Starting phenix.real_space_refine on Sun Mar 17 17:33:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/03_2024/7z22_14455.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/03_2024/7z22_14455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/03_2024/7z22_14455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/03_2024/7z22_14455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/03_2024/7z22_14455.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/03_2024/7z22_14455.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 12396 2.51 5 N 2892 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C ASP 67": "OD1" <-> "OD2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "E TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "F TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F ASP 67": "OD1" <-> "OD2" Residue "F TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "G TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G ASP 67": "OD1" <-> "OD2" Residue "G TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 205": "OE1" <-> "OE2" Residue "H TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H ASP 67": "OD1" <-> "OD2" Residue "H TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 205": "OE1" <-> "OE2" Residue "I TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 47": "OD1" <-> "OD2" Residue "I ASP 67": "OD1" <-> "OD2" Residue "I TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 205": "OE1" <-> "OE2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 47": "OD1" <-> "OD2" Residue "J ASP 67": "OD1" <-> "OD2" Residue "J TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "K TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 47": "OD1" <-> "OD2" Residue "K ASP 67": "OD1" <-> "OD2" Residue "K TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 205": "OE1" <-> "OE2" Residue "L TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 47": "OD1" <-> "OD2" Residue "L ASP 67": "OD1" <-> "OD2" Residue "L TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18492 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "H" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "I" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "J" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Time building chain proxies: 9.60, per 1000 atoms: 0.52 Number of scatterers: 18492 At special positions: 0 Unit cell: (101.37, 98.754, 157.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3108 8.00 N 2892 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 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: 7.00 Conformation dependent library (CDL) restraints added in 3.3 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 77.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.896A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR A 177 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.896A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.543A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR D 177 " --> pdb=" O GLN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR E 177 " --> pdb=" O GLN E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR F 177 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR G 177 " --> pdb=" O GLN G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR H 177 " --> pdb=" O GLN H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR I 177 " --> pdb=" O GLN I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR J 177 " --> pdb=" O GLN J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU K 7 " --> pdb=" O ASP K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR K 177 " --> pdb=" O GLN K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU L 7 " --> pdb=" O ASP L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR L 177 " --> pdb=" O GLN L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1380 hydrogen bonds defined for protein. 4104 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.46 Time building geometry restraints manager: 7.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5401 1.34 - 1.46: 4232 1.46 - 1.58: 9255 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" CB THR L 186 " pdb=" CG2 THR L 186 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CB THR F 186 " pdb=" CG2 THR F 186 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CB THR C 186 " pdb=" CG2 THR C 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.81e-01 bond pdb=" CB THR I 186 " pdb=" CG2 THR I 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.81e-01 bond pdb=" CB THR J 186 " pdb=" CG2 THR J 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.78e-01 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 100.83 - 107.48: 545 107.48 - 114.12: 10871 114.12 - 120.76: 8844 120.76 - 127.41: 5315 127.41 - 134.05: 225 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C VAL J 87 " pdb=" CA VAL J 87 " pdb=" CB VAL J 87 " ideal model delta sigma weight residual 113.70 110.28 3.42 9.50e-01 1.11e+00 1.29e+01 angle pdb=" C VAL I 87 " pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL L 87 " pdb=" CA VAL L 87 " pdb=" CB VAL L 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.46: 9059 8.46 - 16.92: 1148 16.92 - 25.38: 389 25.38 - 33.84: 348 33.84 - 42.30: 120 Dihedral angle restraints: 11064 sinusoidal: 4392 harmonic: 6672 Sorted by residual: dihedral pdb=" CA GLN L 173 " pdb=" CB GLN L 173 " pdb=" CG GLN L 173 " pdb=" CD GLN L 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 dihedral pdb=" CA GLN I 173 " pdb=" CB GLN I 173 " pdb=" CG GLN I 173 " pdb=" CD GLN I 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 dihedral pdb=" CA GLN C 173 " pdb=" CB GLN C 173 " pdb=" CG GLN C 173 " pdb=" CD GLN C 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1895 0.027 - 0.055: 725 0.055 - 0.082: 187 0.082 - 0.109: 108 0.109 - 0.137: 37 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA PRO B 203 " pdb=" N PRO B 203 " pdb=" C PRO B 203 " pdb=" CB PRO B 203 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PRO E 203 " pdb=" N PRO E 203 " pdb=" C PRO E 203 " pdb=" CB PRO E 203 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PRO D 203 " pdb=" N PRO D 203 " pdb=" C PRO D 203 " pdb=" CB PRO D 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 76 " -0.082 9.50e-02 1.11e+02 3.68e-02 9.51e-01 pdb=" NE ARG H 76 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG H 76 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 76 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 76 " -0.081 9.50e-02 1.11e+02 3.65e-02 9.34e-01 pdb=" NE ARG D 76 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG D 76 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 76 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 76 " 0.081 9.50e-02 1.11e+02 3.65e-02 9.33e-01 pdb=" NE ARG J 76 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG J 76 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG J 76 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1161 2.74 - 3.28: 18793 3.28 - 3.82: 32371 3.82 - 4.36: 33981 4.36 - 4.90: 62159 Nonbonded interactions: 148465 Sorted by model distance: nonbonded pdb=" OD1 ASN G 63 " pdb=" NH1 ARG L 53 " model vdw 2.198 2.520 nonbonded pdb=" NH1 ARG E 53 " pdb=" OD1 ASN F 63 " model vdw 2.198 2.520 nonbonded pdb=" NH1 ARG G 53 " pdb=" OD1 ASN H 63 " model vdw 2.199 2.520 nonbonded pdb=" NH1 ARG D 53 " pdb=" OD1 ASN E 63 " model vdw 2.199 2.520 nonbonded pdb=" OD1 ASN A 63 " pdb=" NH1 ARG F 53 " model vdw 2.199 2.520 ... (remaining 148460 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.390 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 47.180 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 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:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 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 : 0.003 0.028 19008 Z= 0.178 Angle : 0.514 4.809 25800 Z= 0.298 Chirality : 0.036 0.137 2952 Planarity : 0.004 0.037 3096 Dihedral : 11.338 42.299 6636 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.18), residues: 2220 helix: 3.02 (0.11), residues: 1632 sheet: -1.64 (0.35), residues: 204 loop : -2.64 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 25 HIS 0.003 0.001 HIS H 74 PHE 0.017 0.001 PHE B 212 TYR 0.011 0.002 TYR K 155 ARG 0.006 0.001 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 754 time to evaluate : 2.001 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 18 residues processed: 754 average time/residue: 1.0520 time to fit residues: 904.5981 Evaluate side-chains 333 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 315 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 211 ILE Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 211 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 196 optimal weight: 0.0980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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: 0.5935 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19008 Z= 0.248 Angle : 0.857 11.566 25800 Z= 0.409 Chirality : 0.042 0.116 2952 Planarity : 0.004 0.020 3096 Dihedral : 4.388 26.546 2472 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.93 % Allowed : 16.03 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2220 helix: 2.34 (0.11), residues: 1644 sheet: -1.12 (0.37), residues: 204 loop : -2.26 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 78 HIS 0.003 0.001 HIS G 95 PHE 0.026 0.003 PHE C 233 TYR 0.022 0.002 TYR J 98 ARG 0.013 0.001 ARG J 76 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 390 time to evaluate : 2.028 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: symmetry clash outliers start: 121 outliers final: 13 residues processed: 463 average time/residue: 0.9135 time to fit residues: 493.1127 Evaluate side-chains 332 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 319 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 212 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 157 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 195 GLN C 195 GLN D 195 GLN E 195 GLN F 195 GLN G 195 GLN H 195 GLN I 195 GLN J 195 GLN K 195 GLN L 195 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.9140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 19008 Z= 0.308 Angle : 0.834 11.518 25800 Z= 0.415 Chirality : 0.045 0.174 2952 Planarity : 0.004 0.033 3096 Dihedral : 4.188 14.501 2436 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 5.44 % Allowed : 18.14 % Favored : 76.42 % 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: 1.15 (0.17), residues: 2220 helix: 1.76 (0.11), residues: 1644 sheet: -1.06 (0.38), residues: 204 loop : -2.73 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 78 HIS 0.007 0.002 HIS A 74 PHE 0.031 0.003 PHE I 77 TYR 0.020 0.003 TYR K 98 ARG 0.015 0.002 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 319 time to evaluate : 2.132 Fit side-chains REVERT: A 53 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7045 (ptp90) REVERT: B 32 PHE cc_start: 0.6622 (t80) cc_final: 0.6349 (t80) REVERT: B 53 ARG cc_start: 0.7166 (OUTLIER) cc_final: 0.6807 (ptp90) REVERT: B 84 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7441 (t80) REVERT: C 53 ARG cc_start: 0.7250 (OUTLIER) cc_final: 0.6973 (ptp90) REVERT: D 53 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.7039 (ptp90) REVERT: E 32 PHE cc_start: 0.6541 (t80) cc_final: 0.6273 (t80) REVERT: E 53 ARG cc_start: 0.7157 (OUTLIER) cc_final: 0.6798 (ptp90) REVERT: E 84 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7444 (t80) REVERT: F 53 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.7046 (ptp90) REVERT: G 53 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.7043 (ptp90) REVERT: H 32 PHE cc_start: 0.6581 (t80) cc_final: 0.6310 (t80) REVERT: H 53 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6805 (ptp90) REVERT: H 84 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7445 (t80) REVERT: I 53 ARG cc_start: 0.7258 (OUTLIER) cc_final: 0.7006 (ptp90) REVERT: J 53 ARG cc_start: 0.7266 (OUTLIER) cc_final: 0.7053 (ptp90) REVERT: K 53 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6794 (ptp90) REVERT: K 84 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7439 (t80) REVERT: L 53 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.7041 (ptp90) outliers start: 111 outliers final: 34 residues processed: 386 average time/residue: 1.0107 time to fit residues: 447.8079 Evaluate side-chains 308 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 258 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain I residue 53 ARG Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 131 optimal weight: 4.9990 chunk 197 optimal weight: 9.9990 chunk 208 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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: 0.7279 moved from start: 0.9964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19008 Z= 0.205 Angle : 0.721 11.954 25800 Z= 0.340 Chirality : 0.037 0.172 2952 Planarity : 0.003 0.024 3096 Dihedral : 3.791 13.736 2436 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 6.47 % Allowed : 21.96 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.17), residues: 2220 helix: 2.41 (0.11), residues: 1644 sheet: -0.70 (0.38), residues: 204 loop : -2.55 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP G 78 HIS 0.004 0.001 HIS L 74 PHE 0.029 0.001 PHE J 32 TYR 0.014 0.002 TYR I 155 ARG 0.004 0.001 ARG L 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 325 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7625 (t80) REVERT: E 84 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7612 (t80) REVERT: K 84 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7623 (t80) outliers start: 132 outliers final: 53 residues processed: 396 average time/residue: 0.9227 time to fit residues: 430.6507 Evaluate side-chains 318 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 262 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 228 LEU Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 228 LEU Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.0060 chunk 118 optimal weight: 10.0000 chunk 3 optimal weight: 0.0970 chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 178 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 106 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- 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: 0.7297 moved from start: 1.0152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19008 Z= 0.166 Angle : 0.733 16.161 25800 Z= 0.331 Chirality : 0.038 0.159 2952 Planarity : 0.003 0.019 3096 Dihedral : 3.665 16.858 2436 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.64 % Allowed : 21.47 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.17), residues: 2220 helix: 2.64 (0.11), residues: 1656 sheet: -0.64 (0.38), residues: 204 loop : -2.48 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 25 HIS 0.001 0.000 HIS E 74 PHE 0.034 0.001 PHE L 32 TYR 0.015 0.002 TYR C 98 ARG 0.003 0.000 ARG A 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 296 time to evaluate : 2.130 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: B 53 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6768 (ptp90) REVERT: B 84 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7585 (t80) REVERT: E 53 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6786 (ptp90) REVERT: E 84 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7577 (t80) REVERT: H 53 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6790 (ptp90) REVERT: K 53 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6764 (ptp90) REVERT: K 84 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.7585 (t80) outliers start: 115 outliers final: 58 residues processed: 356 average time/residue: 0.9964 time to fit residues: 408.4113 Evaluate side-chains 313 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 248 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain H residue 233 PHE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain K residue 233 PHE Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 208 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.7455 moved from start: 1.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19008 Z= 0.176 Angle : 0.731 14.394 25800 Z= 0.331 Chirality : 0.039 0.240 2952 Planarity : 0.003 0.017 3096 Dihedral : 3.541 14.440 2436 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 5.25 % Allowed : 21.86 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.17), residues: 2220 helix: 2.88 (0.11), residues: 1656 sheet: -0.61 (0.38), residues: 204 loop : -2.40 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 174 HIS 0.001 0.000 HIS A 74 PHE 0.030 0.001 PHE G 32 TYR 0.027 0.002 TYR F 230 ARG 0.004 0.001 ARG K 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 315 time to evaluate : 1.952 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7626 (t80) REVERT: E 84 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7628 (t80) REVERT: K 84 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7640 (t80) outliers start: 107 outliers final: 64 residues processed: 365 average time/residue: 1.0906 time to fit residues: 453.4194 Evaluate side-chains 344 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 277 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 233 PHE Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 233 PHE Chi-restraints excluded: chain K residue 82 ILE Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 170 LEU Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 223 LEU Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 175 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 130 optimal weight: 0.1980 chunk 126 optimal weight: 0.3980 chunk 96 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7528 moved from start: 1.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19008 Z= 0.173 Angle : 0.722 14.863 25800 Z= 0.335 Chirality : 0.039 0.240 2952 Planarity : 0.003 0.016 3096 Dihedral : 3.562 18.257 2436 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.83 % Allowed : 23.43 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.17), residues: 2220 helix: 2.89 (0.11), residues: 1656 sheet: -0.72 (0.37), residues: 204 loop : -2.48 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 174 HIS 0.002 0.001 HIS A 95 PHE 0.036 0.001 PHE C 32 TYR 0.038 0.002 TYR E 155 ARG 0.003 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 331 time to evaluate : 1.937 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ARG cc_start: 0.7129 (OUTLIER) cc_final: 0.6719 (ptp90) REVERT: B 84 PHE cc_start: 0.8071 (OUTLIER) cc_final: 0.7694 (t80) REVERT: E 53 ARG cc_start: 0.7123 (OUTLIER) cc_final: 0.6714 (ptp90) REVERT: E 84 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7690 (t80) REVERT: H 53 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6720 (ptp90) REVERT: H 84 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7721 (t80) REVERT: K 53 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.6721 (ptp90) REVERT: K 84 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7691 (t80) outliers start: 119 outliers final: 64 residues processed: 392 average time/residue: 0.9670 time to fit residues: 437.6079 Evaluate side-chains 361 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 289 time to evaluate : 1.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 170 LEU Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 228 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 189 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 1.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19008 Z= 0.216 Angle : 0.776 17.411 25800 Z= 0.367 Chirality : 0.041 0.281 2952 Planarity : 0.003 0.018 3096 Dihedral : 3.698 16.167 2436 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.29 % Allowed : 25.25 % Favored : 69.46 % 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: 2.78 (0.18), residues: 2220 helix: 2.97 (0.11), residues: 1656 sheet: -0.46 (0.38), residues: 204 loop : -2.54 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 174 HIS 0.005 0.001 HIS A 95 PHE 0.032 0.001 PHE C 32 TYR 0.037 0.002 TYR H 155 ARG 0.012 0.001 ARG J 101 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 350 time to evaluate : 2.251 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: A 98 TYR cc_start: 0.6590 (OUTLIER) cc_final: 0.5759 (m-80) REVERT: A 177 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5797 (p90) REVERT: B 53 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6830 (ptp90) REVERT: B 84 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7757 (t80) REVERT: D 177 TYR cc_start: 0.6219 (OUTLIER) cc_final: 0.5840 (p90) REVERT: E 53 ARG cc_start: 0.7184 (OUTLIER) cc_final: 0.6825 (ptp90) REVERT: E 84 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7777 (t80) REVERT: G 98 TYR cc_start: 0.6612 (OUTLIER) cc_final: 0.5793 (m-80) REVERT: G 177 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5799 (p90) REVERT: H 53 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6827 (ptp90) REVERT: H 84 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7828 (t80) REVERT: J 177 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.5830 (p90) REVERT: K 53 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6831 (ptp90) REVERT: K 84 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7773 (t80) outliers start: 108 outliers final: 47 residues processed: 402 average time/residue: 0.8999 time to fit residues: 422.1288 Evaluate side-chains 369 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 308 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 228 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 98 TYR Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 228 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 9.9990 chunk 181 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 116 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 chunk 127 optimal weight: 20.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 1.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 19008 Z= 0.319 Angle : 0.906 15.993 25800 Z= 0.443 Chirality : 0.044 0.238 2952 Planarity : 0.005 0.050 3096 Dihedral : 4.393 24.666 2436 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.02 % Allowed : 28.82 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.18), residues: 2220 helix: 2.58 (0.11), residues: 1656 sheet: -0.23 (0.37), residues: 204 loop : -2.63 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 174 HIS 0.005 0.002 HIS L 95 PHE 0.054 0.003 PHE I 229 TYR 0.043 0.003 TYR B 155 ARG 0.009 0.001 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 311 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.6184 (p90) REVERT: B 53 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.7020 (ptp90) REVERT: B 84 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.7829 (t80) REVERT: D 177 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6199 (p90) REVERT: E 53 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7016 (ptp90) REVERT: E 84 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7878 (t80) REVERT: G 177 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.6193 (p90) REVERT: H 53 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.7017 (ptp90) REVERT: H 84 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.7892 (t80) REVERT: J 177 TYR cc_start: 0.6781 (OUTLIER) cc_final: 0.6175 (p90) REVERT: K 53 ARG cc_start: 0.7262 (OUTLIER) cc_final: 0.7020 (ptp90) REVERT: K 84 PHE cc_start: 0.8255 (OUTLIER) cc_final: 0.7820 (t80) outliers start: 82 outliers final: 37 residues processed: 355 average time/residue: 1.0942 time to fit residues: 442.8300 Evaluate side-chains 305 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 256 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 226 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain I residue 226 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 98 TYR Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 226 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.2980 chunk 125 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 198 optimal weight: 9.9990 chunk 171 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 1.4342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19008 Z= 0.222 Angle : 0.843 17.186 25800 Z= 0.399 Chirality : 0.041 0.220 2952 Planarity : 0.003 0.042 3096 Dihedral : 4.029 19.048 2436 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.35 % Allowed : 30.88 % Favored : 66.76 % 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: 2.64 (0.18), residues: 2220 helix: 2.89 (0.12), residues: 1644 sheet: -0.15 (0.38), residues: 204 loop : -2.72 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 174 HIS 0.002 0.001 HIS K 95 PHE 0.030 0.002 PHE C 32 TYR 0.038 0.002 TYR I 155 ARG 0.003 0.000 ARG K 101 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 298 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.6190 (p90) REVERT: B 53 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6881 (ptp90) REVERT: B 84 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7876 (t80) REVERT: D 177 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6245 (p90) REVERT: E 53 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6947 (ptp90) REVERT: E 84 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7807 (t80) REVERT: E 177 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6547 (p90) REVERT: G 177 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.6209 (p90) REVERT: H 53 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6849 (ptp90) REVERT: H 84 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7867 (t80) REVERT: J 177 TYR cc_start: 0.6802 (OUTLIER) cc_final: 0.6230 (p90) REVERT: K 53 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6855 (ptp90) REVERT: K 84 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7858 (t80) outliers start: 48 outliers final: 31 residues processed: 325 average time/residue: 1.1432 time to fit residues: 421.0405 Evaluate side-chains 321 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 277 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 98 TYR Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 224 ASN F 15 GLN ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 15 GLN ** J 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 GLN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.091408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070350 restraints weight = 49176.850| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.01 r_work: 0.3034 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 1.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19008 Z= 0.208 Angle : 0.828 15.244 25800 Z= 0.387 Chirality : 0.040 0.198 2952 Planarity : 0.003 0.029 3096 Dihedral : 3.947 19.803 2436 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.94 % Allowed : 30.74 % Favored : 66.32 % 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: 2.74 (0.18), residues: 2220 helix: 2.97 (0.12), residues: 1644 sheet: -0.20 (0.37), residues: 204 loop : -2.73 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP E 174 HIS 0.003 0.001 HIS J 95 PHE 0.030 0.002 PHE C 32 TYR 0.029 0.002 TYR H 98 ARG 0.005 0.000 ARG J 101 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7666.20 seconds wall clock time: 135 minutes 46.19 seconds (8146.19 seconds total)