Starting phenix.real_space_refine on Wed Aug 7 00:51:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/08_2024/7z22_14455.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/08_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_14455/08_2024/7z22_14455.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/08_2024/7z22_14455.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/08_2024/7z22_14455.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z22_14455/08_2024/7z22_14455.cif" } 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-5409/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: 10.47, per 1000 atoms: 0.57 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: 7.25 Conformation dependent library (CDL) restraints added in 3.2 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: 1.83 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: 5.26 Time building geometry restraints manager: 7.96 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 3.120 nonbonded pdb=" NH1 ARG E 53 " pdb=" OD1 ASN F 63 " model vdw 2.198 3.120 nonbonded pdb=" NH1 ARG G 53 " pdb=" OD1 ASN H 63 " model vdw 2.199 3.120 nonbonded pdb=" NH1 ARG D 53 " pdb=" OD1 ASN E 63 " model vdw 2.199 3.120 nonbonded pdb=" OD1 ASN A 63 " pdb=" NH1 ARG F 53 " model vdw 2.199 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 14.560 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 49.400 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.360 ------------------------------------------------------------------------------- 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 : 1.982 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: 1.0527 time to fit residues: 903.3463 Evaluate side-chains 333 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 315 time to evaluate : 1.996 ------------------------------------------------------------------------------- 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: 7.9990 chunk 90 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 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: 2.0184 ------------------------------------------------------------------------------- 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: 0.6290 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19008 Z= 0.303 Angle : 0.943 12.120 25800 Z= 0.458 Chirality : 0.046 0.156 2952 Planarity : 0.005 0.026 3096 Dihedral : 4.570 27.095 2472 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.83 % Allowed : 14.75 % Favored : 79.41 % 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: 1.35 (0.17), residues: 2220 helix: 1.91 (0.11), residues: 1632 sheet: -1.18 (0.37), residues: 204 loop : -2.42 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 78 HIS 0.005 0.001 HIS D 95 PHE 0.029 0.003 PHE C 233 TYR 0.026 0.003 TYR J 98 ARG 0.015 0.002 ARG D 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 539 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 420 time to evaluate : 1.976 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 outliers start: 119 outliers final: 17 residues processed: 482 average time/residue: 0.8946 time to fit residues: 501.7876 Evaluate side-chains 342 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 325 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP 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 104 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 104 GLU 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 104 GLU Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain L residue 53 ARG 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: 0.1980 chunk 60 optimal weight: 6.9990 chunk 163 optimal weight: 0.0970 chunk 133 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 196 optimal weight: 4.9990 chunk 212 optimal weight: 0.0070 chunk 175 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 157 optimal weight: 0.8980 overall best weight: 1.0398 ------------------------------------------------------------------------------- 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 E 195 GLN G 195 GLN H 195 GLN K 195 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.6869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19008 Z= 0.187 Angle : 0.693 9.730 25800 Z= 0.327 Chirality : 0.038 0.134 2952 Planarity : 0.003 0.017 3096 Dihedral : 3.790 12.262 2436 Min Nonbonded Distance : 2.661 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.07 % Allowed : 20.98 % Favored : 74.95 % 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: 2.22 (0.18), residues: 2220 helix: 2.53 (0.11), residues: 1644 sheet: -0.57 (0.40), residues: 204 loop : -2.41 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 78 HIS 0.001 0.000 HIS E 74 PHE 0.027 0.001 PHE I 233 TYR 0.017 0.002 TYR I 98 ARG 0.007 0.001 ARG E 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 384 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 301 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 84 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.7050 (t80) outliers start: 83 outliers final: 11 residues processed: 368 average time/residue: 0.8341 time to fit residues: 363.2891 Evaluate side-chains 262 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 250 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 228 LEU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 228 LEU Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain K residue 190 ASP 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: 6.9990 chunk 147 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 131 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN F 195 GLN I 195 GLN J 195 GLN L 195 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 1.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 19008 Z= 0.363 Angle : 1.051 20.473 25800 Z= 0.498 Chirality : 0.050 0.278 2952 Planarity : 0.005 0.042 3096 Dihedral : 4.566 16.355 2436 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.64 % Allowed : 22.16 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.17), residues: 2220 helix: 1.42 (0.11), residues: 1644 sheet: -0.84 (0.37), residues: 204 loop : -2.66 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 25 HIS 0.005 0.002 HIS F 194 PHE 0.033 0.003 PHE A 30 TYR 0.023 0.003 TYR I 98 ARG 0.014 0.002 ARG K 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 527 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 412 time to evaluate : 2.320 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: E 84 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7808 (t80) REVERT: F 53 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6754 (ptp-170) REVERT: K 84 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7821 (t80) outliers start: 115 outliers final: 30 residues processed: 485 average time/residue: 1.1023 time to fit residues: 608.0657 Evaluate side-chains 325 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 292 time to evaluate : 2.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 164 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 12 ASP Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 164 ILE 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: 0.9980 chunk 118 optimal weight: 9.9990 chunk 3 optimal weight: 8.9990 chunk 155 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.7652 moved from start: 1.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19008 Z= 0.189 Angle : 0.726 10.922 25800 Z= 0.348 Chirality : 0.039 0.192 2952 Planarity : 0.003 0.021 3096 Dihedral : 4.020 15.709 2436 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 5.98 % Allowed : 26.03 % Favored : 67.99 % 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: 1.82 (0.18), residues: 2220 helix: 2.33 (0.11), residues: 1632 sheet: -0.63 (0.38), residues: 204 loop : -2.91 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 25 HIS 0.002 0.000 HIS I 74 PHE 0.026 0.001 PHE G 32 TYR 0.039 0.002 TYR B 155 ARG 0.003 0.000 ARG I 76 *********************** 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 465 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 343 time to evaluate : 2.005 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: F 53 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6866 (ptp-170) REVERT: K 76 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7206 (mtm180) outliers start: 122 outliers final: 53 residues processed: 410 average time/residue: 1.1061 time to fit residues: 514.3770 Evaluate side-chains 369 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 314 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 177 TYR 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 177 TYR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 177 TYR 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 105 LYS Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 233 PHE Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 233 PHE Chi-restraints excluded: chain K residue 76 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 225 ILE Chi-restraints excluded: chain L residue 12 ASP Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 233 PHE 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: 4.9990 chunk 41 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 208 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** 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: 0.7915 moved from start: 1.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19008 Z= 0.258 Angle : 0.774 12.478 25800 Z= 0.374 Chirality : 0.040 0.264 2952 Planarity : 0.004 0.035 3096 Dihedral : 3.779 12.789 2436 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.54 % Allowed : 26.76 % Favored : 67.70 % 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: 2.60 (0.18), residues: 2220 helix: 2.83 (0.11), residues: 1656 sheet: -0.23 (0.39), residues: 204 loop : -2.77 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 174 HIS 0.002 0.001 HIS L 194 PHE 0.027 0.002 PHE A 32 TYR 0.039 0.003 TYR E 155 ARG 0.006 0.001 ARG D 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 455 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 342 time to evaluate : 2.129 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: A 177 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5990 (p90) REVERT: B 84 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7858 (t80) REVERT: D 177 TYR cc_start: 0.6381 (OUTLIER) cc_final: 0.6005 (p90) REVERT: E 84 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7824 (t80) REVERT: G 177 TYR cc_start: 0.6364 (OUTLIER) cc_final: 0.5990 (p90) REVERT: H 84 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7850 (t80) REVERT: J 177 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.6007 (p90) REVERT: K 84 PHE cc_start: 0.8244 (OUTLIER) cc_final: 0.7816 (t80) outliers start: 113 outliers final: 37 residues processed: 413 average time/residue: 1.1179 time to fit residues: 522.8448 Evaluate side-chains 325 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL 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 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 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 75 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 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 F residue 64 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 75 VAL 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 H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 98 TYR 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 75 VAL 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 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 84 PHE Chi-restraints excluded: chain L residue 98 TYR Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 225 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 175 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 208 optimal weight: 8.9990 chunk 130 optimal weight: 0.0050 chunk 126 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 GLN ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN K 173 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 1.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19008 Z= 0.216 Angle : 0.775 14.400 25800 Z= 0.356 Chirality : 0.037 0.127 2952 Planarity : 0.003 0.034 3096 Dihedral : 3.808 19.932 2436 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.90 % Allowed : 29.46 % Favored : 65.64 % 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: 2.86 (0.18), residues: 2220 helix: 3.11 (0.12), residues: 1644 sheet: -0.17 (0.39), residues: 204 loop : -2.97 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 174 HIS 0.002 0.001 HIS E 95 PHE 0.023 0.001 PHE G 32 TYR 0.028 0.002 TYR A 98 ARG 0.002 0.000 ARG A 153 *********************** 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 396 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 296 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.6050 (p90) REVERT: B 84 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7834 (t80) REVERT: B 177 TYR cc_start: 0.6773 (OUTLIER) cc_final: 0.6441 (p90) REVERT: C 76 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7397 (mtm180) REVERT: D 177 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.6063 (p90) REVERT: E 84 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7796 (t80) REVERT: E 212 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7745 (t80) REVERT: F 76 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7391 (mtm180) REVERT: G 177 TYR cc_start: 0.6485 (OUTLIER) cc_final: 0.6054 (p90) REVERT: H 84 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7826 (t80) REVERT: I 76 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7383 (mtm180) REVERT: J 177 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.6062 (p90) REVERT: K 84 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7798 (t80) REVERT: K 177 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.6406 (p90) REVERT: K 212 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7763 (t80) REVERT: L 76 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7407 (mtm180) outliers start: 100 outliers final: 48 residues processed: 358 average time/residue: 1.2261 time to fit residues: 493.5583 Evaluate side-chains 348 residues out of total 2040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 284 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL 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 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 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 233 PHE Chi-restraints excluded: chain C residue 76 ARG Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 233 PHE Chi-restraints excluded: chain D residue 75 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 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 98 TYR Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain E residue 233 PHE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 233 PHE Chi-restraints excluded: chain G residue 75 VAL 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 G residue 233 PHE 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 233 PHE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 76 ARG Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain I residue 233 PHE Chi-restraints excluded: chain J residue 75 VAL 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 J residue 233 PHE 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 212 PHE Chi-restraints excluded: chain K residue 233 PHE Chi-restraints excluded: chain L residue 76 ARG Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Chi-restraints excluded: chain L residue 233 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 173 GLN B 173 GLN B 224 ASN ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 173 GLN E 173 GLN ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN G 173 GLN H 173 GLN ** H 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 GLN J 15 GLN J 173 GLN K 173 GLN ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 1.4163 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: