 0.168 4680 Planarity : 0.005 0.055 4810 Dihedral : 11.568 74.487 4920 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.48 % Allowed : 8.66 % Favored : 89.87 % 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: 1.12 (0.14), residues: 3470 helix: 1.40 (0.11), residues: 2300 sheet: -1.67 (0.27), residues: 190 loop : -0.18 (0.20), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 261 HIS 0.004 0.001 HIS O 7 PHE 0.011 0.002 PHE E 169 TYR 0.015 0.002 TYR C 354 ARG 0.003 0.000 ARG E 221 *********************** 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 308 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 3.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 ARG cc_start: 0.6014 (mpt-90) cc_final: 0.5783 (mpt90) REVERT: E 341 ARG cc_start: 0.6227 (mpt-90) cc_final: 0.6018 (mpt90) REVERT: G 113 MET cc_start: 0.4922 (mmm) cc_final: 0.4536 (mmt) REVERT: G 272 MET cc_start: 0.6428 (mmm) cc_final: 0.6204 (mmm) REVERT: I 26 LYS cc_start: 0.8525 (mtmm) cc_final: 0.8286 (mtmm) REVERT: I 46 LEU cc_start: 0.8160 (tp) cc_final: 0.7937 (tp) REVERT: K 341 ARG cc_start: 0.6022 (mpt-90) cc_final: 0.5794 (mpt90) REVERT: O 341 ARG cc_start: 0.6232 (mpt-90) cc_final: 0.6025 (mpt90) REVERT: Q 272 MET cc_start: 0.6423 (mmm) cc_final: 0.6200 (mmm) REVERT: S 26 LYS cc_start: 0.8528 (mtmm) cc_final: 0.8289 (mtmm) REVERT: S 46 LEU cc_start: 0.8160 (tp) cc_final: 0.7938 (tp) outliers start: 44 outliers final: 24 residues processed: 302 average time/residue: 0.4131 time to fit residues: 196.0668 Evaluate side-chains 266 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 242 time to evaluate : 3.031 ------------------------------------------------------------------------------- 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: 0.8980 chunk 239 optimal weight: 0.5980 chunk 165 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 319 optimal weight: 1.9990 chunk 338 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 chunk 302 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS M 275 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29170 Z= 0.206 Angle : 0.505 10.642 39670 Z= 0.262 Chirality : 0.039 0.131 4680 Planarity : 0.004 0.048 4810 Dihedral : 11.511 74.115 4920 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.95 % Allowed : 9.36 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 3470 helix: 1.32 (0.11), residues: 2400 sheet: -1.76 (0.27), residues: 190 loop : -0.71 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP I 261 HIS 0.003 0.001 HIS E 7 PHE 0.010 0.002 PHE M 169 TYR 0.015 0.002 TYR O 354 ARG 0.005 0.000 ARG O 221 *********************** 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 315 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 257 time to evaluate : 3.312 Fit side-chains REVERT: A 113 MET cc_start: 0.4754 (mmm) cc_final: 0.4519 (mmt) REVERT: A 341 ARG cc_start: 0.6042 (mpt-90) cc_final: 0.5816 (mpt90) REVERT: G 113 MET cc_start: 0.4860 (mmm) cc_final: 0.4492 (mmt) REVERT: I 26 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8285 (mtmm) REVERT: I 46 LEU cc_start: 0.8104 (tp) cc_final: 0.7901 (tp) REVERT: K 113 MET cc_start: 0.4746 (mmm) cc_final: 0.4488 (mmt) REVERT: K 341 ARG cc_start: 0.6086 (mpt-90) cc_final: 0.5865 (mpt90) REVERT: S 26 LYS cc_start: 0.8535 (mtmm) cc_final: 0.8289 (mtmm) REVERT: S 46 LEU cc_start: 0.8105 (tp) cc_final: 0.7903 (tp) outliers start: 58 outliers final: 26 residues processed: 304 average time/residue: 0.3917 time to fit residues: 195.2487 Evaluate side-chains 260 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 234 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 135 MET 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 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 I residue 342 VAL Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 135 MET 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 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 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: 0.3980 chunk 192 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 251 optimal weight: 0.8980 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: 0.8980 chunk 303 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 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 E 275 HIS G 85 ASN K 344 ASN O 275 HIS Q 85 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29170 Z= 0.196 Angle : 0.503 11.601 39670 Z= 0.258 Chirality : 0.038 0.122 4680 Planarity : 0.004 0.045 4810 Dihedral : 11.511 74.026 4920 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.74 % Allowed : 10.13 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.15), residues: 3470 helix: 1.46 (0.11), residues: 2380 sheet: -1.65 (0.29), residues: 190 loop : -0.49 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP O 123 HIS 0.003 0.001 HIS E 7 PHE 0.010 0.002 PHE M 169 TYR 0.016 0.002 TYR Q 354 ARG 0.001 0.000 ARG A 221 *********************** 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 329 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 277 time to evaluate : 2.933 Fit side-chains REVERT: A 85 ASN cc_start: 0.7808 (m110) cc_final: 0.7588 (m110) REVERT: A 113 MET cc_start: 0.4762 (mmm) cc_final: 0.4549 (mmt) REVERT: C 181 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7335 (mp0) REVERT: G 113 MET cc_start: 0.4764 (mmm) cc_final: 0.4425 (mmt) REVERT: I 23 TYR cc_start: 0.8164 (m-80) cc_final: 0.7948 (m-80) REVERT: I 26 LYS cc_start: 0.8516 (mtmm) cc_final: 0.8279 (mtmm) REVERT: I 46 LEU cc_start: 0.8049 (tp) cc_final: 0.7849 (tp) REVERT: I 258 MET cc_start: 0.8161 (mmm) cc_final: 0.7525 (mmm) REVERT: K 85 ASN cc_start: 0.7901 (m110) cc_final: 0.7669 (m110) REVERT: K 113 MET cc_start: 0.4748 (mmm) cc_final: 0.4521 (mmt) REVERT: M 181 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7331 (mp0) REVERT: S 23 TYR cc_start: 0.8165 (m-80) cc_final: 0.7947 (m-80) REVERT: S 26 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8282 (mtmm) REVERT: S 46 LEU cc_start: 0.8046 (tp) cc_final: 0.7845 (tp) REVERT: S 258 MET cc_start: 0.8160 (mmm) cc_final: 0.7529 (mmm) outliers start: 52 outliers final: 20 residues processed: 315 average time/residue: 0.3772 time to fit residues: 192.3506 Evaluate side-chains 288 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 266 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 SER Chi-restraints excluded: chain A residue 135 MET 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 G residue 176 ILE Chi-restraints excluded: chain I residue 32 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 135 MET 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 Q residue 176 ILE Chi-restraints excluded: chain S residue 32 THR 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: 0.5980 chunk 304 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 338 optimal weight: 2.9990 chunk 281 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 177 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 HIS A 306 GLN ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN G 41 GLN G 275 HIS I 275 HIS K 306 GLN ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 279 GLN Q 41 GLN Q 275 HIS S 275 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2114 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= 0.294 Angle : 0.565 12.220 39670 Z= 0.287 Chirality : 0.042 0.272 4680 Planarity : 0.005 0.045 4810 Dihedral : 11.524 74.525 4920 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.61 % Allowed : 10.60 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3470 helix: 1.24 (0.11), residues: 2400 sheet: -1.81 (0.29), residues: 190 loop : -0.84 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP O 261 HIS 0.004 0.001 HIS E 7 PHE 0.012 0.002 PHE E 169 TYR 0.014 0.002 TYR G 354 ARG 0.002 0.000 ARG A 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 321 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 273 time to evaluate : 2.823 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: 0.4809 (mmm) cc_final: 0.4548 (mmt) REVERT: C 177 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: C 181 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: G 113 MET cc_start: 0.4996 (mmm) cc_final: 0.4607 (mmt) REVERT: I 26 LYS cc_start: 0.8606 (mtmm) cc_final: 0.8375 (mtmm) REVERT: K 113 MET cc_start: 0.4802 (mmm) cc_final: 0.4561 (mmt) REVERT: M 177 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: M 181 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7304 (mp0) REVERT: S 26 LYS cc_start: 0.8607 (mtmm) cc_final: 0.8379 (mtmm) outliers start: 48 outliers final: 25 residues processed: 312 average time/residue: 0.3880 time to fit residues: 195.4827 Evaluate side-chains 296 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 267 time to evaluate : 2.765 ------------------------------------------------------------------------------- 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 177 GLU 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 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 286 THR Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain K residue 88 SER Chi-restraints excluded: chain K residue 135 MET 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 177 GLU 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 175 THR Chi-restraints excluded: chain O residue 342 VAL Chi-restraints excluded: chain Q residue 176 ILE Chi-restraints excluded: chain Q residue 286 THR 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: 1.9990 chunk 192 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 191 optimal weight: 0.9990 chunk 285 optimal weight: 9.9990 chunk 189 optimal weight: 0.0670 chunk 337 optimal weight: 2.9990 chunk 211 optimal weight: 0.7980 chunk 205 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.7122 ------------------------------------------------------------------------------- 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 279 GLN G 306 GLN K 275 HIS ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 279 GLN Q 306 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29170 Z= 0.204 Angle : 0.514 12.207 39670 Z= 0.262 Chirality : 0.039 0.244 4680 Planarity : 0.004 0.043 4810 Dihedral : 11.481 74.145 4920 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.24 % Allowed : 11.85 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.15), residues: 3470 helix: 1.52 (0.11), residues: 2380 sheet: -1.70 (0.30), residues: 190 loop : -0.58 (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 E 7 PHE 0.010 0.001 PHE M 169 TYR 0.019 0.002 TYR C 354 ARG 0.001 0.000 ARG K 221 *********************** 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 320 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 283 time to evaluate : 3.041 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: 0.4720 (mmm) cc_final: 0.4461 (mmt) REVERT: E 17 ILE cc_start: 0.8218 (mt) cc_final: 0.7936 (mm) REVERT: G 113 MET cc_start: 0.4935 (mmm) cc_final: 0.4575 (mmt) REVERT: I 26 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8366 (mtmm) REVERT: I 279 GLN cc_start: 0.7541 (mm110) cc_final: 0.7301 (mm-40) REVERT: K 113 MET cc_start: 0.4707 (mmm) cc_final: 0.4457 (mmt) REVERT: O 17 ILE cc_start: 0.8177 (mt) cc_final: 0.7913 (mm) REVERT: S 26 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8370 (mtmm) REVERT: S 279 GLN cc_start: 0.7544 (mm110) cc_final: 0.7303 (mm-40) outliers start: 37 outliers final: 22 residues processed: 315 average time/residue: 0.3736 time to fit residues: 191.9952 Evaluate side-chains 285 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 263 time to evaluate : 2.876 ------------------------------------------------------------------------------- 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 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 135 MET 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 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: 8.9990 chunk 134 optimal weight: 0.0770 chunk 201 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 chunk 229 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- 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** I 306 GLN ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29170 Z= 0.243 Angle : 0.559 13.272 39670 Z= 0.279 Chirality : 0.040 0.213 4680 Planarity : 0.004 0.043 4810 Dihedral : 11.504 74.262 4920 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.07 % Allowed : 13.15 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.15), residues: 3470 helix: 1.50 (0.11), residues: 2380 sheet: -1.66 (0.30), residues: 190 loop : -0.66 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 123 HIS 0.003 0.001 HIS O 7 PHE 0.011 0.002 PHE C 169 TYR 0.018 0.002 TYR M 354 ARG 0.002 0.000 ARG K 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 319 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 287 time to evaluate : 3.255 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: 0.4777 (mmm) cc_final: 0.4523 (mmt) REVERT: C 258 MET cc_start: 0.7956 (mmm) cc_final: 0.7113 (mmm) REVERT: E 17 ILE cc_start: 0.8213 (mt) cc_final: 0.7924 (mm) REVERT: E 177 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6802 (mp0) REVERT: G 80 GLN cc_start: 0.8226 (tp40) cc_final: 0.7649 (tp-100) REVERT: G 113 MET cc_start: 0.5014 (mmm) cc_final: 0.4634 (mmt) REVERT: I 26 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8387 (mtmm) REVERT: K 85 ASN cc_start: 0.7913 (m110) cc_final: 0.7690 (m110) REVERT: K 113 MET cc_start: 0.4739 (mmm) cc_final: 0.4466 (mmt) REVERT: M 258 MET cc_start: 0.7952 (mmm) cc_final: 0.7106 (mmm) REVERT: O 17 ILE cc_start: 0.8240 (mt) cc_final: 0.7965 (mm) REVERT: O 177 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: Q 80 GLN cc_start: 0.8224 (tp40) cc_final: 0.7646 (tp-100) REVERT: S 26 LYS cc_start: 0.8612 (mtmm) cc_final: 0.8396 (mtmm) REVERT: S 279 GLN cc_start: 0.7576 (mm110) cc_final: 0.7309 (mm-40) outliers start: 32 outliers final: 24 residues processed: 315 average time/residue: 0.4205 time to fit residues: 215.3998 Evaluate side-chains 302 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 276 time to evaluate : 3.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET 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 175 THR Chi-restraints excluded: chain E residue 177 GLU 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 135 MET 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 175 THR Chi-restraints excluded: chain O residue 177 GLU 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: 1.9990 chunk 323 optimal weight: 0.6980 chunk 294 optimal weight: 0.6980 chunk 314 optimal weight: 5.9990 chunk 189 optimal weight: 0.0570 chunk 136 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 284 optimal weight: 1.9990 chunk 297 optimal weight: 1.9990 chunk 313 optimal weight: 0.8980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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** E 306 GLN ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 306 GLN S 41 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2484 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= 0.197 Angle : 0.532 13.832 39670 Z= 0.266 Chirality : 0.039 0.181 4680 Planarity : 0.004 0.042 4810 Dihedral : 11.479 74.061 4920 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.01 % Allowed : 13.49 % Favored : 85.50 % 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 (0.15), residues: 3470 helix: 1.62 (0.11), residues: 2380 sheet: -1.65 (0.30), residues: 190 loop : -0.61 (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 G 117 PHE 0.010 0.001 PHE C 169 TYR 0.020 0.002 TYR M 354 ARG 0.002 0.000 ARG E 221 *********************** 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 312 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 282 time to evaluate : 2.877 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: 0.4692 (mmm) cc_final: 0.4445 (mmt) REVERT: C 55 LYS cc_start: 0.8043 (tttm) cc_final: 0.7749 (tppt) REVERT: C 258 MET cc_start: 0.7985 (mmm) cc_final: 0.7207 (mmm) REVERT: E 17 ILE cc_start: 0.8172 (mt) cc_final: 0.7880 (mm) REVERT: G 80 GLN cc_start: 0.8192 (tp40) cc_final: 0.7930 (tp40) REVERT: G 113 MET cc_start: 0.4960 (mmm) cc_final: 0.4599 (mmt) REVERT: I 26 LYS cc_start: 0.8610 (mtmm) cc_final: 0.8399 (mtmm) REVERT: K 113 MET cc_start: 0.4688 (mmm) cc_final: 0.4444 (mmt) REVERT: M 258 MET cc_start: 0.7985 (mmm) cc_final: 0.7206 (mmm) REVERT: O 17 ILE cc_start: 0.8161 (mt) cc_final: 0.7911 (mm) REVERT: Q 80 GLN cc_start: 0.8189 (tp40) cc_final: 0.7930 (tp40) REVERT: S 26 LYS cc_start: 0.8627 (mtmm) cc_final: 0.8401 (mtmm) REVERT: S 279 GLN cc_start: 0.7487 (mm110) cc_final: 0.7236 (mm-40) outliers start: 30 outliers final: 26 residues processed: 304 average time/residue: 0.3960 time to fit residues: 194.0299 Evaluate side-chains 303 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 277 time to evaluate : 2.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET 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 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 I residue 295 MET Chi-restraints excluded: chain K residue 135 MET 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 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 Chi-restraints excluded: chain S residue 295 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 4.9990 chunk 332 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 348 optimal weight: 0.9990 chunk 320 optimal weight: 10.0000 chunk 277 optimal weight: 0.0060 chunk 28 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 170 optimal weight: 2.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- 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** ** K 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29170 Z= 0.249 Angle : 0.559 14.337 39670 Z= 0.279 Chirality : 0.040 0.183 4680 Planarity : 0.004 0.043 4810 Dihedral : 11.483 74.267 4920 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.17 % Allowed : 13.69 % Favored : 85.13 % 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: 1.19 (0.15), residues: 3470 helix: 1.56 (0.11), residues: 2380 sheet: -1.56 (0.31), residues: 190 loop : -0.65 (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 E 7 PHE 0.012 0.002 PHE O 169 TYR 0.019 0.002 TYR O 354 ARG 0.002 0.000 ARG K 221 ********************** 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 318 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 283 time to evaluate : 2.822 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: 0.4718 (mmm) cc_final: 0.4472 (mmt) REVERT: C 55 LYS cc_start: 0.8037 (tttm) cc_final: 0.7721 (tppt) REVERT: C 258 MET cc_start: 0.8087 (mmm) cc_final: 0.7276 (mmm) REVERT: E 17 ILE cc_start: 0.8214 (mt) cc_final: 0.7922 (mm) REVERT: G 80 GLN cc_start: 0.8206 (tp40) cc_final: 0.7954 (tp40) REVERT: G 113 MET cc_start: 0.5048 (mmm) cc_final: 0.4716 (mmt) REVERT: I 26 LYS cc_start: 0.8644 (mtmm) cc_final: 0.8409 (mtmm) REVERT: K 113 MET cc_start: 0.4727 (mmm) cc_final: 0.4467 (mmt) REVERT: M 258 MET cc_start: 0.8084 (mmm) cc_final: 0.7273 (mmm) REVERT: O 17 ILE cc_start: 0.8206 (mt) cc_final: 0.7906 (mm) REVERT: Q 80 GLN cc_start: 0.8199 (tp40) cc_final: 0.7949 (tp40) REVERT: S 26 LYS cc_start: 0.8646 (mtmm) cc_final: 0.8412 (mtmm) REVERT: S 279 GLN cc_start: 0.7549 (mm110) cc_final: 0.7293 (mm-40) outliers start: 35 outliers final: 28 residues processed: 309 average time/residue: 0.3802 time to fit residues: 190.2825 Evaluate side-chains 300 residues out of total 2980 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 272 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 MET Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain C residue 10 ASP 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 I residue 295 MET Chi-restraints excluded: chain K residue 135 MET 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 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 Chi-restraints excluded: chain S residue 295 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 278 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 GLN M 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.191992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.164015 restraints weight = 33246.378| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 1.56 r_work: 0.3525 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29170 Z= 0.301 Angle : 0.588 13.682 39670 Z= 0.295 Chirality : 0.041 0.196 4680 Planarity : 0.005 0.043 4810 Dihedral : 11.500 74.479 4920 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.21 % Allowed : 13.76 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.15), residues: 3470 helix: 1.58 (0.11), residues: 2320 sheet: -1.57 (0.31), residues: 190 loop : -0.31 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 261 HIS 0.004 0.001 HIS O 7 PHE 0.013 0.002 PHE E 169 TYR 0.018 0.002 TYR I 354 ARG 0.002 0.000 ARG O 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5539.20 seconds wall clock time: 100 minutes 54.45 seconds (6054.45 seconds total)