Starting phenix.real_space_refine on Fri Mar 15 23:27:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/03_2024/8oq4_17104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/03_2024/8oq4_17104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/03_2024/8oq4_17104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/03_2024/8oq4_17104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/03_2024/8oq4_17104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq4_17104/03_2024/8oq4_17104.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 8256 2.51 5 N 2088 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E GLU 33": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F GLU 33": "OE1" <-> "OE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G GLU 33": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H GLU 33": "OE1" <-> "OE2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I GLU 33": "OE1" <-> "OE2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "L GLU 20": "OE1" <-> "OE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L GLU 33": "OE1" <-> "OE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "M GLU 20": "OE1" <-> "OE2" Residue "M GLU 27": "OE1" <-> "OE2" Residue "M GLU 33": "OE1" <-> "OE2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 27": "OE1" <-> "OE2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O GLU 27": "OE1" <-> "OE2" Residue "O GLU 33": "OE1" <-> "OE2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "P GLU 20": "OE1" <-> "OE2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q GLU 33": "OE1" <-> "OE2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "R GLU 20": "OE1" <-> "OE2" Residue "R GLU 27": "OE1" <-> "OE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S GLU 33": "OE1" <-> "OE2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "T GLU 20": "OE1" <-> "OE2" Residue "T GLU 27": "OE1" <-> "OE2" Residue "T GLU 33": "OE1" <-> "OE2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "U GLU 20": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 33": "OE1" <-> "OE2" Residue "U ARG 54": "NH1" <-> "NH2" Residue "V GLU 20": "OE1" <-> "OE2" Residue "V GLU 27": "OE1" <-> "OE2" Residue "V GLU 33": "OE1" <-> "OE2" Residue "V ARG 54": "NH1" <-> "NH2" Residue "Z GLU 20": "OE1" <-> "OE2" Residue "Z GLU 27": "OE1" <-> "OE2" Residue "Z GLU 33": "OE1" <-> "OE2" Residue "Z ARG 54": "NH1" <-> "NH2" Residue "W GLU 20": "OE1" <-> "OE2" Residue "W GLU 27": "OE1" <-> "OE2" Residue "W GLU 33": "OE1" <-> "OE2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "J GLU 20": "OE1" <-> "OE2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J GLU 33": "OE1" <-> "OE2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "K GLU 20": "OE1" <-> "OE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K ARG 54": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "B" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "C" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "D" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "E" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "F" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "G" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "H" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "I" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "L" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "M" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "N" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "O" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "P" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "Q" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "S" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "T" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "U" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "V" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "Z" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "W" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "J" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Chain: "K" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 544 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 1, 'TRANS': 66} Time building chain proxies: 6.96, per 1000 atoms: 0.53 Number of scatterers: 13056 At special positions: 0 Unit cell: (209.04, 104, 55.12, 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 72 16.00 O 2640 8.00 N 2088 7.00 C 8256 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: 4.65 Conformation dependent library (CDL) restraints added in 2.5 seconds 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 26 sheets defined 0.0% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 15 Processing sheet with id=AA3, first strand: chain 'A' and resid 18 through 26 removed outlier: 6.738A pdb=" N MET A 18 " --> pdb=" O THR E 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR E 21 " --> pdb=" O MET A 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 20 " --> pdb=" O TYR E 21 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS E 23 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLY A 22 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 9.495A pdb=" N LEU E 25 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N ASP A 24 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET E 18 " --> pdb=" O THR I 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR I 21 " --> pdb=" O MET E 18 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU E 20 " --> pdb=" O TYR I 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS I 23 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY E 22 " --> pdb=" O LYS I 23 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LEU I 25 " --> pdb=" O GLY E 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP E 24 " --> pdb=" O LEU I 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET I 18 " --> pdb=" O THR O 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR O 21 " --> pdb=" O MET I 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU I 20 " --> pdb=" O TYR O 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS O 23 " --> pdb=" O GLU I 20 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY I 22 " --> pdb=" O LYS O 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU O 25 " --> pdb=" O GLY I 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP I 24 " --> pdb=" O LEU O 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET O 18 " --> pdb=" O THR S 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR S 21 " --> pdb=" O MET O 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU O 20 " --> pdb=" O TYR S 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS S 23 " --> pdb=" O GLU O 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY O 22 " --> pdb=" O LYS S 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU S 25 " --> pdb=" O GLY O 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP O 24 " --> pdb=" O LEU S 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET S 18 " --> pdb=" O THR Z 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR Z 21 " --> pdb=" O MET S 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU S 20 " --> pdb=" O TYR Z 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS Z 23 " --> pdb=" O GLU S 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY S 22 " --> pdb=" O LYS Z 23 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LEU Z 25 " --> pdb=" O GLY S 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP S 24 " --> pdb=" O LEU Z 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.249A pdb=" N HIS A 46 " --> pdb=" O GLU E 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU E 49 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N GLN A 48 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS E 46 " --> pdb=" O GLU I 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU I 49 " --> pdb=" O HIS E 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN E 48 " --> pdb=" O LEU I 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS I 46 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU O 49 " --> pdb=" O HIS I 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN I 48 " --> pdb=" O LEU O 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS O 46 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU S 49 " --> pdb=" O HIS O 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN O 48 " --> pdb=" O LEU S 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS S 46 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU Z 49 " --> pdb=" O HIS S 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN S 48 " --> pdb=" O LEU Z 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 64 removed outlier: 6.564A pdb=" N SER A 59 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN E 62 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL A 61 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE E 64 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE A 63 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 59 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN I 62 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL E 61 " --> pdb=" O ASN I 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE I 64 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE E 63 " --> pdb=" O PHE I 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER I 59 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN O 62 " --> pdb=" O SER I 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL I 61 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE O 64 " --> pdb=" O VAL I 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE I 63 " --> pdb=" O PHE O 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER O 59 " --> pdb=" O LEU S 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN S 62 " --> pdb=" O SER O 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL O 61 " --> pdb=" O ASN S 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE S 64 " --> pdb=" O VAL O 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE O 63 " --> pdb=" O PHE S 64 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER S 59 " --> pdb=" O LEU Z 60 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN Z 62 " --> pdb=" O SER S 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL S 61 " --> pdb=" O ASN Z 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE Z 64 " --> pdb=" O VAL S 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE S 63 " --> pdb=" O PHE Z 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.231A pdb=" N MET A 68 " --> pdb=" O ASN E 69 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET E 68 " --> pdb=" O ASN I 69 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET I 68 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET O 68 " --> pdb=" O ASN S 69 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N MET S 68 " --> pdb=" O ASN Z 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 15 Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 26 removed outlier: 6.639A pdb=" N MET B 18 " --> pdb=" O THR F 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR F 21 " --> pdb=" O MET B 18 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU B 20 " --> pdb=" O TYR F 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS F 23 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY B 22 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU F 25 " --> pdb=" O GLY B 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP B 24 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET F 18 " --> pdb=" O THR L 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR L 21 " --> pdb=" O MET F 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU F 20 " --> pdb=" O TYR L 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS L 23 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLY F 22 " --> pdb=" O LYS L 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU L 25 " --> pdb=" O GLY F 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP F 24 " --> pdb=" O LEU L 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET L 18 " --> pdb=" O THR P 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR P 21 " --> pdb=" O MET L 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU L 20 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS P 23 " --> pdb=" O GLU L 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY L 22 " --> pdb=" O LYS P 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU P 25 " --> pdb=" O GLY L 22 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASP L 24 " --> pdb=" O LEU P 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET P 18 " --> pdb=" O THR T 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR T 21 " --> pdb=" O MET P 18 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU P 20 " --> pdb=" O TYR T 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS T 23 " --> pdb=" O GLU P 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY P 22 " --> pdb=" O LYS T 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU T 25 " --> pdb=" O GLY P 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP P 24 " --> pdb=" O LEU T 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET T 18 " --> pdb=" O THR W 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR W 21 " --> pdb=" O MET T 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU T 20 " --> pdb=" O TYR W 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS W 23 " --> pdb=" O GLU T 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY T 22 " --> pdb=" O LYS W 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU W 25 " --> pdb=" O GLY T 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP T 24 " --> pdb=" O LEU W 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 46 through 49 removed outlier: 6.311A pdb=" N HIS B 46 " --> pdb=" O GLU F 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU F 49 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN B 48 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS F 46 " --> pdb=" O GLU L 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU L 49 " --> pdb=" O HIS F 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN F 48 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS L 46 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU P 49 " --> pdb=" O HIS L 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN L 48 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N HIS P 46 " --> pdb=" O GLU T 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU T 49 " --> pdb=" O HIS P 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN P 48 " --> pdb=" O LEU T 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS T 46 " --> pdb=" O GLU W 47 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU W 49 " --> pdb=" O HIS T 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN T 48 " --> pdb=" O LEU W 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 64 removed outlier: 6.272A pdb=" N SER B 59 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN F 62 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL B 61 " --> pdb=" O ASN F 62 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE F 64 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE B 63 " --> pdb=" O PHE F 64 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER F 59 " --> pdb=" O LEU L 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN L 62 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL F 61 " --> pdb=" O ASN L 62 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE L 64 " --> pdb=" O VAL F 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE F 63 " --> pdb=" O PHE L 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER L 59 " --> pdb=" O LEU P 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN P 62 " --> pdb=" O SER L 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL L 61 " --> pdb=" O ASN P 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE P 64 " --> pdb=" O VAL L 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE L 63 " --> pdb=" O PHE P 64 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER P 59 " --> pdb=" O LEU T 60 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ASN T 62 " --> pdb=" O SER P 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL P 61 " --> pdb=" O ASN T 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE T 64 " --> pdb=" O VAL P 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE P 63 " --> pdb=" O PHE T 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER T 59 " --> pdb=" O LEU W 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN W 62 " --> pdb=" O SER T 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL T 61 " --> pdb=" O ASN W 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE W 64 " --> pdb=" O VAL T 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE T 63 " --> pdb=" O PHE W 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.108A pdb=" N MET B 68 " --> pdb=" O ASN F 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET F 68 " --> pdb=" O ASN L 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET L 68 " --> pdb=" O ASN P 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET P 68 " --> pdb=" O ASN T 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET T 68 " --> pdb=" O ASN W 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 15 Processing sheet with id=AB7, first strand: chain 'C' and resid 18 through 26 removed outlier: 6.738A pdb=" N MET C 18 " --> pdb=" O THR G 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR G 21 " --> pdb=" O MET C 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU C 20 " --> pdb=" O TYR G 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS G 23 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY C 22 " --> pdb=" O LYS G 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU G 25 " --> pdb=" O GLY C 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP C 24 " --> pdb=" O LEU G 25 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET G 18 " --> pdb=" O THR M 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR M 21 " --> pdb=" O MET G 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU G 20 " --> pdb=" O TYR M 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS M 23 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY G 22 " --> pdb=" O LYS M 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU M 25 " --> pdb=" O GLY G 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP G 24 " --> pdb=" O LEU M 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET M 18 " --> pdb=" O THR Q 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR Q 21 " --> pdb=" O MET M 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU M 20 " --> pdb=" O TYR Q 21 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS Q 23 " --> pdb=" O GLU M 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY M 22 " --> pdb=" O LYS Q 23 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LEU Q 25 " --> pdb=" O GLY M 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP M 24 " --> pdb=" O LEU Q 25 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N MET Q 18 " --> pdb=" O THR U 19 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N TYR U 21 " --> pdb=" O MET Q 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU Q 20 " --> pdb=" O TYR U 21 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS U 23 " --> pdb=" O GLU Q 20 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N GLY Q 22 " --> pdb=" O LYS U 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU U 25 " --> pdb=" O GLY Q 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP Q 24 " --> pdb=" O LEU U 25 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET U 18 " --> pdb=" O THR J 19 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N TYR J 21 " --> pdb=" O MET U 18 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU U 20 " --> pdb=" O TYR J 21 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N LYS J 23 " --> pdb=" O GLU U 20 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N GLY U 22 " --> pdb=" O LYS J 23 " (cutoff:3.500A) removed outlier: 9.493A pdb=" N LEU J 25 " --> pdb=" O GLY U 22 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ASP U 24 " --> pdb=" O LEU J 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 46 through 49 removed outlier: 6.249A pdb=" N HIS C 46 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU G 49 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN C 48 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS G 46 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU M 49 " --> pdb=" O HIS G 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN G 48 " --> pdb=" O LEU M 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS M 46 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU Q 49 " --> pdb=" O HIS M 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN M 48 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS Q 46 " --> pdb=" O GLU U 47 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N LEU U 49 " --> pdb=" O HIS Q 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN Q 48 " --> pdb=" O LEU U 49 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N HIS U 46 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU J 49 " --> pdb=" O HIS U 46 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N GLN U 48 " --> pdb=" O LEU J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 58 through 64 removed outlier: 6.564A pdb=" N SER C 59 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASN G 62 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL C 61 " --> pdb=" O ASN G 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE G 64 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE C 63 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER G 59 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN M 62 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL G 61 " --> pdb=" O ASN M 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE M 64 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE G 63 " --> pdb=" O PHE M 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER M 59 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN Q 62 " --> pdb=" O SER M 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL M 61 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE Q 64 " --> pdb=" O VAL M 61 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N PHE M 63 " --> pdb=" O PHE Q 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER Q 59 " --> pdb=" O LEU U 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN U 62 " --> pdb=" O SER Q 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL Q 61 " --> pdb=" O ASN U 62 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE U 64 " --> pdb=" O VAL Q 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE Q 63 " --> pdb=" O PHE U 64 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER U 59 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASN J 62 " --> pdb=" O SER U 59 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL U 61 " --> pdb=" O ASN J 62 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE J 64 " --> pdb=" O VAL U 61 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N PHE U 63 " --> pdb=" O PHE J 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.231A pdb=" N MET C 68 " --> pdb=" O ASN G 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET G 68 " --> pdb=" O ASN M 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET M 68 " --> pdb=" O ASN Q 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET Q 68 " --> pdb=" O ASN U 69 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N MET U 68 " --> pdb=" O ASN J 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 15 Processing sheet with id=AC4, first strand: chain 'D' and resid 18 through 26 removed outlier: 6.638A pdb=" N MET D 18 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR H 21 " --> pdb=" O MET D 18 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU D 20 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS H 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY D 22 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU H 25 " --> pdb=" O GLY D 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP D 24 " --> pdb=" O LEU H 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H 18 " --> pdb=" O THR N 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR N 21 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU H 20 " --> pdb=" O TYR N 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS N 23 " --> pdb=" O GLU H 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY H 22 " --> pdb=" O LYS N 23 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N LEU N 25 " --> pdb=" O GLY H 22 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASP H 24 " --> pdb=" O LEU N 25 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N MET N 18 " --> pdb=" O THR R 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR R 21 " --> pdb=" O MET N 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU N 20 " --> pdb=" O TYR R 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS R 23 " --> pdb=" O GLU N 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY N 22 " --> pdb=" O LYS R 23 " (cutoff:3.500A) removed outlier: 9.345A pdb=" N LEU R 25 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASP N 24 " --> pdb=" O LEU R 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET R 18 " --> pdb=" O THR V 19 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR V 21 " --> pdb=" O MET R 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU R 20 " --> pdb=" O TYR V 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS V 23 " --> pdb=" O GLU R 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY R 22 " --> pdb=" O LYS V 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU V 25 " --> pdb=" O GLY R 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP R 24 " --> pdb=" O LEU V 25 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET V 18 " --> pdb=" O THR K 19 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR K 21 " --> pdb=" O MET V 18 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU V 20 " --> pdb=" O TYR K 21 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS K 23 " --> pdb=" O GLU V 20 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY V 22 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N LEU K 25 " --> pdb=" O GLY V 22 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ASP V 24 " --> pdb=" O LEU K 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.311A pdb=" N HIS D 46 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU H 49 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN D 48 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS H 46 " --> pdb=" O GLU N 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU N 49 " --> pdb=" O HIS H 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN H 48 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS N 46 " --> pdb=" O GLU R 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU R 49 " --> pdb=" O HIS N 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN N 48 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N HIS R 46 " --> pdb=" O GLU V 47 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU V 49 " --> pdb=" O HIS R 46 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLN R 48 " --> pdb=" O LEU V 49 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N HIS V 46 " --> pdb=" O GLU K 47 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU K 49 " --> pdb=" O HIS V 46 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLN V 48 " --> pdb=" O LEU K 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AC7, first strand: chain 'D' and resid 58 through 64 removed outlier: 6.273A pdb=" N SER D 59 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN H 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL D 61 " --> pdb=" O ASN H 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE H 64 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE D 63 " --> pdb=" O PHE H 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER H 59 " --> pdb=" O LEU N 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN N 62 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL H 61 " --> pdb=" O ASN N 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE N 64 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE H 63 " --> pdb=" O PHE N 64 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N SER N 59 " --> pdb=" O LEU R 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN R 62 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL N 61 " --> pdb=" O ASN R 62 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N PHE R 64 " --> pdb=" O VAL N 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE N 63 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER R 59 " --> pdb=" O LEU V 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN V 62 " --> pdb=" O SER R 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL R 61 " --> pdb=" O ASN V 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE V 64 " --> pdb=" O VAL R 61 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE R 63 " --> pdb=" O PHE V 64 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N SER V 59 " --> pdb=" O LEU K 60 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ASN K 62 " --> pdb=" O SER V 59 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL V 61 " --> pdb=" O ASN K 62 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N PHE K 64 " --> pdb=" O VAL V 61 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N PHE V 63 " --> pdb=" O PHE K 64 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.107A pdb=" N MET D 68 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET H 68 " --> pdb=" O ASN N 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET N 68 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET R 68 " --> pdb=" O ASN V 69 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET V 68 " --> pdb=" O ASN K 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 150 hydrogen bonds defined for protein. 450 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: 3.59 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2232 1.29 - 1.42: 3372 1.42 - 1.55: 7464 1.55 - 1.68: 60 1.68 - 1.81: 144 Bond restraints: 13272 Sorted by residual: bond pdb=" C TYR I 21 " pdb=" O TYR I 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.48e+01 bond pdb=" C TYR G 21 " pdb=" O TYR G 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.47e+01 bond pdb=" C TYR E 21 " pdb=" O TYR E 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.46e+01 bond pdb=" C TYR J 21 " pdb=" O TYR J 21 " ideal model delta sigma weight residual 1.233 1.164 0.069 1.17e-02 7.31e+03 3.46e+01 bond pdb=" C TYR Z 21 " pdb=" O TYR Z 21 " ideal model delta sigma weight residual 1.233 1.165 0.069 1.17e-02 7.31e+03 3.46e+01 ... (remaining 13267 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.34: 492 106.34 - 112.59: 5460 112.59 - 118.84: 5949 118.84 - 125.08: 5655 125.08 - 131.33: 252 Bond angle restraints: 17808 Sorted by residual: angle pdb=" N SER C 55 " pdb=" CA SER C 55 " pdb=" C SER C 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.35e+01 angle pdb=" N SER Z 55 " pdb=" CA SER Z 55 " pdb=" C SER Z 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.35e+01 angle pdb=" N SER S 55 " pdb=" CA SER S 55 " pdb=" C SER S 55 " ideal model delta sigma weight residual 111.74 119.55 -7.81 1.35e+00 5.49e-01 3.34e+01 angle pdb=" N SER M 55 " pdb=" CA SER M 55 " pdb=" C SER M 55 " ideal model delta sigma weight residual 111.74 119.53 -7.79 1.35e+00 5.49e-01 3.33e+01 angle pdb=" N SER A 55 " pdb=" CA SER A 55 " pdb=" C SER A 55 " ideal model delta sigma weight residual 111.74 119.51 -7.77 1.35e+00 5.49e-01 3.31e+01 ... (remaining 17803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.29: 6516 10.29 - 20.57: 828 20.57 - 30.86: 324 30.86 - 41.15: 180 41.15 - 51.43: 192 Dihedral angle restraints: 8040 sinusoidal: 3240 harmonic: 4800 Sorted by residual: dihedral pdb=" CA ALA D 40 " pdb=" C ALA D 40 " pdb=" N TYR D 41 " pdb=" CA TYR D 41 " ideal model delta harmonic sigma weight residual -180.00 -152.54 -27.46 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA M 40 " pdb=" C ALA M 40 " pdb=" N TYR M 41 " pdb=" CA TYR M 41 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA L 40 " pdb=" C ALA L 40 " pdb=" N TYR L 41 " pdb=" CA TYR L 41 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 783 0.066 - 0.133: 669 0.133 - 0.199: 383 0.199 - 0.266: 121 0.266 - 0.332: 12 Chirality restraints: 1968 Sorted by residual: chirality pdb=" CA SER C 55 " pdb=" N SER C 55 " pdb=" C SER C 55 " pdb=" CB SER C 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER M 55 " pdb=" N SER M 55 " pdb=" C SER M 55 " pdb=" CB SER M 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA SER Z 55 " pdb=" N SER Z 55 " pdb=" C SER Z 55 " pdb=" CB SER Z 55 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 1965 not shown) Planarity restraints: 2280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 35 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C GLN B 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN B 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER B 36 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 35 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLN F 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN F 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER F 36 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN W 35 " 0.022 2.00e-02 2.50e+03 4.32e-02 1.87e+01 pdb=" C GLN W 35 " -0.075 2.00e-02 2.50e+03 pdb=" O GLN W 35 " 0.027 2.00e-02 2.50e+03 pdb=" N SER W 36 " 0.026 2.00e-02 2.50e+03 ... (remaining 2277 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 6998 3.00 - 3.48: 11643 3.48 - 3.95: 25251 3.95 - 4.43: 27624 4.43 - 4.90: 50006 Nonbonded interactions: 121522 Sorted by model distance: nonbonded pdb=" N GLU K 20 " pdb=" O GLU K 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU H 20 " pdb=" O GLU H 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU T 20 " pdb=" O GLU T 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU V 20 " pdb=" O GLU V 20 " model vdw 2.528 2.496 nonbonded pdb=" N GLU R 20 " pdb=" O GLU R 20 " model vdw 2.528 2.496 ... (remaining 121517 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.020 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 36.590 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.015 0.069 13272 Z= 0.963 Angle : 2.023 9.784 17808 Z= 1.403 Chirality : 0.112 0.332 1968 Planarity : 0.010 0.043 2280 Dihedral : 15.006 51.432 4920 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % 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: -5.03 (0.11), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.09), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 46 PHE 0.008 0.002 PHE Z 42 TYR 0.033 0.005 TYR E 21 ARG 0.002 0.001 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 1.679 Fit side-chains REVERT: E 6 ASP cc_start: 0.8069 (m-30) cc_final: 0.7825 (m-30) REVERT: E 62 ASN cc_start: 0.8224 (m-40) cc_final: 0.8006 (m110) REVERT: L 7 MET cc_start: 0.7625 (mtp) cc_final: 0.7378 (mtt) REVERT: O 6 ASP cc_start: 0.8098 (m-30) cc_final: 0.7866 (m-30) REVERT: U 6 ASP cc_start: 0.8005 (m-30) cc_final: 0.7793 (m-30) REVERT: K 52 LEU cc_start: 0.8698 (mp) cc_final: 0.8472 (mp) outliers start: 0 outliers final: 1 residues processed: 652 average time/residue: 1.0333 time to fit residues: 742.4127 Evaluate side-chains 466 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 465 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 63 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN E 5 GLN G 48 GLN ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 GLN I 62 ASN ** M 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 5 GLN O 62 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN S 5 GLN S 62 ASN U 5 GLN ** U 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 5 GLN Z 62 ASN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 GLN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13272 Z= 0.231 Angle : 0.639 8.450 17808 Z= 0.341 Chirality : 0.045 0.152 1968 Planarity : 0.004 0.030 2280 Dihedral : 6.175 39.047 1706 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.85 % Allowed : 25.20 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS Q 46 PHE 0.012 0.002 PHE N 11 TYR 0.011 0.002 TYR D 14 ARG 0.007 0.001 ARG C 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 459 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 27 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6675 (mm-30) REVERT: I 54 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7819 (ttm170) REVERT: L 7 MET cc_start: 0.7685 (mtp) cc_final: 0.7372 (mtt) REVERT: L 28 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7909 (mptp) REVERT: L 33 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: N 10 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8465 (tt) REVERT: P 33 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7333 (tm-30) REVERT: Q 54 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7812 (ttm170) REVERT: R 28 LYS cc_start: 0.8289 (mttp) cc_final: 0.8065 (mttm) outliers start: 71 outliers final: 9 residues processed: 486 average time/residue: 1.2592 time to fit residues: 665.3180 Evaluate side-chains 417 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 402 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain Z residue 10 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN C 62 ASN G 62 ASN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 GLN M 62 ASN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 GLN R 37 GLN T 37 GLN ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 62 ASN V 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 GLN J 62 ASN K 37 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13272 Z= 0.281 Angle : 0.678 8.907 17808 Z= 0.354 Chirality : 0.046 0.129 1968 Planarity : 0.004 0.033 2280 Dihedral : 6.058 21.405 1704 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.44 % Allowed : 27.12 % Favored : 68.44 % 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: -4.24 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS U 46 PHE 0.014 0.002 PHE W 11 TYR 0.013 0.002 TYR N 21 ARG 0.005 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 436 time to evaluate : 1.300 Fit side-chains REVERT: D 10 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8417 (mt) REVERT: D 33 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: D 71 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6588 (tm-30) REVERT: E 30 LYS cc_start: 0.8024 (mtpm) cc_final: 0.7805 (mtpm) REVERT: H 43 GLU cc_start: 0.8263 (tt0) cc_final: 0.8061 (tt0) REVERT: I 27 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6554 (mm-30) REVERT: I 54 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7796 (ttm170) REVERT: L 7 MET cc_start: 0.7882 (mtp) cc_final: 0.7578 (mtt) REVERT: L 28 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7843 (mptp) REVERT: L 33 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: Q 5 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8287 (mt0) REVERT: Q 54 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7585 (ttm170) REVERT: R 33 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7213 (tm-30) REVERT: T 33 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: U 10 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8366 (tt) REVERT: V 10 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8571 (mt) REVERT: J 5 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8452 (mt0) REVERT: J 24 ASP cc_start: 0.8380 (m-30) cc_final: 0.8146 (m-30) REVERT: K 33 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7388 (tm-30) outliers start: 65 outliers final: 17 residues processed: 455 average time/residue: 1.2436 time to fit residues: 613.7019 Evaluate side-chains 450 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 419 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 47 GLU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 5 GLN Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 68 MET Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 13272 Z= 0.503 Angle : 0.806 10.072 17808 Z= 0.416 Chirality : 0.049 0.148 1968 Planarity : 0.004 0.047 2280 Dihedral : 6.586 23.418 1704 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.81 % Allowed : 26.84 % Favored : 67.35 % 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: -4.03 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 46 PHE 0.018 0.002 PHE W 11 TYR 0.014 0.003 TYR R 21 ARG 0.005 0.001 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 441 time to evaluate : 1.638 Fit side-chains REVERT: B 33 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7285 (tt0) REVERT: D 28 LYS cc_start: 0.8431 (mttp) cc_final: 0.8208 (mttt) REVERT: D 33 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7434 (tt0) REVERT: E 30 LYS cc_start: 0.8062 (mtpm) cc_final: 0.7769 (mtpm) REVERT: F 33 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7332 (tt0) REVERT: F 47 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7563 (mt-10) REVERT: H 28 LYS cc_start: 0.8344 (mttp) cc_final: 0.8042 (mttt) REVERT: H 33 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: I 27 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6784 (mm-30) REVERT: I 45 THR cc_start: 0.8844 (p) cc_final: 0.8637 (m) REVERT: I 54 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7628 (ttm170) REVERT: L 7 MET cc_start: 0.8061 (mtp) cc_final: 0.7834 (mtt) REVERT: L 33 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: N 33 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7520 (tt0) REVERT: P 33 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: Q 5 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8345 (mt0) REVERT: Q 54 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7569 (ttm170) REVERT: R 33 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: S 39 LYS cc_start: 0.7852 (mmmt) cc_final: 0.7648 (mmmm) REVERT: S 43 GLU cc_start: 0.7208 (tm-30) cc_final: 0.7005 (tm-30) REVERT: T 10 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8724 (tt) REVERT: T 33 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: U 71 GLU cc_start: 0.7132 (tm-30) cc_final: 0.6824 (tm-30) REVERT: V 10 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8567 (OUTLIER) REVERT: V 33 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7578 (tt0) REVERT: W 33 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7268 (tt0) REVERT: K 33 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7560 (tt0) outliers start: 85 outliers final: 26 residues processed: 468 average time/residue: 1.3477 time to fit residues: 681.1920 Evaluate side-chains 466 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 423 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain I residue 27 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain N residue 71 GLU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 5 GLN Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 52 LEU Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 12 THR Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 33 GLU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain W residue 10 LEU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain J residue 5 GLN Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 GLN L 37 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN T 69 ASN U 48 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13272 Z= 0.216 Angle : 0.634 8.229 17808 Z= 0.328 Chirality : 0.043 0.116 1968 Planarity : 0.003 0.031 2280 Dihedral : 5.811 20.128 1704 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.30 % Allowed : 29.17 % Favored : 66.53 % 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: -4.05 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 46 PHE 0.012 0.001 PHE W 11 TYR 0.011 0.002 TYR N 21 ARG 0.002 0.001 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 436 time to evaluate : 1.636 Fit side-chains REVERT: D 33 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: E 30 LYS cc_start: 0.8050 (mtpm) cc_final: 0.7782 (mtpm) REVERT: F 33 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7433 (tt0) REVERT: H 33 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7037 (tt0) REVERT: I 45 THR cc_start: 0.8753 (p) cc_final: 0.8550 (m) REVERT: I 54 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7868 (ttm170) REVERT: L 7 MET cc_start: 0.7999 (mtp) cc_final: 0.7739 (mtt) REVERT: L 33 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: N 33 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7212 (tt0) REVERT: P 10 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8308 (mt) REVERT: Q 5 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8229 (mt0) REVERT: Q 54 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7485 (ttm170) REVERT: R 33 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: T 10 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8660 (tt) REVERT: T 33 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: U 30 LYS cc_start: 0.8033 (mtpm) cc_final: 0.7757 (mtpm) REVERT: U 71 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6780 (tm-30) REVERT: V 10 LEU cc_start: 0.8773 (tt) cc_final: 0.8548 (mt) REVERT: K 33 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7521 (tt0) outliers start: 63 outliers final: 23 residues processed: 459 average time/residue: 1.2631 time to fit residues: 628.6247 Evaluate side-chains 450 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 414 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 28 LYS Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 33 GLU Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 5 GLN Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 67 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 37 GLN ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 GLN ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 13272 Z= 0.444 Angle : 0.765 9.763 17808 Z= 0.395 Chirality : 0.047 0.144 1968 Planarity : 0.004 0.044 2280 Dihedral : 6.334 22.433 1704 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.58 % Allowed : 28.96 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS S 46 PHE 0.016 0.002 PHE W 11 TYR 0.013 0.003 TYR N 21 ARG 0.004 0.001 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 422 time to evaluate : 1.534 Fit side-chains REVERT: B 33 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: D 33 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7424 (tt0) REVERT: E 30 LYS cc_start: 0.8092 (mtpm) cc_final: 0.7725 (mttm) REVERT: F 33 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: H 33 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: I 54 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7648 (ttm170) REVERT: L 7 MET cc_start: 0.8140 (mtp) cc_final: 0.7904 (mtt) REVERT: L 33 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: M 39 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7779 (mmmm) REVERT: N 23 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8053 (mmtp) REVERT: P 10 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8336 (mt) REVERT: P 33 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: Q 5 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8368 (mt0) REVERT: Q 54 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7536 (ttm170) REVERT: R 33 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: S 39 LYS cc_start: 0.7863 (mmmt) cc_final: 0.7656 (mmmm) REVERT: T 10 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8673 (tt) REVERT: T 33 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7309 (tt0) REVERT: U 10 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8145 (tt) REVERT: U 71 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6817 (tm-30) REVERT: V 10 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8563 (mt) REVERT: Z 43 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6810 (tm-30) REVERT: W 33 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: K 33 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7554 (tt0) outliers start: 67 outliers final: 27 residues processed: 443 average time/residue: 1.3390 time to fit residues: 640.2185 Evaluate side-chains 462 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 416 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain P residue 33 GLU Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain R residue 33 GLU Chi-restraints excluded: chain S residue 5 GLN Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 31 THR Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain U residue 10 LEU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 33 GLU Chi-restraints excluded: chain K residue 49 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 0.2980 chunk 79 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 78 optimal weight: 0.0870 chunk 117 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN L 37 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 GLN T 37 GLN ** W 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13272 Z= 0.165 Angle : 0.592 7.563 17808 Z= 0.309 Chirality : 0.042 0.117 1968 Planarity : 0.002 0.022 2280 Dihedral : 5.430 18.332 1704 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.21 % Allowed : 31.97 % Favored : 64.82 % 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: -3.99 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS U 46 PHE 0.009 0.001 PHE W 11 TYR 0.009 0.001 TYR O 14 ARG 0.002 0.001 ARG J 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 437 time to evaluate : 1.589 Fit side-chains REVERT: E 30 LYS cc_start: 0.8016 (mtpm) cc_final: 0.7743 (mtpm) REVERT: F 33 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: F 71 GLU cc_start: 0.6704 (tt0) cc_final: 0.6367 (tt0) REVERT: G 30 LYS cc_start: 0.7688 (ttpt) cc_final: 0.7437 (mtmt) REVERT: H 33 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: I 54 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7844 (ttm170) REVERT: L 7 MET cc_start: 0.8061 (mtp) cc_final: 0.7774 (mtt) REVERT: L 33 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: P 10 LEU cc_start: 0.8667 (tt) cc_final: 0.8347 (mt) REVERT: Q 54 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7250 (ttm170) REVERT: R 10 LEU cc_start: 0.8732 (tt) cc_final: 0.8410 (mt) REVERT: T 33 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: U 30 LYS cc_start: 0.8010 (mtpm) cc_final: 0.7738 (mtpm) REVERT: U 71 GLU cc_start: 0.7100 (tm-30) cc_final: 0.6816 (tm-30) outliers start: 47 outliers final: 15 residues processed: 462 average time/residue: 1.2023 time to fit residues: 604.1965 Evaluate side-chains 437 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 416 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain S residue 5 GLN Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN C 5 GLN F 37 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN M 5 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN P 35 GLN P 37 GLN R 37 GLN T 37 GLN V 37 GLN W 35 GLN W 37 GLN K 37 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.065 13272 Z= 0.724 Angle : 0.925 10.753 17808 Z= 0.480 Chirality : 0.054 0.183 1968 Planarity : 0.005 0.057 2280 Dihedral : 6.765 24.073 1704 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.78 % Allowed : 30.12 % Favored : 65.10 % 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: -3.88 (0.15), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 46 PHE 0.020 0.003 PHE W 11 TYR 0.017 0.003 TYR C 14 ARG 0.008 0.001 ARG F 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 424 time to evaluate : 1.578 Fit side-chains REVERT: D 10 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8476 (mt) REVERT: D 33 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: E 30 LYS cc_start: 0.8086 (mtpm) cc_final: 0.7738 (mttm) REVERT: E 52 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8144 (mp) REVERT: E 54 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7314 (ttm-80) REVERT: F 33 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7539 (tt0) REVERT: H 33 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: I 54 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7698 (ttm170) REVERT: L 5 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: L 7 MET cc_start: 0.8156 (mtp) cc_final: 0.7941 (mtt) REVERT: L 33 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7561 (tt0) REVERT: M 39 LYS cc_start: 0.8083 (mmmm) cc_final: 0.7757 (mttp) REVERT: N 23 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8096 (mmtp) REVERT: Q 5 GLN cc_start: 0.8616 (OUTLIER) cc_final: 0.8373 (mt0) REVERT: Q 54 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7602 (ttm170) REVERT: T 10 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8445 (mt) REVERT: T 33 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7320 (tt0) REVERT: U 71 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6861 (tm-30) REVERT: Z 43 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6900 (tm-30) REVERT: W 33 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7286 (tt0) REVERT: J 18 MET cc_start: 0.7829 (ttm) cc_final: 0.7570 (mtp) REVERT: K 33 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7573 (tt0) outliers start: 70 outliers final: 25 residues processed: 449 average time/residue: 1.3834 time to fit residues: 669.7055 Evaluate side-chains 459 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 417 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 33 GLU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain H residue 7 MET Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain L residue 5 GLN Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 31 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain P residue 10 LEU Chi-restraints excluded: chain Q residue 5 GLN Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain S residue 5 GLN Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 36 SER Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 28 LYS Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain W residue 33 GLU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.8980 chunk 121 optimal weight: 0.7980 chunk 129 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN F 37 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN P 37 GLN R 37 GLN T 37 GLN V 37 GLN W 37 GLN K 37 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13272 Z= 0.228 Angle : 0.673 10.592 17808 Z= 0.345 Chirality : 0.044 0.125 1968 Planarity : 0.003 0.032 2280 Dihedral : 5.925 19.907 1704 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.14 % Allowed : 33.06 % Favored : 63.80 % 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: -3.96 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS S 46 PHE 0.012 0.001 PHE W 11 TYR 0.014 0.002 TYR V 14 ARG 0.003 0.001 ARG H 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 425 time to evaluate : 1.593 Fit side-chains REVERT: E 30 LYS cc_start: 0.8058 (mtpm) cc_final: 0.7724 (mttm) REVERT: F 33 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: H 33 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7016 (tt0) REVERT: I 54 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7840 (ttm170) REVERT: L 7 MET cc_start: 0.8106 (mtp) cc_final: 0.7831 (mtt) REVERT: L 33 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: N 23 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8018 (mmtp) REVERT: Q 54 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7513 (ttm170) REVERT: T 33 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7282 (tm-30) REVERT: U 71 GLU cc_start: 0.7029 (tm-30) cc_final: 0.6796 (tm-30) REVERT: K 33 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7523 (tt0) outliers start: 46 outliers final: 22 residues processed: 443 average time/residue: 1.3553 time to fit residues: 648.1991 Evaluate side-chains 449 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 419 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain S residue 5 GLN Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN F 37 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN M 5 GLN ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.6028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13272 Z= 0.280 Angle : 0.709 10.240 17808 Z= 0.362 Chirality : 0.045 0.121 1968 Planarity : 0.003 0.037 2280 Dihedral : 5.966 20.331 1704 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.53 % Allowed : 33.95 % Favored : 63.52 % 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: -3.99 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS S 46 PHE 0.013 0.001 PHE W 11 TYR 0.013 0.002 TYR V 14 ARG 0.002 0.001 ARG H 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3168 Ramachandran restraints generated. 1584 Oldfield, 0 Emsley, 1584 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 427 time to evaluate : 1.471 Fit side-chains REVERT: D 10 LEU cc_start: 0.8610 (mt) cc_final: 0.8375 (mt) REVERT: E 30 LYS cc_start: 0.8058 (mtpm) cc_final: 0.7699 (mttm) REVERT: F 33 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: H 33 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: I 54 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7878 (ttm170) REVERT: L 7 MET cc_start: 0.8080 (mtp) cc_final: 0.7836 (mtt) REVERT: L 33 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: N 23 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8009 (mmtp) REVERT: Q 54 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7491 (ttm170) REVERT: T 7 MET cc_start: 0.8210 (mtp) cc_final: 0.8007 (mtm) REVERT: T 10 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8414 (mt) REVERT: T 33 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: U 30 LYS cc_start: 0.8010 (mtpm) cc_final: 0.7757 (mtpm) REVERT: U 71 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6829 (tm-30) REVERT: K 33 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7537 (tt0) outliers start: 37 outliers final: 25 residues processed: 441 average time/residue: 1.3591 time to fit residues: 647.8147 Evaluate side-chains 454 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 420 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 54 ARG Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain L residue 33 GLU Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain Q residue 54 ARG Chi-restraints excluded: chain S residue 5 GLN Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain T residue 10 LEU Chi-restraints excluded: chain T residue 33 GLU Chi-restraints excluded: chain V residue 10 LEU Chi-restraints excluded: chain V residue 12 THR Chi-restraints excluded: chain V residue 49 LEU Chi-restraints excluded: chain Z residue 10 LEU Chi-restraints excluded: chain W residue 49 LEU Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 52 LEU Chi-restraints excluded: chain K residue 33 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.097575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.084799 restraints weight = 16894.147| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.30 r_work: 0.3228 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.6013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13272 Z= 0.378 Angle : 0.753 10.459 17808 Z= 0.388 Chirality : 0.047 0.133 1968 Planarity : 0.004 0.042 2280 Dihedral : 6.246 21.693 1704 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.14 % Allowed : 33.06 % Favored : 63.80 % 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: -3.99 (0.14), residues: 1584 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.11), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 46 PHE 0.015 0.002 PHE W 11 TYR 0.013 0.002 TYR V 14 ARG 0.003 0.001 ARG H 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8646.50 seconds wall clock time: 151 minutes 31.24 seconds (9091.24 seconds total)