Starting phenix.real_space_refine on Mon Jul 22 06:39:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/07_2024/8tpa_41471.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/07_2024/8tpa_41471.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/07_2024/8tpa_41471.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/07_2024/8tpa_41471.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/07_2024/8tpa_41471.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tpa_41471/07_2024/8tpa_41471.cif" } resolution = 3.0 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= 0.058 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 69 5.16 5 C 10875 2.51 5 N 2961 2.21 5 O 3381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 278": "OD1" <-> "OD2" Residue "G PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17286 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "L" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "B" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 1, 'TRANS': 161} Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "D" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "F" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 1, 'TRANS': 161} Chain: "G" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2530 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "J" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "K" Number of atoms: 1328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1328 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 1, 'TRANS': 161} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 9.29, per 1000 atoms: 0.54 Number of scatterers: 17286 At special positions: 0 Unit cell: (132.25, 127.65, 148.35, 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 69 16.00 O 3381 8.00 N 2961 7.00 C 10875 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.05 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.02 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.06 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS F 137 " distance=2.05 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.06 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS K 137 " distance=2.05 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.02 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.06 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.02 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Simple disulfide: pdb=" SG CYS K 144 " - pdb=" SG CYS K 148 " 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 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 401 " - " ASN A 132 " " NAG A 402 " - " ASN A 163 " " NAG A 403 " - " ASN A 289 " " NAG A 404 " - " ASN A 63 " " NAG C 401 " - " ASN C 132 " " NAG C 402 " - " ASN C 163 " " NAG C 403 " - " ASN C 289 " " NAG C 404 " - " ASN C 63 " " NAG G 401 " - " ASN G 132 " " NAG G 402 " - " ASN G 163 " " NAG G 403 " - " ASN G 289 " " NAG G 404 " - " ASN G 63 " " NAG M 1 " - " ASN A 95 " " NAG N 1 " - " ASN C 95 " " NAG O 1 " - " ASN G 95 " Time building additional restraints: 5.76 Conformation dependent library (CDL) restraints added in 2.9 seconds 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3960 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 51 sheets defined 21.4% alpha, 34.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.773A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU A 78 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 125 through 130 removed outlier: 4.213A pdb=" N TRP A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.772A pdb=" N GLU C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LEU C 78 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 125 through 130 removed outlier: 4.213A pdb=" N TRP C 130 " --> pdb=" O LYS C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 37 through 58 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 65 through 72 Processing helix chain 'G' and resid 73 through 80 removed outlier: 3.773A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LEU G 78 " --> pdb=" O GLU G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 125 through 130 removed outlier: 4.213A pdb=" N TRP G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 196 Processing helix chain 'I' and resid 73 through 75 No H-bonds generated for 'chain 'I' and resid 73 through 75' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'K' and resid 37 through 58 Processing helix chain 'K' and resid 74 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 159 through 161 No H-bonds generated for 'chain 'K' and resid 159 through 161' Processing helix chain 'K' and resid 162 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 33 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 removed outlier: 4.353A pdb=" N ASP A 24 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 6.121A pdb=" N LEU A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS A 277 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.632A pdb=" N LEU A 59 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR A 256 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU A 175 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.368A pdb=" N SER A 138 " --> pdb=" O LYS A 144 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N LYS A 144 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR H 35 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP H 35A" --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.411A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 33 through 36 Processing sheet with id=AC1, first strand: chain 'C' and resid 24 through 26 removed outlier: 4.354A pdb=" N ASP C 24 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC3, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC4, first strand: chain 'C' and resid 51 through 54 removed outlier: 6.121A pdb=" N LEU C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.632A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 115 through 122 removed outlier: 6.508A pdb=" N TYR C 256 " --> pdb=" O LEU C 179 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU C 175 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.369A pdb=" N SER C 138 " --> pdb=" O LYS C 144 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LYS C 144 " --> pdb=" O SER C 138 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD1, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AD2, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR D 35 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP D 35A" --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR D 50 " --> pdb=" O TRP D 35A" (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AD5, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.410A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.410A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 33 through 36 Processing sheet with id=AD9, first strand: chain 'G' and resid 24 through 26 removed outlier: 4.353A pdb=" N ASP G 24 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'G' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'G' and resid 51 through 54 removed outlier: 6.121A pdb=" N LEU G 51 " --> pdb=" O ASP G 275 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N CYS G 277 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 59 through 60 removed outlier: 6.632A pdb=" N LEU G 59 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.509A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU G 179 " --> pdb=" O PRO G 254 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 115 through 122 removed outlier: 6.509A pdb=" N TYR G 256 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU G 179 " --> pdb=" O TYR G 256 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLU G 175 " --> pdb=" O LEU G 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 136 through 141 removed outlier: 7.368A pdb=" N SER G 138 " --> pdb=" O LYS G 144 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N LYS G 144 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 164 through 169 Processing sheet with id=AE9, first strand: chain 'G' and resid 286 through 287 Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.858A pdb=" N TYR I 35 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP I 35A" --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N TYR I 50 " --> pdb=" O TRP I 35A" (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.409A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.409A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA J 84 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2070 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: 5.82 Time building geometry restraints manager: 6.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 5199 1.33 - 1.47: 5392 1.47 - 1.61: 7013 1.61 - 1.75: 12 1.75 - 1.89: 81 Bond restraints: 17697 Sorted by residual: bond pdb=" CB ILE I 37 " pdb=" CG1 ILE I 37 " ideal model delta sigma weight residual 1.530 1.425 0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb=" CB ILE D 37 " pdb=" CG1 ILE D 37 " ideal model delta sigma weight residual 1.530 1.425 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" CB ILE H 37 " pdb=" CG1 ILE H 37 " ideal model delta sigma weight residual 1.530 1.426 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" CB ASN G 48 " pdb=" CG ASN G 48 " ideal model delta sigma weight residual 1.516 1.391 0.125 2.50e-02 1.60e+03 2.49e+01 bond pdb=" CB ASN C 48 " pdb=" CG ASN C 48 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.46e+01 ... (remaining 17692 not shown) Histogram of bond angle deviations from ideal: 96.08 - 109.35: 3157 109.35 - 122.61: 18403 122.61 - 135.88: 2461 135.88 - 149.14: 0 149.14 - 162.41: 6 Bond angle restraints: 24027 Sorted by residual: angle pdb=" C2 NAG C 402 " pdb=" N2 NAG C 402 " pdb=" C7 NAG C 402 " ideal model delta sigma weight residual 124.56 162.41 -37.85 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG G 402 " pdb=" N2 NAG G 402 " pdb=" C7 NAG G 402 " ideal model delta sigma weight residual 124.56 162.34 -37.78 3.00e+00 1.11e-01 1.59e+02 angle pdb=" C2 NAG A 402 " pdb=" N2 NAG A 402 " pdb=" C7 NAG A 402 " ideal model delta sigma weight residual 124.56 162.31 -37.75 3.00e+00 1.11e-01 1.58e+02 angle pdb=" C2 NAG C 403 " pdb=" N2 NAG C 403 " pdb=" C7 NAG C 403 " ideal model delta sigma weight residual 124.56 160.05 -35.49 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C2 NAG A 403 " pdb=" N2 NAG A 403 " pdb=" C7 NAG A 403 " ideal model delta sigma weight residual 124.56 160.01 -35.45 3.00e+00 1.11e-01 1.40e+02 ... (remaining 24022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 10329 17.80 - 35.61: 273 35.61 - 53.41: 109 53.41 - 71.22: 38 71.22 - 89.02: 9 Dihedral angle restraints: 10758 sinusoidal: 4539 harmonic: 6219 Sorted by residual: dihedral pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " pdb=" SG CYS F 148 " pdb=" CB CYS F 148 " ideal model delta sinusoidal sigma weight residual 93.00 146.69 -53.69 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CB CYS K 144 " pdb=" SG CYS K 144 " pdb=" SG CYS K 148 " pdb=" CB CYS K 148 " ideal model delta sinusoidal sigma weight residual 93.00 146.67 -53.67 1 1.00e+01 1.00e-02 3.91e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual 93.00 146.66 -53.66 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 10755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1731 0.089 - 0.178: 663 0.178 - 0.267: 150 0.267 - 0.356: 60 0.356 - 0.445: 21 Chirality restraints: 2625 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.03e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.93e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.79e+01 ... (remaining 2622 not shown) Planarity restraints: 3114 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 113 " 0.034 2.00e-02 2.50e+03 6.99e-02 4.89e+01 pdb=" C SER D 113 " -0.121 2.00e-02 2.50e+03 pdb=" O SER D 113 " 0.043 2.00e-02 2.50e+03 pdb=" OXT SER D 113 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER I 113 " 0.034 2.00e-02 2.50e+03 6.96e-02 4.84e+01 pdb=" C SER I 113 " -0.120 2.00e-02 2.50e+03 pdb=" O SER I 113 " 0.043 2.00e-02 2.50e+03 pdb=" OXT SER I 113 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 113 " -0.034 2.00e-02 2.50e+03 6.96e-02 4.84e+01 pdb=" C SER H 113 " 0.120 2.00e-02 2.50e+03 pdb=" O SER H 113 " -0.043 2.00e-02 2.50e+03 pdb=" OXT SER H 113 " -0.043 2.00e-02 2.50e+03 ... (remaining 3111 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 5534 2.85 - 3.36: 15252 3.36 - 3.88: 30199 3.88 - 4.39: 35145 4.39 - 4.90: 58402 Nonbonded interactions: 144532 Sorted by model distance: nonbonded pdb=" NZ LYS B 83 " pdb=" OD1 ASP F 85 " model vdw 2.338 2.520 nonbonded pdb=" OD1 ASP B 85 " pdb=" NZ LYS K 83 " model vdw 2.338 2.520 nonbonded pdb=" NZ LYS F 83 " pdb=" OD1 ASP K 85 " model vdw 2.338 2.520 nonbonded pdb=" N ALA J 50 " pdb=" O ALA J 50 " model vdw 2.355 2.496 nonbonded pdb=" N ALA L 50 " pdb=" O ALA L 50 " model vdw 2.355 2.496 ... (remaining 144527 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 1.560 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: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 45.520 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.090 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:11.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 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 : 0.022 0.152 17697 Z= 1.418 Angle : 1.807 37.848 24027 Z= 1.159 Chirality : 0.106 0.445 2625 Planarity : 0.009 0.070 3099 Dihedral : 10.431 89.023 6726 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.17), residues: 2130 helix: 1.50 (0.24), residues: 357 sheet: 0.96 (0.20), residues: 528 loop : 0.54 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.009 TRP C 84 HIS 0.014 0.003 HIS B 142 PHE 0.033 0.006 PHE C 118 TYR 0.086 0.009 TYR I 50 ARG 0.007 0.001 ARG G 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7298 (mm110) REVERT: B 162 TYR cc_start: 0.7328 (m-80) cc_final: 0.6700 (m-80) REVERT: C 60 GLN cc_start: 0.8554 (mt0) cc_final: 0.8319 (mt0) REVERT: G 274 MET cc_start: 0.7003 (tpt) cc_final: 0.6397 (tpt) outliers start: 0 outliers final: 3 residues processed: 400 average time/residue: 1.4302 time to fit residues: 630.1881 Evaluate side-chains 198 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain G residue 323 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN L 28 ASN B 26 HIS B 46 ASN C 33 ASN D 3 GLN F 26 HIS F 42 GLN F 46 ASN G 33 ASN ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 295 GLN I 60 ASN J 28 ASN K 26 HIS K 46 ASN K 154 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17697 Z= 0.274 Angle : 0.706 13.133 24027 Z= 0.369 Chirality : 0.049 0.331 2625 Planarity : 0.005 0.041 3099 Dihedral : 6.388 77.940 2745 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.68 % Allowed : 8.37 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.18), residues: 2130 helix: 2.45 (0.25), residues: 360 sheet: 0.75 (0.21), residues: 549 loop : 0.31 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 47 HIS 0.006 0.001 HIS A 47 PHE 0.035 0.003 PHE A 118 TYR 0.031 0.002 TYR H 50 ARG 0.007 0.001 ARG I 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 256 time to evaluate : 1.938 Fit side-chains REVERT: A 173 GLU cc_start: 0.6482 (tp30) cc_final: 0.6173 (tp30) REVERT: D 63 LEU cc_start: 0.7932 (mt) cc_final: 0.7566 (mt) REVERT: F 69 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7765 (mm-30) REVERT: G 145 SER cc_start: 0.8461 (m) cc_final: 0.8138 (p) REVERT: G 274 MET cc_start: 0.7265 (tpt) cc_final: 0.6642 (tpt) REVERT: I 5 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7610 (mmp-170) REVERT: J 68 ARG cc_start: 0.8535 (mtp85) cc_final: 0.8254 (mtp85) REVERT: K 72 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8288 (mttt) outliers start: 69 outliers final: 23 residues processed: 297 average time/residue: 1.2863 time to fit residues: 425.2448 Evaluate side-chains 212 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain I residue 5 ARG Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain K residue 72 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 170 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 105 GLN F 26 HIS G 199 ASN G 295 GLN K 26 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 17697 Z= 0.519 Angle : 0.801 11.292 24027 Z= 0.409 Chirality : 0.053 0.328 2625 Planarity : 0.006 0.042 3099 Dihedral : 6.470 71.215 2739 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.64 % Allowed : 10.35 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.39 (0.17), residues: 2130 helix: 1.89 (0.25), residues: 360 sheet: 0.30 (0.20), residues: 597 loop : -0.22 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 47 HIS 0.012 0.002 HIS F 142 PHE 0.034 0.003 PHE C 118 TYR 0.039 0.003 TYR H 50 ARG 0.008 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 216 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7815 (mp0) cc_final: 0.7589 (mp0) REVERT: H 43 ARG cc_start: 0.6877 (OUTLIER) cc_final: 0.6556 (mmt90) REVERT: L 22 THR cc_start: 0.8553 (m) cc_final: 0.8315 (m) REVERT: C 127 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6820 (pt0) REVERT: D 53 TYR cc_start: 0.5819 (m-80) cc_final: 0.5489 (m-80) REVERT: E 68 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7455 (mtp85) REVERT: G 274 MET cc_start: 0.7670 (tpt) cc_final: 0.6808 (tpt) REVERT: J 24 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6735 (ttt90) REVERT: K 72 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8362 (mttt) outliers start: 87 outliers final: 36 residues processed: 272 average time/residue: 1.3193 time to fit residues: 398.9985 Evaluate side-chains 235 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 194 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 43 ARG Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain K residue 72 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 202 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN H 76 ASN B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN D 3 GLN D 76 ASN D 105 GLN F 26 HIS ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 28 ASN J 31 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17697 Z= 0.202 Angle : 0.606 9.679 24027 Z= 0.310 Chirality : 0.046 0.363 2625 Planarity : 0.004 0.034 3099 Dihedral : 5.918 70.936 2739 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.63 % Allowed : 13.28 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.41 (0.17), residues: 2130 helix: 2.00 (0.26), residues: 363 sheet: 0.18 (0.21), residues: 522 loop : -0.15 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 47 HIS 0.004 0.001 HIS K 26 PHE 0.016 0.002 PHE G 118 TYR 0.029 0.002 TYR H 50 ARG 0.009 0.000 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 209 time to evaluate : 2.096 Fit side-chains REVERT: C 127 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6667 (pt0) REVERT: E 68 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7376 (mtp85) REVERT: G 274 MET cc_start: 0.7376 (tpt) cc_final: 0.6494 (tpt) outliers start: 68 outliers final: 28 residues processed: 257 average time/residue: 1.2250 time to fit residues: 352.2870 Evaluate side-chains 214 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 8.9990 chunk 140 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 182 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN F 26 HIS G 199 ASN K 26 HIS K 129 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 17697 Z= 0.531 Angle : 0.778 10.302 24027 Z= 0.393 Chirality : 0.052 0.343 2625 Planarity : 0.006 0.043 3099 Dihedral : 6.385 65.941 2739 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.91 % Allowed : 13.39 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.08 (0.17), residues: 2130 helix: 1.60 (0.26), residues: 363 sheet: 0.20 (0.20), residues: 567 loop : -0.47 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 35A HIS 0.009 0.002 HIS C 47 PHE 0.031 0.003 PHE C 118 TYR 0.038 0.003 TYR H 50 ARG 0.008 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 207 time to evaluate : 1.914 Fit side-chains revert: symmetry clash REVERT: L 100 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.6702 (tt0) REVERT: C 127 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6795 (pt0) REVERT: D 105 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7270 (pm20) REVERT: E 68 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.7563 (mtp85) REVERT: G 119 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: I 64 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.6726 (ttp80) REVERT: J 68 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8317 (mtp85) REVERT: K 72 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8350 (mttt) outliers start: 92 outliers final: 49 residues processed: 267 average time/residue: 1.2675 time to fit residues: 377.2851 Evaluate side-chains 250 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 193 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 50 TYR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 118 PHE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 118 PHE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 50 TYR Chi-restraints excluded: chain I residue 64 ARG Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 168 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS C 33 ASN D 3 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS G 199 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17697 Z= 0.192 Angle : 0.590 9.473 24027 Z= 0.301 Chirality : 0.045 0.311 2625 Planarity : 0.004 0.042 3099 Dihedral : 5.797 67.713 2739 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.15 % Allowed : 15.95 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.13 (0.18), residues: 2130 helix: 1.94 (0.26), residues: 363 sheet: 0.05 (0.22), residues: 507 loop : -0.41 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.006 0.001 HIS K 26 PHE 0.013 0.001 PHE C 118 TYR 0.026 0.002 TYR H 50 ARG 0.010 0.001 ARG H 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 214 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: L 100 GLN cc_start: 0.6824 (OUTLIER) cc_final: 0.6611 (tt0) REVERT: C 127 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6707 (pt0) REVERT: D 63 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6787 (mt) REVERT: E 68 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7764 (mtp85) REVERT: G 274 MET cc_start: 0.7349 (tpt) cc_final: 0.6416 (tpt) REVERT: J 4 MET cc_start: 0.7830 (mmm) cc_final: 0.7507 (mmm) REVERT: J 68 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8181 (mtp85) outliers start: 59 outliers final: 24 residues processed: 257 average time/residue: 1.2676 time to fit residues: 363.3838 Evaluate side-chains 222 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN B 26 HIS B 154 ASN C 199 ASN ** D 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 77 GLN F 26 HIS G 199 ASN J 3 GLN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 17697 Z= 0.535 Angle : 0.771 10.653 24027 Z= 0.388 Chirality : 0.051 0.358 2625 Planarity : 0.005 0.041 3099 Dihedral : 6.335 67.642 2739 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.84 % Allowed : 15.95 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.04 (0.17), residues: 2130 helix: 1.71 (0.25), residues: 363 sheet: 0.16 (0.21), residues: 567 loop : -0.65 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 97 HIS 0.008 0.002 HIS C 47 PHE 0.032 0.003 PHE C 118 TYR 0.044 0.003 TYR D 50 ARG 0.009 0.001 ARG I 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 216 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 100 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6717 (tt0) REVERT: C 127 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6687 (pt0) REVERT: D 53 TYR cc_start: 0.6000 (m-10) cc_final: 0.5695 (m-80) REVERT: D 63 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7029 (mt) REVERT: E 68 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7732 (mtp85) REVERT: G 119 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: G 219 LYS cc_start: 0.8341 (tptt) cc_final: 0.8078 (tppp) REVERT: G 274 MET cc_start: 0.7592 (tpt) cc_final: 0.6552 (tpt) REVERT: J 68 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8216 (mtp85) outliers start: 72 outliers final: 45 residues processed: 265 average time/residue: 1.2791 time to fit residues: 378.1794 Evaluate side-chains 251 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 200 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 50 TYR Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 54 ASN Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 120 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 100 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN B 26 HIS C 33 ASN C 133 HIS D 3 GLN D 76 ASN D 77 GLN F 26 HIS F 142 HIS G 92 ASN G 199 ASN I 76 ASN K 26 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17697 Z= 0.239 Angle : 0.620 9.520 24027 Z= 0.314 Chirality : 0.045 0.306 2625 Planarity : 0.004 0.038 3099 Dihedral : 5.935 69.595 2739 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.84 % Allowed : 16.96 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.01 (0.17), residues: 2130 helix: 1.96 (0.26), residues: 363 sheet: 0.04 (0.23), residues: 477 loop : -0.60 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.005 0.001 HIS K 26 PHE 0.016 0.002 PHE C 118 TYR 0.034 0.002 TYR H 50 ARG 0.010 0.000 ARG D 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 202 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 100 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6667 (tt0) REVERT: B 116 LYS cc_start: 0.8294 (mttt) cc_final: 0.7851 (mptt) REVERT: C 127 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6747 (pt0) REVERT: D 53 TYR cc_start: 0.5880 (m-10) cc_final: 0.5642 (m-10) REVERT: E 68 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7654 (mtp85) REVERT: G 119 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: G 219 LYS cc_start: 0.8210 (tptt) cc_final: 0.7957 (tppp) REVERT: G 274 MET cc_start: 0.7385 (tpt) cc_final: 0.6357 (tpt) REVERT: J 68 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.8096 (mtp85) outliers start: 72 outliers final: 42 residues processed: 253 average time/residue: 1.2439 time to fit residues: 352.9506 Evaluate side-chains 241 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 194 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 121 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 63 LEU Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain J residue 68 ARG Chi-restraints excluded: chain K residue 121 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.0670 chunk 176 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 170 optimal weight: 0.3980 chunk 178 optimal weight: 0.6980 chunk 187 optimal weight: 0.8980 chunk 123 optimal weight: 0.1980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN H 76 ASN B 26 HIS C 285 GLN D 3 GLN D 76 ASN D 77 GLN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS G 92 ASN G 199 ASN I 76 ASN J 31 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17697 Z= 0.178 Angle : 0.598 10.466 24027 Z= 0.302 Chirality : 0.045 0.256 2625 Planarity : 0.004 0.036 3099 Dihedral : 5.747 70.733 2739 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.20 % Allowed : 17.33 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.10 (0.18), residues: 2130 helix: 2.13 (0.26), residues: 363 sheet: 0.07 (0.23), residues: 477 loop : -0.52 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 92 HIS 0.004 0.001 HIS K 26 PHE 0.014 0.001 PHE F 110 TYR 0.030 0.002 TYR I 50 ARG 0.010 0.000 ARG I 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 206 time to evaluate : 2.066 Fit side-chains revert: symmetry clash REVERT: L 100 GLN cc_start: 0.6838 (OUTLIER) cc_final: 0.6633 (tt0) REVERT: B 116 LYS cc_start: 0.8233 (mttt) cc_final: 0.7785 (mptt) REVERT: C 127 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6704 (pt0) REVERT: D 53 TYR cc_start: 0.5966 (m-10) cc_final: 0.5719 (m-80) REVERT: G 119 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: G 219 LYS cc_start: 0.8141 (tptt) cc_final: 0.7906 (tppp) REVERT: G 274 MET cc_start: 0.7309 (tpt) cc_final: 0.6293 (tpt) REVERT: J 68 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8077 (mtp85) outliers start: 60 outliers final: 36 residues processed: 248 average time/residue: 1.3003 time to fit residues: 362.9422 Evaluate side-chains 237 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 285 GLN Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain D residue 76 ASN Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 145 SER Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 68 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.0170 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 10.0000 chunk 192 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 132 optimal weight: 2.9990 overall best weight: 1.8424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN B 26 HIS C 199 ASN C 285 GLN ** D 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN I 76 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 17697 Z= 0.352 Angle : 0.659 9.570 24027 Z= 0.333 Chirality : 0.047 0.305 2625 Planarity : 0.005 0.039 3099 Dihedral : 5.919 71.270 2739 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.88 % Allowed : 17.76 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.07 (0.18), residues: 2130 helix: 2.07 (0.26), residues: 363 sheet: 0.23 (0.21), residues: 546 loop : -0.66 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 35A HIS 0.006 0.001 HIS C 47 PHE 0.022 0.002 PHE C 118 TYR 0.038 0.002 TYR L 49 ARG 0.011 0.001 ARG H 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4260 Ramachandran restraints generated. 2130 Oldfield, 0 Emsley, 2130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 207 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: L 100 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: B 116 LYS cc_start: 0.8266 (mttt) cc_final: 0.7822 (mptt) REVERT: C 127 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6837 (pt0) REVERT: D 53 TYR cc_start: 0.5934 (m-10) cc_final: 0.5639 (m-80) REVERT: G 119 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: G 219 LYS cc_start: 0.8234 (tptt) cc_final: 0.8008 (tppp) REVERT: G 274 MET cc_start: 0.7422 (tpt) cc_final: 0.6418 (tpt) REVERT: J 68 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8112 (mtp85) outliers start: 54 outliers final: 37 residues processed: 247 average time/residue: 1.2562 time to fit residues: 346.9466 Evaluate side-chains 241 residues out of total 1875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 211 ARG Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 100 GLN Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 127 GLU Chi-restraints excluded: chain C residue 145 SER Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 295 GLN Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 57 THR Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain F residue 121 LYS Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 77 GLU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain G residue 261 SER Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 105 GLN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 68 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 171 optimal weight: 0.0030 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS C 33 ASN C 199 ASN C 285 GLN ** D 35BASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 ASN F 26 HIS ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN I 76 ASN K 26 HIS ** K 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.140077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.116347 restraints weight = 23825.218| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.63 r_work: 0.3173 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.208 17697 Z= 0.360 Angle : 0.826 59.199 24027 Z= 0.463 Chirality : 0.051 1.121 2625 Planarity : 0.005 0.040 3099 Dihedral : 5.924 71.288 2739 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.72 % Allowed : 17.87 % Favored : 79.41 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.12 % 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: 0.07 (0.18), residues: 2130 helix: 2.08 (0.26), residues: 363 sheet: 0.22 (0.21), residues: 546 loop : -0.67 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP K 14 HIS 0.005 0.001 HIS C 47 PHE 0.021 0.002 PHE C 118 TYR 0.035 0.002 TYR H 50 ARG 0.008 0.000 ARG H 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6488.30 seconds wall clock time: 114 minutes 24.28 seconds (6864.28 seconds total)