Starting phenix.real_space_refine on Tue Apr 9 19:38:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0l_23098/04_2024/7l0l_23098.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0l_23098/04_2024/7l0l_23098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0l_23098/04_2024/7l0l_23098.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0l_23098/04_2024/7l0l_23098.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0l_23098/04_2024/7l0l_23098.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l0l_23098/04_2024/7l0l_23098.pdb" } resolution = 2.85 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= 0.003 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 10782 2.51 5 N 2955 2.21 5 O 3378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 60": "OE1" <-> "OE2" Residue "A ASP 63": "OD1" <-> "OD2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 95": "OD1" <-> "OD2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A GLU 255": "OE1" <-> "OE2" Residue "B ASP 29": "OD1" <-> "OD2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 82": "OD1" <-> "OD2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 77": "OD1" <-> "OD2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C GLU 216": "OE1" <-> "OE2" Residue "C TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E GLU 139": "OE1" <-> "OE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 10": "OE1" <-> "OE2" Residue "G TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 82": "OD1" <-> "OD2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D ASP 187": "OD1" <-> "OD2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F ASP 19": "OD1" <-> "OD2" Residue "F TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 29": "OD1" <-> "OD2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 120": "OD1" <-> "OD2" Residue "F TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17211 Number of models: 1 Model: "" Number of chains: 18 Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "A" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2521 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain: "B" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "J" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2521 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain: "E" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "G" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "K" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 824 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "D" Number of atoms: 2521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2521 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 18, 'TRANS': 303} Chain: "F" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1398 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 1, 'TRANS': 170} Chain: "I" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.40, per 1000 atoms: 0.55 Number of scatterers: 17211 At special positions: 0 Unit cell: (139.707, 125.628, 150.537, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3378 8.00 N 2955 7.00 C 10782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS F 47 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 47 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS E 137 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 47 " - pdb=" SG CYS D 30 " distance=2.03 Simple disulfide: pdb=" SG CYS E 144 " - pdb=" SG CYS E 148 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 277 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 76 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 305 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " 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 NAG-ASN " NAG A 401 " - " ASN A 33 " " NAG A 402 " - " ASN A 169 " " NAG A 403 " - " ASN A 21 " " NAG A 404 " - " ASN A 289 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 33 " " NAG C 402 " - " ASN C 169 " " NAG C 403 " - " ASN C 21 " " NAG C 404 " - " ASN C 289 " " NAG D 401 " - " ASN D 33 " " NAG D 402 " - " ASN D 169 " " NAG D 403 " - " ASN D 21 " " NAG D 404 " - " ASN D 289 " " NAG E 301 " - " ASN E 154 " " NAG F 301 " - " ASN F 154 " Time building additional restraints: 6.46 Conformation dependent library (CDL) restraints added in 2.9 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 48 sheets defined 20.3% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'L' and resid 28 through 31 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.602A pdb=" N SER A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.547A pdb=" N ARG A 126 " --> pdb=" O PRO A 122 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 127' Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 37 through 59 removed outlier: 3.660A pdb=" N MET B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 62 No H-bonds generated for 'chain 'B' and resid 60 through 62' Processing helix chain 'B' and resid 74 through 124 removed outlier: 3.806A pdb=" N VAL B 115 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 154 Processing helix chain 'B' and resid 158 through 172 removed outlier: 3.619A pdb=" N TYR B 162 " --> pdb=" O ASP B 158 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 31 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.944A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG 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 122 through 127 removed outlier: 3.641A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'E' and resid 37 through 59 removed outlier: 3.507A pdb=" N MET E 59 " --> pdb=" O VAL E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 62 No H-bonds generated for 'chain 'E' and resid 60 through 62' Processing helix chain 'E' and resid 74 through 124 removed outlier: 3.756A pdb=" N VAL E 115 " --> pdb=" O HIS E 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 116 " --> pdb=" O ASP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 154 Processing helix chain 'E' and resid 158 through 172 removed outlier: 3.546A pdb=" N TYR E 162 " --> pdb=" O ASP E 158 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU E 164 " --> pdb=" O PRO E 160 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N GLU E 165 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.705A pdb=" N GLN G 64 " --> pdb=" O GLN G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'K' and resid 28 through 31 Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 80 removed outlier: 3.761A pdb=" N ASP D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ARG D 78 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 122 through 127 removed outlier: 3.595A pdb=" N TRP D 127 " --> pdb=" O LYS D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'F' and resid 37 through 59 removed outlier: 3.636A pdb=" N MET F 59 " --> pdb=" O VAL F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 62 No H-bonds generated for 'chain 'F' and resid 60 through 62' Processing helix chain 'F' and resid 74 through 126 removed outlier: 3.551A pdb=" N VAL F 115 " --> pdb=" O HIS F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 158 through 172 removed outlier: 3.660A pdb=" N TYR F 162 " --> pdb=" O ASP F 158 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLU F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU F 165 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.513A pdb=" N VAL L 85 " --> pdb=" O HIS L 38 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 36 Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA7, first strand: chain 'A' and resid 51 through 53A removed outlier: 7.875A pdb=" N LEU A 51 " --> pdb=" O CYS A 277 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N THR A 279 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LYS A 53 " --> pdb=" O THR A 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 59 through 60 removed outlier: 6.568A pdb=" N LEU A 59 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 87 " --> pdb=" O MET A 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.624A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N ILE A 179 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TYR A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS A 116A" --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 263 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 115 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 100 through 102 removed outlier: 6.624A pdb=" N SER A 101 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N TRP A 234 " --> pdb=" O SER A 101 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.467A pdb=" N ALA A 138 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ASN A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB4, first strand: chain 'A' and resid 281 through 282 Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.591A pdb=" N THR H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.515A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.702A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.605A pdb=" N VAL J 85 " --> pdb=" O HIS J 38 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 32 through 36 Processing sheet with id=AC2, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC5, first strand: chain 'C' and resid 51 through 53A removed outlier: 6.067A pdb=" N LEU C 51 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N CYS C 277 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.614A pdb=" N LEU C 59 " --> pdb=" O MET C 88 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE C 87 " --> pdb=" O MET C 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.698A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N ILE C 179 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS C 116A" --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 263 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL C 115 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.698A pdb=" N SER C 101 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N TRP C 234 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 136 through 141 removed outlier: 4.725A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 146 " --> pdb=" O CYS C 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AD2, first strand: chain 'C' and resid 281 through 282 Processing sheet with id=AD3, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.601A pdb=" N THR G 77 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.692A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.489A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'K' and resid 53 through 54 removed outlier: 6.570A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL K 85 " --> pdb=" O HIS K 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 32 through 36 Processing sheet with id=AD9, first strand: chain 'D' and resid 25 through 26 Processing sheet with id=AE1, first strand: chain 'D' and resid 39 through 41 Processing sheet with id=AE2, first strand: chain 'D' and resid 43 through 44 Processing sheet with id=AE3, first strand: chain 'D' and resid 51 through 53A removed outlier: 7.955A pdb=" N LEU D 51 " --> pdb=" O CYS D 277 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N THR D 279 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS D 53 " --> pdb=" O THR D 279 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'D' and resid 59 through 60 removed outlier: 6.592A pdb=" N LEU D 59 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE D 87 " --> pdb=" O MET D 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.705A pdb=" N SER D 101 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N TRP D 234 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ILE D 179 " --> pdb=" O TYR D 256 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TYR D 256 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N HIS D 116A" --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG D 263 " --> pdb=" O VAL D 115 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL D 115 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 100 through 102 removed outlier: 6.705A pdb=" N SER D 101 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N TRP D 234 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE D 179 " --> pdb=" O PRO D 254 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 136 through 141 removed outlier: 4.774A pdb=" N CYS D 139 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D 146 " --> pdb=" O CYS D 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 164 through 169 Processing sheet with id=AE9, first strand: chain 'D' and resid 281 through 282 Processing sheet with id=AF1, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.525A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR I 77 " --> pdb=" O ASP I 72 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.530A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 10 through 11 removed outlier: 6.582A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1818 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: 6.04 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5651 1.34 - 1.46: 4301 1.46 - 1.58: 7505 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 17595 Sorted by residual: bond pdb=" C1 NAG C 404 " pdb=" O5 NAG C 404 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG A 404 " pdb=" O5 NAG A 404 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG D 404 " pdb=" O5 NAG D 404 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG D 401 " pdb=" O5 NAG D 401 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG B 301 " pdb=" O5 NAG B 301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 ... (remaining 17590 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.28: 429 106.28 - 113.25: 9519 113.25 - 120.21: 5896 120.21 - 127.17: 7757 127.17 - 134.13: 216 Bond angle restraints: 23817 Sorted by residual: angle pdb=" C TYR A 195 " pdb=" N GLN A 196 " pdb=" CA GLN A 196 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.11e+00 angle pdb=" C TYR D 195 " pdb=" N GLN D 196 " pdb=" CA GLN D 196 " ideal model delta sigma weight residual 121.54 126.52 -4.98 1.91e+00 2.74e-01 6.80e+00 angle pdb=" N GLY H 106 " pdb=" CA GLY H 106 " pdb=" C GLY H 106 " ideal model delta sigma weight residual 111.72 114.79 -3.07 1.31e+00 5.83e-01 5.49e+00 angle pdb=" C LEU E 126 " pdb=" N ARG E 127 " pdb=" CA ARG E 127 " ideal model delta sigma weight residual 120.82 124.07 -3.25 1.50e+00 4.44e-01 4.70e+00 angle pdb=" C LEU F 126 " pdb=" N ARG F 127 " pdb=" CA ARG F 127 " ideal model delta sigma weight residual 120.82 124.03 -3.21 1.50e+00 4.44e-01 4.59e+00 ... (remaining 23812 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 9742 17.62 - 35.25: 737 35.25 - 52.87: 163 52.87 - 70.49: 20 70.49 - 88.11: 15 Dihedral angle restraints: 10677 sinusoidal: 4497 harmonic: 6180 Sorted by residual: dihedral pdb=" CB CYS A 30 " pdb=" SG CYS A 30 " pdb=" SG CYS F 47 " pdb=" CB CYS F 47 " ideal model delta sinusoidal sigma weight residual -86.00 -45.15 -40.85 1 1.00e+01 1.00e-02 2.34e+01 dihedral pdb=" CB CYS E 47 " pdb=" SG CYS E 47 " pdb=" SG CYS D 30 " pdb=" CB CYS D 30 " ideal model delta sinusoidal sigma weight residual -86.00 -47.19 -38.81 1 1.00e+01 1.00e-02 2.12e+01 dihedral pdb=" CA LEU E 126 " pdb=" C LEU E 126 " pdb=" N ARG E 127 " pdb=" CA ARG E 127 " ideal model delta harmonic sigma weight residual -180.00 -162.37 -17.63 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 10674 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1508 0.027 - 0.054: 649 0.054 - 0.081: 214 0.081 - 0.108: 152 0.108 - 0.135: 75 Chirality restraints: 2598 Sorted by residual: chirality pdb=" CA ILE K 48 " pdb=" N ILE K 48 " pdb=" C ILE K 48 " pdb=" CB ILE K 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.56e-01 chirality pdb=" CA ILE D 260 " pdb=" N ILE D 260 " pdb=" C ILE D 260 " pdb=" CB ILE D 260 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA ILE C 260 " pdb=" N ILE C 260 " pdb=" C ILE C 260 " pdb=" CB ILE C 260 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2595 not shown) Planarity restraints: 3090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 73 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 74 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 73 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO C 74 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 74 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 74 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 13 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO I 14 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO I 14 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO I 14 " -0.027 5.00e-02 4.00e+02 ... (remaining 3087 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1194 2.74 - 3.28: 16017 3.28 - 3.82: 27752 3.82 - 4.36: 34852 4.36 - 4.90: 60950 Nonbonded interactions: 140765 Sorted by model distance: nonbonded pdb=" OG1 THR C 283 " pdb=" O GLY C 286 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR D 283 " pdb=" O GLY D 286 " model vdw 2.236 2.440 nonbonded pdb=" NH2 ARG A 126 " pdb=" O GLN A 165 " model vdw 2.254 2.520 nonbonded pdb=" OH TYR J 96 " pdb=" O ILE G 100 " model vdw 2.256 2.440 nonbonded pdb=" OH TYR K 96 " pdb=" O ILE I 100 " model vdw 2.257 2.440 ... (remaining 140760 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 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.960 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 46.910 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17595 Z= 0.205 Angle : 0.522 6.058 23817 Z= 0.297 Chirality : 0.042 0.135 2598 Planarity : 0.004 0.051 3075 Dihedral : 13.077 88.114 6675 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2142 helix: 1.45 (0.25), residues: 357 sheet: 0.35 (0.24), residues: 507 loop : 0.32 (0.17), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 69 HIS 0.005 0.001 HIS C 18 PHE 0.009 0.001 PHE D 232 TYR 0.032 0.001 TYR E 22 ARG 0.008 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 253 time to evaluate : 2.105 Fit side-chains revert: symmetry clash REVERT: A 105 TYR cc_start: 0.8600 (t80) cc_final: 0.8393 (t80) REVERT: A 187 ASP cc_start: 0.7230 (p0) cc_final: 0.7016 (p0) REVERT: C 211 LYS cc_start: 0.7479 (tttm) cc_final: 0.7083 (ttpt) REVERT: E 75 ARG cc_start: 0.7954 (mmp-170) cc_final: 0.7721 (mmp-170) REVERT: G 23 LYS cc_start: 0.8645 (tttp) cc_final: 0.8403 (ttpp) REVERT: F 40 SER cc_start: 0.8690 (m) cc_final: 0.8473 (m) outliers start: 1 outliers final: 0 residues processed: 254 average time/residue: 1.4201 time to fit residues: 399.4260 Evaluate side-chains 190 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 191 GLN B 60 ASN ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN D 12 GLN D 191 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN F 169 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17595 Z= 0.402 Angle : 0.598 8.960 23817 Z= 0.318 Chirality : 0.047 0.148 2598 Planarity : 0.004 0.053 3075 Dihedral : 4.894 57.218 2661 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.78 % Allowed : 7.76 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2142 helix: 2.14 (0.26), residues: 357 sheet: 0.47 (0.24), residues: 501 loop : 0.07 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 21 HIS 0.009 0.001 HIS C 18 PHE 0.018 0.003 PHE D 232 TYR 0.039 0.002 TYR E 22 ARG 0.007 0.001 ARG H 82B *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 2.125 Fit side-chains revert: symmetry clash REVERT: L 37 ARG cc_start: 0.7490 (ttp-170) cc_final: 0.7253 (ttp-170) REVERT: L 45 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7148 (ttt90) REVERT: A 231 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7702 (tt0) REVERT: A 312 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: B 147 GLU cc_start: 0.6950 (tt0) cc_final: 0.6749 (tt0) REVERT: H 81 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: H 105 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6793 (pp30) REVERT: C 211 LYS cc_start: 0.7480 (tttm) cc_final: 0.7246 (tttt) REVERT: C 304 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7392 (mt-10) REVERT: E 17 MET cc_start: 0.8370 (tpp) cc_final: 0.7969 (tpp) REVERT: G 3 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: G 23 LYS cc_start: 0.8455 (tttp) cc_final: 0.8117 (ttmm) REVERT: K 37 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7429 (ttp80) REVERT: K 103 LYS cc_start: 0.6776 (tptp) cc_final: 0.6567 (tptp) REVERT: D 238 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.8053 (t0) REVERT: D 304 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: I 3 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8079 (pt0) outliers start: 52 outliers final: 21 residues processed: 218 average time/residue: 1.4366 time to fit residues: 346.5816 Evaluate side-chains 213 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 45 ARG Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain H residue 81 GLU Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain D residue 304 GLU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 62 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 7.9990 chunk 60 optimal weight: 0.0670 chunk 160 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 172 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN D 12 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17595 Z= 0.244 Angle : 0.529 13.743 23817 Z= 0.280 Chirality : 0.044 0.227 2598 Planarity : 0.004 0.054 3075 Dihedral : 4.512 52.310 2661 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.51 % Allowed : 10.22 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.18), residues: 2142 helix: 2.49 (0.26), residues: 360 sheet: 0.52 (0.24), residues: 495 loop : 0.05 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 21 HIS 0.006 0.001 HIS D 18 PHE 0.013 0.002 PHE D 232 TYR 0.037 0.001 TYR E 22 ARG 0.008 0.000 ARG H 82B *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 196 time to evaluate : 2.117 Fit side-chains revert: symmetry clash REVERT: L 37 ARG cc_start: 0.7499 (ttp-170) cc_final: 0.7280 (ttp-170) REVERT: A 312 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: B 102 MET cc_start: 0.7776 (mtm) cc_final: 0.7388 (mtm) REVERT: H 105 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.6659 (pp30) REVERT: C 211 LYS cc_start: 0.7473 (tttm) cc_final: 0.7012 (ttpt) REVERT: C 304 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7422 (mt-10) REVERT: E 17 MET cc_start: 0.8584 (tpp) cc_final: 0.8088 (tpp) REVERT: G 3 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7670 (pm20) REVERT: G 23 LYS cc_start: 0.8452 (tttp) cc_final: 0.8118 (ttmm) REVERT: I 3 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.8113 (pt0) outliers start: 47 outliers final: 22 residues processed: 219 average time/residue: 1.3901 time to fit residues: 337.8201 Evaluate side-chains 211 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 184 time to evaluate : 2.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 30 CYS Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain I residue 3 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN D 12 GLN ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17595 Z= 0.332 Angle : 0.546 9.449 23817 Z= 0.287 Chirality : 0.045 0.144 2598 Planarity : 0.004 0.053 3075 Dihedral : 4.365 46.749 2661 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.37 % Allowed : 11.50 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2142 helix: 2.46 (0.26), residues: 360 sheet: 0.42 (0.24), residues: 495 loop : -0.03 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 21 HIS 0.008 0.001 HIS D 18 PHE 0.017 0.002 PHE D 232 TYR 0.020 0.002 TYR A 17 ARG 0.008 0.001 ARG H 82B *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 188 time to evaluate : 2.205 Fit side-chains revert: symmetry clash REVERT: L 70 ASP cc_start: 0.7893 (t0) cc_final: 0.7655 (t70) REVERT: A 304 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: A 312 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7426 (tp30) REVERT: B 59 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7263 (mmm) REVERT: B 102 MET cc_start: 0.7825 (mtm) cc_final: 0.7385 (mtm) REVERT: H 105 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.6713 (pp30) REVERT: C 211 LYS cc_start: 0.7578 (tttm) cc_final: 0.7343 (tttt) REVERT: C 304 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7463 (mt-10) REVERT: E 17 MET cc_start: 0.8527 (tpp) cc_final: 0.8081 (tpp) REVERT: G 3 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: G 23 LYS cc_start: 0.8446 (tttp) cc_final: 0.8116 (ttmm) REVERT: F 22 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: F 59 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7512 (mtp) REVERT: F 156 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8347 (p) REVERT: I 3 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8147 (pt0) REVERT: I 105 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7497 (pm20) outliers start: 63 outliers final: 29 residues processed: 217 average time/residue: 1.3657 time to fit residues: 331.0464 Evaluate side-chains 221 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 42 GLN J 89 GLN ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17595 Z= 0.321 Angle : 0.539 8.947 23817 Z= 0.284 Chirality : 0.044 0.146 2598 Planarity : 0.004 0.052 3075 Dihedral : 4.217 39.604 2661 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.48 % Allowed : 12.52 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 2142 helix: 2.43 (0.26), residues: 360 sheet: 0.34 (0.24), residues: 495 loop : -0.07 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 21 HIS 0.008 0.001 HIS D 18 PHE 0.017 0.002 PHE D 232 TYR 0.013 0.002 TYR L 49 ARG 0.008 0.000 ARG H 82B *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 185 time to evaluate : 2.119 Fit side-chains REVERT: A 304 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7783 (mp0) REVERT: A 312 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7437 (tp30) REVERT: B 102 MET cc_start: 0.7838 (mtm) cc_final: 0.7476 (mtm) REVERT: H 105 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6708 (pp30) REVERT: C 211 LYS cc_start: 0.7583 (tttm) cc_final: 0.7329 (tttt) REVERT: C 304 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7474 (mt-10) REVERT: E 17 MET cc_start: 0.8457 (tpp) cc_final: 0.8039 (tpp) REVERT: E 22 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7449 (m-80) REVERT: G 3 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8113 (pm20) REVERT: G 23 LYS cc_start: 0.8446 (tttp) cc_final: 0.8117 (ttmm) REVERT: D 29 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7849 (mm) REVERT: D 239 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7056 (mmm) REVERT: F 22 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8218 (m-80) REVERT: F 59 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7613 (mtp) REVERT: I 3 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8154 (pt0) REVERT: I 105 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7498 (pm20) outliers start: 65 outliers final: 33 residues processed: 219 average time/residue: 1.3844 time to fit residues: 337.1140 Evaluate side-chains 222 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 177 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 312 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 3 GLN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 171 optimal weight: 0.0060 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17595 Z= 0.264 Angle : 0.516 8.395 23817 Z= 0.272 Chirality : 0.043 0.147 2598 Planarity : 0.004 0.051 3075 Dihedral : 4.013 29.588 2661 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.37 % Allowed : 13.70 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 2142 helix: 2.56 (0.26), residues: 360 sheet: 0.34 (0.24), residues: 495 loop : -0.06 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 21 HIS 0.006 0.001 HIS D 18 PHE 0.014 0.002 PHE D 232 TYR 0.012 0.001 TYR L 49 ARG 0.008 0.000 ARG G 82B *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 189 time to evaluate : 2.196 Fit side-chains revert: symmetry clash REVERT: A 304 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: B 102 MET cc_start: 0.7815 (mtm) cc_final: 0.7453 (mtm) REVERT: H 101 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7849 (t0) REVERT: H 105 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.6558 (pp30) REVERT: C 211 LYS cc_start: 0.7576 (tttm) cc_final: 0.7319 (tttt) REVERT: C 304 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7455 (mt-10) REVERT: E 17 MET cc_start: 0.8386 (tpp) cc_final: 0.8002 (tpp) REVERT: E 22 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: G 23 LYS cc_start: 0.8441 (tttp) cc_final: 0.8121 (ttmm) REVERT: D 239 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.7021 (mmm) REVERT: F 22 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: F 59 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7666 (mtp) REVERT: I 3 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: I 105 GLN cc_start: 0.7729 (OUTLIER) cc_final: 0.7485 (pm20) outliers start: 63 outliers final: 33 residues processed: 220 average time/residue: 1.3811 time to fit residues: 339.5826 Evaluate side-chains 226 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 183 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 17 TYR Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 173 optimal weight: 0.0370 chunk 115 optimal weight: 0.5980 chunk 205 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17595 Z= 0.198 Angle : 0.488 7.429 23817 Z= 0.258 Chirality : 0.042 0.148 2598 Planarity : 0.004 0.051 3075 Dihedral : 3.840 23.070 2661 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.05 % Allowed : 14.45 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2142 helix: 2.77 (0.26), residues: 360 sheet: 0.35 (0.24), residues: 495 loop : -0.02 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 21 HIS 0.005 0.001 HIS D 18 PHE 0.010 0.001 PHE D 232 TYR 0.010 0.001 TYR J 49 ARG 0.009 0.000 ARG J 100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 189 time to evaluate : 2.028 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: A 304 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 102 MET cc_start: 0.7815 (mtm) cc_final: 0.7490 (mtm) REVERT: H 101 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7783 (t0) REVERT: C 211 LYS cc_start: 0.7610 (tttm) cc_final: 0.7353 (tttt) REVERT: C 304 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7460 (mt-10) REVERT: E 17 MET cc_start: 0.8346 (tpp) cc_final: 0.8009 (tpp) REVERT: E 22 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: G 23 LYS cc_start: 0.8444 (tttp) cc_final: 0.8144 (ttmm) REVERT: G 105 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: D 239 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.6962 (mmm) REVERT: F 22 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: F 59 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7689 (mtp) REVERT: I 3 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: I 105 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7486 (pm20) outliers start: 57 outliers final: 31 residues processed: 219 average time/residue: 1.3464 time to fit residues: 328.9996 Evaluate side-chains 226 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17595 Z= 0.197 Angle : 0.495 11.356 23817 Z= 0.258 Chirality : 0.042 0.148 2598 Planarity : 0.004 0.052 3075 Dihedral : 3.757 20.877 2661 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.78 % Allowed : 15.20 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.18), residues: 2142 helix: 2.84 (0.26), residues: 360 sheet: 0.38 (0.24), residues: 495 loop : 0.01 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 21 HIS 0.005 0.001 HIS D 18 PHE 0.020 0.001 PHE H 63 TYR 0.015 0.001 TYR A 17 ARG 0.010 0.000 ARG G 82B *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 186 time to evaluate : 2.196 Fit side-chains revert: symmetry clash REVERT: A 91 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: A 304 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: B 102 MET cc_start: 0.7816 (mtm) cc_final: 0.7552 (mtm) REVERT: H 101 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7763 (t0) REVERT: C 211 LYS cc_start: 0.7612 (tttm) cc_final: 0.7372 (tttt) REVERT: C 304 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: E 17 MET cc_start: 0.8320 (tpp) cc_final: 0.7961 (tpp) REVERT: E 22 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.7361 (m-80) REVERT: G 23 LYS cc_start: 0.8421 (tttp) cc_final: 0.8143 (ttmm) REVERT: G 105 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: D 239 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6980 (mmm) REVERT: F 22 TYR cc_start: 0.8792 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: F 59 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7767 (mtp) REVERT: I 3 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8163 (pt0) REVERT: I 105 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7438 (pm20) outliers start: 52 outliers final: 33 residues processed: 213 average time/residue: 1.3330 time to fit residues: 317.1554 Evaluate side-chains 224 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 27 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 172 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 190 optimal weight: 0.4980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17595 Z= 0.318 Angle : 0.544 10.357 23817 Z= 0.283 Chirality : 0.044 0.145 2598 Planarity : 0.004 0.051 3075 Dihedral : 3.913 20.457 2661 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.84 % Allowed : 15.09 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2142 helix: 2.48 (0.27), residues: 366 sheet: 0.28 (0.24), residues: 498 loop : -0.08 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 21 HIS 0.007 0.001 HIS D 18 PHE 0.024 0.002 PHE H 63 TYR 0.014 0.002 TYR L 49 ARG 0.009 0.000 ARG I 82B *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 183 time to evaluate : 2.109 Fit side-chains REVERT: A 91 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: A 304 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: B 59 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7734 (mtp) REVERT: B 102 MET cc_start: 0.7866 (mtm) cc_final: 0.7589 (mtm) REVERT: H 101 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7882 (t0) REVERT: C 211 LYS cc_start: 0.7639 (tttm) cc_final: 0.7184 (ttpt) REVERT: C 304 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: E 17 MET cc_start: 0.8348 (tpp) cc_final: 0.7988 (tpp) REVERT: E 22 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7267 (m-80) REVERT: G 23 LYS cc_start: 0.8416 (tttp) cc_final: 0.8139 (ttmm) REVERT: G 105 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6938 (pm20) REVERT: F 22 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: F 59 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7918 (mtp) REVERT: F 168 LEU cc_start: 0.8654 (mp) cc_final: 0.8262 (tt) REVERT: I 3 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8184 (pt0) REVERT: I 105 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7456 (pm20) outliers start: 53 outliers final: 32 residues processed: 209 average time/residue: 1.4058 time to fit residues: 327.9817 Evaluate side-chains 225 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 62 ASN Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 59 MET Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17595 Z= 0.296 Angle : 0.541 11.269 23817 Z= 0.281 Chirality : 0.044 0.145 2598 Planarity : 0.004 0.051 3075 Dihedral : 3.943 20.952 2661 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.51 % Allowed : 15.62 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.18), residues: 2142 helix: 2.47 (0.26), residues: 366 sheet: 0.24 (0.24), residues: 498 loop : -0.11 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 21 HIS 0.007 0.001 HIS D 18 PHE 0.029 0.002 PHE H 63 TYR 0.013 0.001 TYR L 49 ARG 0.009 0.000 ARG I 82B ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 183 time to evaluate : 2.079 Fit side-chains REVERT: A 91 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 304 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7859 (mp0) REVERT: B 102 MET cc_start: 0.7849 (mtm) cc_final: 0.7577 (mtm) REVERT: C 211 LYS cc_start: 0.7668 (tttm) cc_final: 0.7200 (ttpt) REVERT: E 17 MET cc_start: 0.8346 (tpp) cc_final: 0.7999 (tpp) REVERT: E 22 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: G 23 LYS cc_start: 0.8413 (tttp) cc_final: 0.8137 (ttmm) REVERT: G 105 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.6940 (pm20) REVERT: K 42 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7210 (mp10) REVERT: F 22 TYR cc_start: 0.8786 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: F 168 LEU cc_start: 0.8653 (mp) cc_final: 0.8253 (tt) REVERT: I 3 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: I 105 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7458 (pm20) outliers start: 47 outliers final: 31 residues processed: 208 average time/residue: 1.4190 time to fit residues: 328.2082 Evaluate side-chains 218 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain J residue 85 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain C residue 11 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 22 TYR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 105 GLN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain D residue 291 THR Chi-restraints excluded: chain F residue 22 TYR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 ILE Chi-restraints excluded: chain I residue 62 ASN Chi-restraints excluded: chain I residue 105 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 31 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.084717 restraints weight = 25532.046| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.59 r_work: 0.2962 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17595 Z= 0.193 Angle : 0.500 10.962 23817 Z= 0.260 Chirality : 0.042 0.142 2598 Planarity : 0.004 0.052 3075 Dihedral : 3.779 19.834 2661 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.09 % Allowed : 16.32 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2142 helix: 2.79 (0.26), residues: 363 sheet: 0.31 (0.24), residues: 498 loop : -0.06 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 92 HIS 0.005 0.001 HIS D 18 PHE 0.029 0.001 PHE H 63 TYR 0.010 0.001 TYR J 49 ARG 0.010 0.000 ARG G 82B Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.95 seconds wall clock time: 109 minutes 20.25 seconds (6560.25 seconds total)