Starting phenix.real_space_refine on Sun Mar 17 07:47:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/03_2024/8gtb_34248.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/03_2024/8gtb_34248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/03_2024/8gtb_34248.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/03_2024/8gtb_34248.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/03_2024/8gtb_34248.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtb_34248/03_2024/8gtb_34248.pdb" } resolution = 3.43 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= 0.009 sd= 0.097 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 54 5.16 5 C 10548 2.51 5 N 2898 2.21 5 O 3636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ASP 61": "OD1" <-> "OD2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ASP 73": "OD1" <-> "OD2" Residue "B TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ASP 61": "OD1" <-> "OD2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D ASP 61": "OD1" <-> "OD2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ASP 61": "OD1" <-> "OD2" Residue "E GLU 70": "OE1" <-> "OE2" Residue "E ASP 73": "OD1" <-> "OD2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 51": "NH1" <-> "NH2" Residue "F ASP 61": "OD1" <-> "OD2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ASP 61": "OD1" <-> "OD2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I ASP 73": "OD1" <-> "OD2" Residue "I TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ASP 61": "OD1" <-> "OD2" Residue "G GLU 70": "OE1" <-> "OE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ASP 61": "OD1" <-> "OD2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "K ASP 73": "OD1" <-> "OD2" Residue "K TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ASP 61": "OD1" <-> "OD2" Residue "M GLU 70": "OE1" <-> "OE2" Residue "M ASP 73": "OD1" <-> "OD2" Residue "M TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 51": "NH1" <-> "NH2" Residue "O ASP 61": "OD1" <-> "OD2" Residue "O GLU 70": "OE1" <-> "OE2" Residue "O ASP 73": "OD1" <-> "OD2" Residue "O TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ASP 61": "OD1" <-> "OD2" Residue "Q GLU 70": "OE1" <-> "OE2" Residue "Q ASP 73": "OD1" <-> "OD2" Residue "Q TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ASP 61": "OD1" <-> "OD2" Residue "J GLU 70": "OE1" <-> "OE2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H ASP 73": "OD1" <-> "OD2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 51": "NH1" <-> "NH2" Residue "L ASP 61": "OD1" <-> "OD2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L ASP 73": "OD1" <-> "OD2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ASP 61": "OD1" <-> "OD2" Residue "N GLU 70": "OE1" <-> "OE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ASP 61": "OD1" <-> "OD2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "P ASP 73": "OD1" <-> "OD2" Residue "P TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 51": "NH1" <-> "NH2" Residue "R ASP 61": "OD1" <-> "OD2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ASP 73": "OD1" <-> "OD2" Residue "R TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17136 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "A" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "C" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "D" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "E" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "I" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "G" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "K" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "M" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "O" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "Q" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "J" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "H" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "L" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "N" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "P" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Chain: "R" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 952 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 6, 'TRANS': 123} Time building chain proxies: 8.51, per 1000 atoms: 0.50 Number of scatterers: 17136 At special positions: 0 Unit cell: (104.904, 104.904, 142.128, 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 54 16.00 O 3636 8.00 N 2898 7.00 C 10548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.12 Conformation dependent library (CDL) restraints added in 3.2 seconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4068 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 3 sheets defined 0.0% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 11 removed outlier: 3.706A pdb=" N ASP B 16 " --> pdb=" O ASN B 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 16 through 17 current: chain 'B' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 44 through 59 current: chain 'B' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN B 116 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 101 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR B 114 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU B 103 " --> pdb=" O MET B 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET B 112 " --> pdb=" O GLU B 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 112 through 119 current: chain 'A' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 16 through 17 current: chain 'A' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 44 through 59 current: chain 'A' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN A 116 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR A 101 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR A 114 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU A 103 " --> pdb=" O MET A 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET A 112 " --> pdb=" O GLU A 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 112 through 119 current: chain 'C' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 16 through 17 current: chain 'C' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 44 through 59 current: chain 'C' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN C 116 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR C 101 " --> pdb=" O THR C 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR C 114 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 103 " --> pdb=" O MET C 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET C 112 " --> pdb=" O GLU C 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 112 through 119 current: chain 'D' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 16 through 17 current: chain 'D' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 44 through 59 current: chain 'D' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN D 116 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR D 101 " --> pdb=" O THR D 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR D 114 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU D 103 " --> pdb=" O MET D 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET D 112 " --> pdb=" O GLU D 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 112 through 119 current: chain 'E' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 16 through 17 current: chain 'E' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 44 through 59 current: chain 'E' and resid 91 through 104 removed outlier: 6.940A pdb=" N ASN E 116 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR E 101 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR E 114 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU E 103 " --> pdb=" O MET E 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET E 112 " --> pdb=" O GLU E 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 112 through 119 current: chain 'F' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 16 through 17 current: chain 'F' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 44 through 59 current: chain 'F' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN F 116 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR F 101 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR F 114 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU F 103 " --> pdb=" O MET F 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET F 112 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 8 through 11 removed outlier: 3.706A pdb=" N ASP I 16 " --> pdb=" O ASN I 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 16 through 17 current: chain 'I' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 44 through 59 current: chain 'I' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN I 116 " --> pdb=" O LEU I 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR I 101 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR I 114 " --> pdb=" O THR I 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU I 103 " --> pdb=" O MET I 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET I 112 " --> pdb=" O GLU I 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 112 through 119 current: chain 'G' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 16 through 17 current: chain 'G' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 44 through 59 current: chain 'G' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN G 116 " --> pdb=" O LEU G 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR G 101 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR G 114 " --> pdb=" O THR G 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU G 103 " --> pdb=" O MET G 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET G 112 " --> pdb=" O GLU G 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 112 through 119 current: chain 'K' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 16 through 17 current: chain 'K' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 44 through 59 current: chain 'K' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN K 116 " --> pdb=" O LEU K 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR K 101 " --> pdb=" O THR K 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR K 114 " --> pdb=" O THR K 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU K 103 " --> pdb=" O MET K 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET K 112 " --> pdb=" O GLU K 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 112 through 119 current: chain 'M' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 16 through 17 current: chain 'M' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 44 through 59 current: chain 'M' and resid 91 through 106 removed outlier: 6.940A pdb=" N ASN M 116 " --> pdb=" O LEU M 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR M 101 " --> pdb=" O THR M 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR M 114 " --> pdb=" O THR M 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU M 103 " --> pdb=" O MET M 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET M 112 " --> pdb=" O GLU M 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 112 through 119 current: chain 'O' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 16 through 17 current: chain 'O' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 44 through 59 current: chain 'O' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN O 116 " --> pdb=" O LEU O 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR O 101 " --> pdb=" O THR O 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR O 114 " --> pdb=" O THR O 101 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU O 103 " --> pdb=" O MET O 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET O 112 " --> pdb=" O GLU O 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 112 through 119 current: chain 'Q' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 16 through 17 current: chain 'Q' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 44 through 59 current: chain 'Q' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN Q 116 " --> pdb=" O LEU Q 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR Q 101 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR Q 114 " --> pdb=" O THR Q 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU Q 103 " --> pdb=" O MET Q 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET Q 112 " --> pdb=" O GLU Q 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 8 through 11 removed outlier: 3.707A pdb=" N ASP J 16 " --> pdb=" O ASN J 11 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 16 through 17 current: chain 'J' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 44 through 59 current: chain 'J' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN J 116 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR J 101 " --> pdb=" O THR J 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR J 114 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU J 103 " --> pdb=" O MET J 112 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET J 112 " --> pdb=" O GLU J 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 112 through 119 current: chain 'H' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 16 through 17 current: chain 'H' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 44 through 59 current: chain 'H' and resid 91 through 104 removed outlier: 6.940A pdb=" N ASN H 116 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR H 101 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR H 114 " --> pdb=" O THR H 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU H 103 " --> pdb=" O MET H 112 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N MET H 112 " --> pdb=" O GLU H 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 112 through 119 current: chain 'L' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 16 through 17 current: chain 'L' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 44 through 59 current: chain 'L' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN L 116 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR L 101 " --> pdb=" O THR L 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR L 114 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU L 103 " --> pdb=" O MET L 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET L 112 " --> pdb=" O GLU L 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 112 through 119 current: chain 'N' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 16 through 17 current: chain 'N' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 44 through 59 current: chain 'N' and resid 91 through 106 removed outlier: 6.941A pdb=" N ASN N 116 " --> pdb=" O LEU N 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR N 101 " --> pdb=" O THR N 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR N 114 " --> pdb=" O THR N 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU N 103 " --> pdb=" O MET N 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET N 112 " --> pdb=" O GLU N 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 112 through 119 current: chain 'P' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 16 through 17 current: chain 'P' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 44 through 59 current: chain 'P' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN P 116 " --> pdb=" O LEU P 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR P 101 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR P 114 " --> pdb=" O THR P 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU P 103 " --> pdb=" O MET P 112 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET P 112 " --> pdb=" O GLU P 103 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 112 through 119 current: chain 'R' and resid 16 through 17 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 16 through 17 current: chain 'R' and resid 44 through 59 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 44 through 59 current: chain 'R' and resid 91 through 104 removed outlier: 6.941A pdb=" N ASN R 116 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR R 101 " --> pdb=" O THR R 114 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR R 114 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU R 103 " --> pdb=" O MET R 112 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET R 112 " --> pdb=" O GLU R 103 " (cutoff:3.500A) 57 hydrogen bonds defined for protein. 171 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: 3.56 Time building geometry restraints manager: 6.65 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: 5904 1.34 - 1.45: 3242 1.45 - 1.57: 8188 1.57 - 1.68: 0 1.68 - 1.80: 108 Bond restraints: 17442 Sorted by residual: bond pdb=" CA GLY R 19 " pdb=" C GLY R 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.10e+00 bond pdb=" CA GLY J 19 " pdb=" C GLY J 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.09e+00 bond pdb=" CA GLY D 19 " pdb=" C GLY D 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.06e+00 bond pdb=" CA GLY K 19 " pdb=" C GLY K 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.05e+00 bond pdb=" CA GLY N 19 " pdb=" C GLY N 19 " ideal model delta sigma weight residual 1.524 1.507 0.017 1.20e-02 6.94e+03 2.01e+00 ... (remaining 17437 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.89: 558 106.89 - 113.67: 9735 113.67 - 120.44: 6213 120.44 - 127.22: 6948 127.22 - 134.00: 234 Bond angle restraints: 23688 Sorted by residual: angle pdb=" C ARG J 51 " pdb=" CA ARG J 51 " pdb=" CB ARG J 51 " ideal model delta sigma weight residual 113.19 108.89 4.30 2.37e+00 1.78e-01 3.29e+00 angle pdb=" C ARG E 51 " pdb=" CA ARG E 51 " pdb=" CB ARG E 51 " ideal model delta sigma weight residual 113.19 108.89 4.30 2.37e+00 1.78e-01 3.29e+00 angle pdb=" C ARG B 51 " pdb=" CA ARG B 51 " pdb=" CB ARG B 51 " ideal model delta sigma weight residual 113.19 108.90 4.29 2.37e+00 1.78e-01 3.28e+00 angle pdb=" C ARG P 51 " pdb=" CA ARG P 51 " pdb=" CB ARG P 51 " ideal model delta sigma weight residual 113.19 108.91 4.28 2.37e+00 1.78e-01 3.27e+00 angle pdb=" C ARG K 51 " pdb=" CA ARG K 51 " pdb=" CB ARG K 51 " ideal model delta sigma weight residual 113.19 108.91 4.28 2.37e+00 1.78e-01 3.26e+00 ... (remaining 23683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 9155 15.61 - 31.21: 975 31.21 - 46.82: 148 46.82 - 62.43: 0 62.43 - 78.03: 18 Dihedral angle restraints: 10296 sinusoidal: 3852 harmonic: 6444 Sorted by residual: dihedral pdb=" CA LYS P 10 " pdb=" C LYS P 10 " pdb=" N ASN P 11 " pdb=" CA ASN P 11 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LYS J 10 " pdb=" C LYS J 10 " pdb=" N ASN J 11 " pdb=" CA ASN J 11 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA LYS A 10 " pdb=" C LYS A 10 " pdb=" N ASN A 11 " pdb=" CA ASN A 11 " ideal model delta harmonic sigma weight residual 180.00 163.72 16.28 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 10293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1285 0.025 - 0.049: 865 0.049 - 0.074: 198 0.074 - 0.099: 146 0.099 - 0.123: 134 Chirality restraints: 2628 Sorted by residual: chirality pdb=" CA VAL O 33 " pdb=" N VAL O 33 " pdb=" C VAL O 33 " pdb=" CB VAL O 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL J 33 " pdb=" N VAL J 33 " pdb=" C VAL J 33 " pdb=" CB VAL J 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA VAL M 33 " pdb=" N VAL M 33 " pdb=" C VAL M 33 " pdb=" CB VAL M 33 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 2625 not shown) Planarity restraints: 3150 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP R 64 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO R 65 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO R 65 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO R 65 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 64 " 0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO E 65 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO E 65 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 65 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 64 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.79e+00 pdb=" N PRO H 65 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " -0.019 5.00e-02 4.00e+02 ... (remaining 3147 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2724 2.75 - 3.29: 15622 3.29 - 3.83: 26022 3.83 - 4.36: 30477 4.36 - 4.90: 57153 Nonbonded interactions: 131998 Sorted by model distance: nonbonded pdb=" OE2 GLU J 43 " pdb=" NH2 ARG R 118 " model vdw 2.213 2.520 nonbonded pdb=" NH2 ARG A 118 " pdb=" OE2 GLU C 43 " model vdw 2.268 2.520 nonbonded pdb=" O SER F 120 " pdb=" OG SER F 120 " model vdw 2.269 2.440 nonbonded pdb=" O SER R 120 " pdb=" OG SER R 120 " model vdw 2.269 2.440 nonbonded pdb=" O SER P 120 " pdb=" OG SER P 120 " model vdw 2.270 2.440 ... (remaining 131993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.090 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 42.040 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2580 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 : 0.007 0.027 17442 Z= 0.478 Angle : 0.714 4.714 23688 Z= 0.411 Chirality : 0.042 0.123 2628 Planarity : 0.004 0.034 3150 Dihedral : 12.850 78.033 6228 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % 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: -3.27 (0.14), residues: 2304 helix: None (None), residues: 0 sheet: -2.06 (0.13), residues: 1260 loop : -2.13 (0.13), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 24 HIS 0.002 0.001 HIS M 20 PHE 0.007 0.002 PHE L 56 TYR 0.007 0.001 TYR O 90 ARG 0.001 0.000 ARG M 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ASN cc_start: 0.6859 (t0) cc_final: 0.6631 (t0) REVERT: A 76 ASP cc_start: 0.6058 (m-30) cc_final: 0.5723 (p0) REVERT: C 18 ILE cc_start: 0.4028 (mm) cc_final: 0.3571 (mm) REVERT: G 93 VAL cc_start: 0.3844 (t) cc_final: 0.3612 (t) REVERT: K 1 MET cc_start: 0.3647 (ttm) cc_final: 0.3159 (tmm) REVERT: K 80 TYR cc_start: 0.2891 (m-80) cc_final: 0.2336 (m-80) REVERT: H 11 ASN cc_start: 0.6636 (t0) cc_final: 0.6372 (t0) REVERT: H 93 VAL cc_start: 0.3150 (t) cc_final: 0.2908 (t) REVERT: H 112 MET cc_start: 0.1221 (mtt) cc_final: 0.0606 (mtm) REVERT: H 113 LEU cc_start: 0.5032 (tp) cc_final: 0.4649 (tp) REVERT: L 81 PRO cc_start: 0.3394 (Cg_exo) cc_final: 0.2815 (Cg_endo) REVERT: P 38 MET cc_start: 0.3380 (mtp) cc_final: 0.2608 (ttt) REVERT: R 38 MET cc_start: 0.4885 (mtp) cc_final: 0.2711 (tmm) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.3293 time to fit residues: 197.1815 Evaluate side-chains 205 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 1.9990 chunk 177 optimal weight: 9.9990 chunk 98 optimal weight: 8.9990 chunk 60 optimal weight: 0.0770 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN A 125 GLN C 22 GLN D 22 GLN D 125 GLN E 125 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 125 GLN G 125 GLN K 125 GLN M 22 GLN O 22 GLN O 125 GLN H 125 GLN L 22 GLN L 125 GLN ** N 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 ASN P 125 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3873 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17442 Z= 0.218 Angle : 0.712 12.222 23688 Z= 0.344 Chirality : 0.045 0.175 2628 Planarity : 0.005 0.060 3150 Dihedral : 4.352 21.741 2466 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.41 % Allowed : 12.10 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.15), residues: 2304 helix: None (None), residues: 0 sheet: -1.25 (0.13), residues: 1260 loop : -1.17 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 117 HIS 0.004 0.001 HIS D 20 PHE 0.035 0.002 PHE N 56 TYR 0.026 0.002 TYR D 59 ARG 0.007 0.001 ARG N 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 332 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.6652 (pmm) cc_final: 0.6281 (mtp) REVERT: B 11 ASN cc_start: 0.7023 (t0) cc_final: 0.6681 (t0) REVERT: A 106 SER cc_start: 0.4894 (OUTLIER) cc_final: 0.4651 (t) REVERT: C 1 MET cc_start: 0.3894 (tmm) cc_final: 0.3638 (tpp) REVERT: C 9 VAL cc_start: 0.1027 (OUTLIER) cc_final: 0.0498 (m) REVERT: E 123 LEU cc_start: 0.3859 (tp) cc_final: 0.3652 (tp) REVERT: I 38 MET cc_start: 0.5037 (ttp) cc_final: 0.4624 (ttm) REVERT: K 1 MET cc_start: 0.4099 (ttm) cc_final: 0.3098 (tmm) REVERT: K 78 GLU cc_start: 0.5394 (pt0) cc_final: 0.4718 (pt0) REVERT: J 1 MET cc_start: 0.5848 (pmm) cc_final: 0.5398 (ptp) REVERT: H 11 ASN cc_start: 0.6583 (t0) cc_final: 0.6274 (t0) REVERT: H 93 VAL cc_start: 0.5143 (t) cc_final: 0.4910 (t) REVERT: N 1 MET cc_start: 0.4749 (tmm) cc_final: 0.4463 (tpp) REVERT: P 38 MET cc_start: 0.4293 (mtp) cc_final: 0.2965 (tmm) REVERT: P 112 MET cc_start: 0.5891 (mmt) cc_final: 0.5628 (mmm) REVERT: R 38 MET cc_start: 0.6352 (mtp) cc_final: 0.3417 (tmm) outliers start: 62 outliers final: 29 residues processed: 365 average time/residue: 0.2966 time to fit residues: 159.1588 Evaluate side-chains 267 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 236 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain D residue 5 LYS Chi-restraints excluded: chain D residue 8 VAL Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain F residue 46 PHE Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 144 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 212 optimal weight: 0.0570 chunk 229 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 chunk 211 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 overall best weight: 2.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 ASN P 11 ASN ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 1.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 17442 Z= 0.484 Angle : 1.122 19.141 23688 Z= 0.573 Chirality : 0.056 0.365 2628 Planarity : 0.008 0.098 3150 Dihedral : 7.304 39.450 2466 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 5.72 % Allowed : 18.21 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.15), residues: 2304 helix: None (None), residues: 0 sheet: -1.78 (0.15), residues: 1078 loop : -1.96 (0.14), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 24 HIS 0.009 0.003 HIS K 20 PHE 0.041 0.004 PHE N 56 TYR 0.042 0.003 TYR D 59 ARG 0.011 0.002 ARG Q 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 669 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 GLN cc_start: 0.8736 (tp40) cc_final: 0.8237 (tp40) REVERT: B 110 ILE cc_start: 0.8748 (mp) cc_final: 0.8515 (mm) REVERT: B 126 LYS cc_start: 0.7931 (tmtt) cc_final: 0.6524 (ttmt) REVERT: A 3 LYS cc_start: 0.8900 (mmtm) cc_final: 0.8684 (tppt) REVERT: A 90 TYR cc_start: 0.8240 (p90) cc_final: 0.7884 (p90) REVERT: A 123 LEU cc_start: 0.8516 (mt) cc_final: 0.8177 (mt) REVERT: A 125 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7190 (mm-40) REVERT: C 21 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8171 (tp) REVERT: C 38 MET cc_start: 0.6077 (mmt) cc_final: 0.5799 (mmm) REVERT: C 68 ASP cc_start: 0.7431 (m-30) cc_final: 0.7161 (p0) REVERT: C 123 LEU cc_start: 0.7710 (mt) cc_final: 0.7495 (mm) REVERT: D 38 MET cc_start: 0.6183 (mmm) cc_final: 0.5775 (mmt) REVERT: D 43 GLU cc_start: 0.7853 (pp20) cc_final: 0.7439 (pp20) REVERT: E 27 ASP cc_start: 0.7016 (t70) cc_final: 0.6193 (t0) REVERT: E 70 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7623 (mt-10) REVERT: F 11 ASN cc_start: 0.7077 (t0) cc_final: 0.6835 (t0) REVERT: F 27 ASP cc_start: 0.6823 (t70) cc_final: 0.5808 (t70) REVERT: F 68 ASP cc_start: 0.7586 (m-30) cc_final: 0.7325 (m-30) REVERT: I 11 ASN cc_start: 0.6669 (t0) cc_final: 0.6067 (t0) REVERT: I 125 GLN cc_start: 0.8079 (tp40) cc_final: 0.7877 (tm-30) REVERT: G 84 GLU cc_start: 0.7996 (tt0) cc_final: 0.7590 (tt0) REVERT: K 78 GLU cc_start: 0.7403 (pt0) cc_final: 0.7097 (pp20) REVERT: M 9 VAL cc_start: 0.8842 (t) cc_final: 0.8610 (m) REVERT: M 43 GLU cc_start: 0.7574 (pp20) cc_final: 0.6726 (pp20) REVERT: O 70 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7602 (mm-30) REVERT: Q 27 ASP cc_start: 0.6612 (t70) cc_final: 0.6145 (t70) REVERT: Q 80 TYR cc_start: 0.5336 (m-80) cc_final: 0.4777 (m-10) REVERT: J 27 ASP cc_start: 0.7713 (t70) cc_final: 0.7449 (t70) REVERT: J 73 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8223 (t70) REVERT: J 93 VAL cc_start: 0.8092 (t) cc_final: 0.7813 (m) REVERT: J 125 GLN cc_start: 0.8043 (tp-100) cc_final: 0.7799 (tm-30) REVERT: J 126 LYS cc_start: 0.8084 (tptp) cc_final: 0.7460 (tppp) REVERT: H 9 VAL cc_start: 0.7282 (t) cc_final: 0.6941 (t) REVERT: H 11 ASN cc_start: 0.6761 (t0) cc_final: 0.6495 (t0) REVERT: H 103 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6965 (mt-10) REVERT: H 110 ILE cc_start: 0.9223 (mp) cc_final: 0.9015 (mm) REVERT: N 29 GLN cc_start: 0.7848 (mt0) cc_final: 0.7597 (mp10) REVERT: P 70 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7293 (mm-30) REVERT: P 112 MET cc_start: 0.8738 (mmt) cc_final: 0.8380 (mmm) REVERT: R 6 ASP cc_start: 0.8808 (OUTLIER) cc_final: 0.8477 (t0) REVERT: R 16 ASP cc_start: 0.7028 (p0) cc_final: 0.6783 (p0) REVERT: R 27 ASP cc_start: 0.7117 (t70) cc_final: 0.6745 (t70) REVERT: R 75 VAL cc_start: 0.7455 (OUTLIER) cc_final: 0.7236 (p) outliers start: 104 outliers final: 40 residues processed: 731 average time/residue: 0.2864 time to fit residues: 311.3971 Evaluate side-chains 469 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 425 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 16 ASP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 2 LEU Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain F residue 73 ASP Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 68 ASP Chi-restraints excluded: chain M residue 73 ASP Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain Q residue 14 THR Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain J residue 73 ASP Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain L residue 16 ASP Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 67 ASP Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 64 ASP Chi-restraints excluded: chain N residue 68 ASP Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain P residue 11 ASN Chi-restraints excluded: chain P residue 31 ASP Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain R residue 6 ASP Chi-restraints excluded: chain R residue 20 HIS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 75 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 110 optimal weight: 0.0970 chunk 23 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 142 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 226 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 202 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN B 29 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS E 22 GLN K 11 ASN Q 22 GLN J 22 GLN ** H 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 1.8789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17442 Z= 0.224 Angle : 0.705 10.863 23688 Z= 0.338 Chirality : 0.045 0.168 2628 Planarity : 0.005 0.050 3150 Dihedral : 4.649 24.924 2466 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.73 % Allowed : 25.69 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.19 (0.14), residues: 1206 loop : -1.45 (0.16), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 24 HIS 0.006 0.001 HIS C 20 PHE 0.021 0.002 PHE C 56 TYR 0.031 0.002 TYR I 90 ARG 0.006 0.001 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 478 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ASN cc_start: 0.6464 (t0) cc_final: 0.6125 (t0) REVERT: B 16 ASP cc_start: 0.7256 (m-30) cc_final: 0.6883 (p0) REVERT: B 125 GLN cc_start: 0.7842 (tp40) cc_final: 0.6847 (tm-30) REVERT: A 68 ASP cc_start: 0.8223 (m-30) cc_final: 0.7947 (p0) REVERT: A 104 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7849 (p) REVERT: C 68 ASP cc_start: 0.7957 (m-30) cc_final: 0.7439 (p0) REVERT: C 112 MET cc_start: 0.8770 (mmt) cc_final: 0.8504 (mmm) REVERT: D 27 ASP cc_start: 0.6792 (t0) cc_final: 0.6247 (t0) REVERT: D 38 MET cc_start: 0.7992 (mmm) cc_final: 0.7694 (mmm) REVERT: D 43 GLU cc_start: 0.8001 (pp20) cc_final: 0.7319 (pt0) REVERT: E 29 GLN cc_start: 0.7985 (mp10) cc_final: 0.7402 (mp10) REVERT: E 70 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7506 (mt-10) REVERT: E 126 LYS cc_start: 0.8097 (tptm) cc_final: 0.7696 (tptp) REVERT: F 11 ASN cc_start: 0.7147 (t0) cc_final: 0.6786 (t0) REVERT: F 123 LEU cc_start: 0.7706 (pt) cc_final: 0.7478 (tp) REVERT: I 60 LEU cc_start: 0.7518 (tt) cc_final: 0.7275 (tp) REVERT: I 70 GLU cc_start: 0.8202 (mp0) cc_final: 0.7997 (mp0) REVERT: I 73 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8597 (t70) REVERT: I 112 MET cc_start: 0.6900 (mmm) cc_final: 0.6604 (mmt) REVERT: I 125 GLN cc_start: 0.8340 (tp40) cc_final: 0.7969 (tm-30) REVERT: I 129 VAL cc_start: 0.5966 (p) cc_final: 0.5480 (p) REVERT: K 3 LYS cc_start: 0.6354 (tppt) cc_final: 0.5901 (tppt) REVERT: K 38 MET cc_start: 0.4032 (mmm) cc_final: 0.3300 (tpp) REVERT: M 80 TYR cc_start: 0.7857 (m-80) cc_final: 0.7597 (m-80) REVERT: M 113 LEU cc_start: 0.8586 (mt) cc_final: 0.8376 (mp) REVERT: O 99 LEU cc_start: 0.8312 (tp) cc_final: 0.8042 (tp) REVERT: Q 27 ASP cc_start: 0.6679 (t70) cc_final: 0.6324 (t70) REVERT: Q 29 GLN cc_start: 0.7616 (pm20) cc_final: 0.7200 (pm20) REVERT: Q 70 GLU cc_start: 0.8190 (mp0) cc_final: 0.7934 (mp0) REVERT: J 70 GLU cc_start: 0.8427 (mp0) cc_final: 0.8050 (mp0) REVERT: J 125 GLN cc_start: 0.8422 (tp-100) cc_final: 0.8050 (tm-30) REVERT: J 126 LYS cc_start: 0.8064 (tptp) cc_final: 0.7674 (tppp) REVERT: H 44 ARG cc_start: 0.8008 (mmt90) cc_final: 0.7802 (mmm-85) REVERT: H 51 ARG cc_start: 0.8360 (ptt-90) cc_final: 0.8085 (ptp90) REVERT: L 84 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7985 (mt-10) REVERT: L 123 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7887 (mm) REVERT: L 125 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7585 (mm-40) REVERT: N 29 GLN cc_start: 0.7970 (mt0) cc_final: 0.7618 (mp10) REVERT: N 78 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7837 (mt-10) REVERT: P 70 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7531 (mm-30) REVERT: R 27 ASP cc_start: 0.7092 (t70) cc_final: 0.6318 (t70) REVERT: R 29 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6646 (pm20) outliers start: 86 outliers final: 51 residues processed: 536 average time/residue: 0.2770 time to fit residues: 222.7147 Evaluate side-chains 461 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 406 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 11 ASN Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 73 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 78 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 2 LEU Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain P residue 67 ASP Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 193 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 203 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN E 20 HIS K 22 GLN O 11 ASN O 20 HIS L 22 GLN ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 2.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 17442 Z= 0.374 Angle : 0.802 11.543 23688 Z= 0.397 Chirality : 0.048 0.221 2628 Planarity : 0.005 0.044 3150 Dihedral : 5.782 32.610 2466 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 7.10 % Allowed : 25.41 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.16), residues: 2304 helix: None (None), residues: 0 sheet: -1.43 (0.13), residues: 1350 loop : -1.44 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 24 HIS 0.005 0.001 HIS I 20 PHE 0.016 0.002 PHE R 46 TYR 0.034 0.003 TYR L 90 ARG 0.009 0.001 ARG L 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 400 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 78 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7874 (tm-30) REVERT: A 68 ASP cc_start: 0.8563 (m-30) cc_final: 0.8142 (p0) REVERT: A 125 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7618 (mm-40) REVERT: C 11 ASN cc_start: 0.7719 (t0) cc_final: 0.7485 (t0) REVERT: C 44 ARG cc_start: 0.7724 (mpp-170) cc_final: 0.7494 (mpp80) REVERT: C 51 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7969 (ptp90) REVERT: C 91 ARG cc_start: 0.7919 (mpt180) cc_final: 0.7460 (mmt-90) REVERT: E 10 LYS cc_start: 0.8639 (mttt) cc_final: 0.8239 (mtpp) REVERT: E 29 GLN cc_start: 0.8465 (mp10) cc_final: 0.8212 (mp10) REVERT: E 91 ARG cc_start: 0.8646 (mpt90) cc_final: 0.7795 (mpt180) REVERT: E 126 LYS cc_start: 0.8325 (tptm) cc_final: 0.7464 (tptp) REVERT: F 27 ASP cc_start: 0.8111 (t70) cc_final: 0.7863 (t70) REVERT: F 29 GLN cc_start: 0.8264 (pm20) cc_final: 0.7864 (pm20) REVERT: F 116 ASN cc_start: 0.8610 (m-40) cc_final: 0.8372 (m-40) REVERT: I 78 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7650 (mt-10) REVERT: I 125 GLN cc_start: 0.8681 (tp40) cc_final: 0.8142 (tm-30) REVERT: I 126 LYS cc_start: 0.8527 (tptp) cc_final: 0.8192 (tppp) REVERT: G 27 ASP cc_start: 0.8074 (t70) cc_final: 0.7791 (p0) REVERT: K 27 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8153 (p0) REVERT: K 38 MET cc_start: 0.5901 (mmm) cc_final: 0.5686 (mmm) REVERT: M 1 MET cc_start: 0.6753 (tmm) cc_final: 0.6223 (ttt) REVERT: M 43 GLU cc_start: 0.8211 (pm20) cc_final: 0.7946 (pt0) REVERT: M 57 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8035 (tm-30) REVERT: M 79 LEU cc_start: 0.8873 (tp) cc_final: 0.8614 (tp) REVERT: O 29 GLN cc_start: 0.8533 (mp10) cc_final: 0.8058 (mp10) REVERT: Q 16 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7202 (p0) REVERT: J 125 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8138 (tm-30) REVERT: J 126 LYS cc_start: 0.8460 (tptp) cc_final: 0.8183 (ttpt) REVERT: H 44 ARG cc_start: 0.8006 (mmt90) cc_final: 0.7763 (mmm-85) REVERT: H 57 GLU cc_start: 0.7477 (pm20) cc_final: 0.7223 (pm20) REVERT: H 112 MET cc_start: 0.8351 (mmm) cc_final: 0.7962 (mmt) REVERT: L 1 MET cc_start: 0.8714 (ttt) cc_final: 0.8504 (ttt) REVERT: L 98 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8194 (pp) REVERT: L 123 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8874 (mm) REVERT: L 125 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8102 (mm110) REVERT: P 57 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7963 (tm-30) REVERT: R 26 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8313 (tt) REVERT: R 29 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7858 (pm20) outliers start: 129 outliers final: 73 residues processed: 488 average time/residue: 0.2890 time to fit residues: 206.4601 Evaluate side-chains 421 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 340 time to evaluate : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 GLN Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 8 VAL Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 48 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 55 ASN Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 14 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 16 ASP Chi-restraints excluded: chain K residue 27 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 33 VAL Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 11 ASN Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 16 ASP Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 98 ILE Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 8 VAL Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 77 LEU Chi-restraints excluded: chain N residue 116 ASN Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 104 SER Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN D 22 GLN D 125 GLN ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN H 125 GLN ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 2.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17442 Z= 0.280 Angle : 0.645 8.666 23688 Z= 0.314 Chirality : 0.044 0.298 2628 Planarity : 0.004 0.036 3150 Dihedral : 4.555 18.674 2466 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.06 % Allowed : 28.77 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -1.20 (0.14), residues: 1350 loop : -1.29 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 24 HIS 0.003 0.001 HIS A 20 PHE 0.026 0.002 PHE Q 46 TYR 0.027 0.002 TYR L 90 ARG 0.007 0.001 ARG M 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 359 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 13 SER cc_start: 0.8338 (m) cc_final: 0.7890 (p) REVERT: B 26 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8069 (tt) REVERT: B 84 GLU cc_start: 0.8340 (tt0) cc_final: 0.8080 (tt0) REVERT: B 112 MET cc_start: 0.8485 (mmm) cc_final: 0.8258 (mmm) REVERT: B 125 GLN cc_start: 0.8298 (tp40) cc_final: 0.7246 (tm-30) REVERT: A 11 ASN cc_start: 0.8311 (m110) cc_final: 0.8083 (t0) REVERT: A 68 ASP cc_start: 0.8509 (m-30) cc_final: 0.8289 (p0) REVERT: A 103 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7379 (mt-10) REVERT: C 1 MET cc_start: 0.6518 (tmm) cc_final: 0.6082 (tpp) REVERT: C 29 GLN cc_start: 0.8128 (mt0) cc_final: 0.7913 (mt0) REVERT: C 32 GLU cc_start: 0.8291 (pp20) cc_final: 0.7807 (pp20) REVERT: C 91 ARG cc_start: 0.8101 (mpt180) cc_final: 0.7710 (mmt-90) REVERT: E 17 SER cc_start: 0.8274 (OUTLIER) cc_final: 0.7931 (t) REVERT: I 125 GLN cc_start: 0.8574 (tp40) cc_final: 0.8257 (tm-30) REVERT: I 126 LYS cc_start: 0.8514 (tptp) cc_final: 0.8181 (tptp) REVERT: G 32 GLU cc_start: 0.8226 (pt0) cc_final: 0.7925 (pt0) REVERT: G 70 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7759 (mm-30) REVERT: G 112 MET cc_start: 0.8296 (mmt) cc_final: 0.7872 (mmt) REVERT: M 1 MET cc_start: 0.7487 (tmm) cc_final: 0.7252 (ttt) REVERT: O 1 MET cc_start: 0.8505 (ptt) cc_final: 0.8222 (ptm) REVERT: O 29 GLN cc_start: 0.8248 (mp10) cc_final: 0.7940 (mp10) REVERT: Q 1 MET cc_start: 0.9258 (ptm) cc_final: 0.8939 (ptm) REVERT: Q 26 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8056 (tt) REVERT: Q 123 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8936 (mp) REVERT: J 29 GLN cc_start: 0.8475 (pm20) cc_final: 0.8069 (pm20) REVERT: J 125 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8162 (tm-30) REVERT: J 126 LYS cc_start: 0.8460 (tptp) cc_final: 0.8195 (ttpt) REVERT: H 57 GLU cc_start: 0.7448 (pm20) cc_final: 0.7177 (pm20) REVERT: P 57 GLU cc_start: 0.8340 (tm-30) cc_final: 0.7673 (tm-30) REVERT: R 27 ASP cc_start: 0.8072 (t70) cc_final: 0.7365 (t70) REVERT: R 29 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7555 (pm20) outliers start: 92 outliers final: 66 residues processed: 419 average time/residue: 0.3062 time to fit residues: 186.5369 Evaluate side-chains 395 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 324 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 31 ASP Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 76 ASP Chi-restraints excluded: chain M residue 101 THR Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 116 ASN Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 20 HIS Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 123 LEU Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 53 SER Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 104 SER Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 126 optimal weight: 5.9990 chunk 225 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 139 optimal weight: 0.8980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN L 22 GLN L 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 2.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17442 Z= 0.386 Angle : 0.693 8.831 23688 Z= 0.339 Chirality : 0.045 0.207 2628 Planarity : 0.005 0.035 3150 Dihedral : 5.013 20.560 2466 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 6.11 % Allowed : 27.39 % Favored : 66.50 % 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: -2.13 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -1.35 (0.13), residues: 1386 loop : -1.22 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 24 HIS 0.004 0.001 HIS E 20 PHE 0.034 0.002 PHE Q 46 TYR 0.027 0.002 TYR L 90 ARG 0.008 0.001 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 308 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 GLN cc_start: 0.8428 (pp30) cc_final: 0.8063 (pm20) REVERT: B 125 GLN cc_start: 0.8325 (tp40) cc_final: 0.7374 (tm-30) REVERT: A 68 ASP cc_start: 0.8644 (m-30) cc_final: 0.8372 (p0) REVERT: A 103 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7427 (mt-10) REVERT: A 125 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8080 (mm-40) REVERT: C 51 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7635 (ptp-110) REVERT: C 91 ARG cc_start: 0.8094 (mpt180) cc_final: 0.7649 (mmt-90) REVERT: D 1 MET cc_start: 0.8268 (tmm) cc_final: 0.7956 (tmm) REVERT: D 103 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7486 (tm-30) REVERT: E 97 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8390 (tt) REVERT: I 125 GLN cc_start: 0.8634 (tp40) cc_final: 0.8281 (tm-30) REVERT: G 32 GLU cc_start: 0.8370 (pt0) cc_final: 0.8086 (pt0) REVERT: G 112 MET cc_start: 0.8258 (mmt) cc_final: 0.7992 (mmm) REVERT: G 125 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8111 (mm110) REVERT: M 57 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7951 (tm-30) REVERT: Q 1 MET cc_start: 0.9253 (ptm) cc_final: 0.8936 (ptm) REVERT: Q 26 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8293 (tt) REVERT: Q 32 GLU cc_start: 0.8127 (pt0) cc_final: 0.7924 (pt0) REVERT: J 1 MET cc_start: 0.8651 (ptp) cc_final: 0.8233 (ptp) REVERT: J 29 GLN cc_start: 0.8656 (pm20) cc_final: 0.8221 (pm20) REVERT: J 125 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8053 (tm-30) REVERT: H 57 GLU cc_start: 0.7447 (pm20) cc_final: 0.7183 (pm20) REVERT: H 125 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8181 (mm110) REVERT: L 103 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: N 57 GLU cc_start: 0.8343 (tm-30) cc_final: 0.8000 (tm-30) REVERT: R 1 MET cc_start: 0.9204 (ptt) cc_final: 0.8841 (ptt) REVERT: R 26 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8342 (tt) REVERT: R 27 ASP cc_start: 0.8204 (t70) cc_final: 0.7527 (t70) REVERT: R 29 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7542 (pm20) outliers start: 111 outliers final: 86 residues processed: 378 average time/residue: 0.3207 time to fit residues: 174.1992 Evaluate side-chains 386 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 294 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 104 SER Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 123 LEU Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 20 HIS Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 27 ASP Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain P residue 58 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 104 SER Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 57 GLU Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 7.9990 chunk 134 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 177 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 overall best weight: 1.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 GLN L 125 GLN ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 2.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17442 Z= 0.174 Angle : 0.578 10.184 23688 Z= 0.277 Chirality : 0.042 0.172 2628 Planarity : 0.004 0.033 3150 Dihedral : 4.111 16.734 2466 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.73 % Allowed : 28.16 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -1.00 (0.14), residues: 1350 loop : -1.15 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 24 HIS 0.002 0.001 HIS F 20 PHE 0.017 0.002 PHE Q 46 TYR 0.021 0.001 TYR L 90 ARG 0.007 0.001 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 332 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 ASP cc_start: 0.8661 (m-30) cc_final: 0.8382 (p0) REVERT: A 103 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7367 (mt-10) REVERT: C 32 GLU cc_start: 0.8282 (pp20) cc_final: 0.7771 (pp20) REVERT: C 91 ARG cc_start: 0.7982 (mpt180) cc_final: 0.7515 (mmt-90) REVERT: D 103 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7395 (tm-30) REVERT: E 17 SER cc_start: 0.8224 (OUTLIER) cc_final: 0.7903 (t) REVERT: F 84 GLU cc_start: 0.8082 (tt0) cc_final: 0.7736 (tt0) REVERT: I 125 GLN cc_start: 0.8574 (tp40) cc_final: 0.8294 (tm-30) REVERT: G 32 GLU cc_start: 0.8276 (pt0) cc_final: 0.8037 (pt0) REVERT: G 91 ARG cc_start: 0.8527 (mpt90) cc_final: 0.7975 (mmt-90) REVERT: G 112 MET cc_start: 0.8180 (mmt) cc_final: 0.7820 (mmt) REVERT: G 125 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8043 (mm-40) REVERT: K 27 ASP cc_start: 0.8408 (p0) cc_final: 0.8199 (p0) REVERT: O 29 GLN cc_start: 0.8079 (mp10) cc_final: 0.7795 (mp10) REVERT: Q 1 MET cc_start: 0.9248 (ptm) cc_final: 0.8915 (ptm) REVERT: J 1 MET cc_start: 0.8663 (ptp) cc_final: 0.8171 (ptp) REVERT: J 29 GLN cc_start: 0.8528 (pm20) cc_final: 0.8229 (pm20) REVERT: J 125 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8183 (tm-30) REVERT: H 57 GLU cc_start: 0.7457 (pm20) cc_final: 0.7198 (pm20) REVERT: H 125 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8135 (mm110) REVERT: L 103 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7841 (pt0) REVERT: P 123 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8952 (mt) REVERT: R 1 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8756 (ptt) REVERT: R 26 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8261 (tt) REVERT: R 27 ASP cc_start: 0.8096 (t70) cc_final: 0.7456 (t70) REVERT: R 29 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: R 91 ARG cc_start: 0.8567 (mpt180) cc_final: 0.8179 (mmt-90) outliers start: 86 outliers final: 66 residues processed: 386 average time/residue: 0.3144 time to fit residues: 173.8364 Evaluate side-chains 390 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 318 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 GLN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 27 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 126 LYS Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 20 HIS Chi-restraints excluded: chain J residue 31 ASP Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 104 SER Chi-restraints excluded: chain P residue 123 LEU Chi-restraints excluded: chain P residue 128 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 7.9990 chunk 197 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 189 optimal weight: 7.9990 chunk 198 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 GLN L 125 GLN ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 2.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17442 Z= 0.156 Angle : 0.560 9.192 23688 Z= 0.266 Chirality : 0.041 0.134 2628 Planarity : 0.004 0.033 3150 Dihedral : 3.844 15.859 2466 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.96 % Allowed : 28.49 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.76 (0.14), residues: 1350 loop : -1.01 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 24 HIS 0.002 0.000 HIS F 20 PHE 0.021 0.002 PHE Q 46 TYR 0.021 0.001 TYR L 90 ARG 0.006 0.001 ARG E 44 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 332 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 GLN cc_start: 0.8488 (pp30) cc_final: 0.7892 (pm20) REVERT: B 125 GLN cc_start: 0.8380 (mm-40) cc_final: 0.7906 (mm110) REVERT: A 68 ASP cc_start: 0.8638 (m-30) cc_final: 0.8288 (p0) REVERT: A 103 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7315 (mt-10) REVERT: C 32 GLU cc_start: 0.8266 (pp20) cc_final: 0.7777 (pp20) REVERT: C 91 ARG cc_start: 0.7978 (mpt180) cc_final: 0.7526 (mmt-90) REVERT: D 103 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7223 (tm-30) REVERT: E 17 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7896 (t) REVERT: E 74 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9126 (mm) REVERT: F 84 GLU cc_start: 0.8069 (tt0) cc_final: 0.7695 (tt0) REVERT: F 112 MET cc_start: 0.8251 (mmm) cc_final: 0.8044 (mmm) REVERT: I 125 GLN cc_start: 0.8539 (tp40) cc_final: 0.8298 (tm-30) REVERT: I 126 LYS cc_start: 0.8538 (tptp) cc_final: 0.7892 (ttmm) REVERT: G 32 GLU cc_start: 0.8266 (pt0) cc_final: 0.8060 (pt0) REVERT: G 91 ARG cc_start: 0.8559 (mpt90) cc_final: 0.8044 (mmt-90) REVERT: G 112 MET cc_start: 0.8127 (mmt) cc_final: 0.7902 (mmm) REVERT: G 125 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8051 (mm-40) REVERT: K 27 ASP cc_start: 0.8412 (p0) cc_final: 0.8068 (p0) REVERT: O 29 GLN cc_start: 0.7937 (mp10) cc_final: 0.7609 (mp10) REVERT: Q 1 MET cc_start: 0.9244 (ptm) cc_final: 0.8897 (ptm) REVERT: J 1 MET cc_start: 0.8556 (ptp) cc_final: 0.8077 (ptp) REVERT: J 29 GLN cc_start: 0.8464 (pm20) cc_final: 0.8144 (pm20) REVERT: J 125 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8129 (tm-30) REVERT: H 57 GLU cc_start: 0.7429 (pm20) cc_final: 0.7177 (pm20) REVERT: H 125 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8130 (mm110) REVERT: L 103 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7817 (pt0) REVERT: R 26 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8261 (tt) REVERT: R 27 ASP cc_start: 0.8032 (t70) cc_final: 0.7412 (t70) REVERT: R 29 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: R 44 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8094 (mtp180) REVERT: R 91 ARG cc_start: 0.8565 (mpt180) cc_final: 0.8196 (mmt-90) outliers start: 72 outliers final: 58 residues processed: 373 average time/residue: 0.3274 time to fit residues: 174.4934 Evaluate side-chains 378 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 315 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 57 GLU Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 20 HIS Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain K residue 6 ASP Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain K residue 101 THR Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 113 LEU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 53 SER Chi-restraints excluded: chain O residue 100 SER Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 101 THR Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain L residue 123 LEU Chi-restraints excluded: chain N residue 29 GLN Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 91 ARG Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 103 GLU Chi-restraints excluded: chain P residue 104 SER Chi-restraints excluded: chain R residue 26 LEU Chi-restraints excluded: chain R residue 29 GLN Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 101 THR Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.0970 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 0.0270 chunk 154 optimal weight: 5.9990 chunk 233 optimal weight: 0.9980 chunk 214 optimal weight: 0.0570 chunk 185 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 143 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN ** P 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 2.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17442 Z= 0.122 Angle : 0.537 9.534 23688 Z= 0.253 Chirality : 0.040 0.134 2628 Planarity : 0.004 0.033 3150 Dihedral : 3.366 15.360 2466 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.48 % Allowed : 29.59 % Favored : 67.93 % 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: -1.01 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.45 (0.14), residues: 1350 loop : -0.83 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 24 HIS 0.001 0.000 HIS F 20 PHE 0.016 0.001 PHE Q 46 TYR 0.019 0.001 TYR L 90 ARG 0.007 0.001 ARG E 44 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 338 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 29 GLN cc_start: 0.8511 (pp30) cc_final: 0.7908 (pm20) REVERT: A 68 ASP cc_start: 0.8652 (m-30) cc_final: 0.8299 (p0) REVERT: A 103 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7242 (mt-10) REVERT: C 1 MET cc_start: 0.6853 (tpp) cc_final: 0.6303 (ttt) REVERT: C 32 GLU cc_start: 0.8266 (pp20) cc_final: 0.7773 (pp20) REVERT: C 91 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7540 (mmt-90) REVERT: D 103 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7027 (tm-30) REVERT: F 84 GLU cc_start: 0.8153 (tt0) cc_final: 0.7889 (tt0) REVERT: I 125 GLN cc_start: 0.8400 (tp40) cc_final: 0.8143 (tm-30) REVERT: I 126 LYS cc_start: 0.8408 (tptp) cc_final: 0.7700 (ttmm) REVERT: G 91 ARG cc_start: 0.8513 (mpt90) cc_final: 0.8054 (mmt-90) REVERT: G 125 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8122 (mm110) REVERT: K 27 ASP cc_start: 0.8337 (p0) cc_final: 0.8021 (p0) REVERT: M 44 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7770 (mtm-85) REVERT: O 29 GLN cc_start: 0.7777 (mp10) cc_final: 0.7491 (mp10) REVERT: Q 1 MET cc_start: 0.9167 (ptm) cc_final: 0.8794 (ptm) REVERT: Q 29 GLN cc_start: 0.8301 (pm20) cc_final: 0.7896 (pm20) REVERT: J 29 GLN cc_start: 0.8336 (pm20) cc_final: 0.7979 (pm20) REVERT: J 125 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8107 (tm-30) REVERT: H 1 MET cc_start: 0.8644 (ptm) cc_final: 0.8223 (ttp) REVERT: H 125 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8102 (mm110) REVERT: L 29 GLN cc_start: 0.7911 (pt0) cc_final: 0.7649 (pm20) REVERT: L 103 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: P 29 GLN cc_start: 0.7710 (pm20) cc_final: 0.7304 (pm20) REVERT: R 44 ARG cc_start: 0.8298 (mtp85) cc_final: 0.7989 (mtp180) REVERT: R 91 ARG cc_start: 0.8528 (mpt180) cc_final: 0.8217 (mmt-90) outliers start: 45 outliers final: 34 residues processed: 361 average time/residue: 0.3328 time to fit residues: 170.4738 Evaluate side-chains 355 residues out of total 1818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 319 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 GLU Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain F residue 20 HIS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 128 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 69 LEU Chi-restraints excluded: chain M residue 31 ASP Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain O residue 128 THR Chi-restraints excluded: chain Q residue 128 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 31 ASP Chi-restraints excluded: chain L residue 57 GLU Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 103 GLU Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 104 SER Chi-restraints excluded: chain R residue 128 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 185 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 ASN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 GLN ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.061522 restraints weight = 36663.090| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.38 r_work: 0.2766 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 2.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17442 Z= 0.221 Angle : 0.578 8.676 23688 Z= 0.274 Chirality : 0.041 0.131 2628 Planarity : 0.004 0.032 3150 Dihedral : 3.865 15.473 2466 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.03 % Allowed : 29.26 % Favored : 67.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.17), residues: 2304 helix: None (None), residues: 0 sheet: -0.44 (0.14), residues: 1350 loop : -0.82 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 24 HIS 0.002 0.001 HIS E 20 PHE 0.020 0.002 PHE Q 46 TYR 0.021 0.001 TYR L 90 ARG 0.006 0.001 ARG Q 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.94 seconds wall clock time: 73 minutes 15.88 seconds (4395.88 seconds total)