Starting phenix.real_space_refine on Tue Feb 20 06:20:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fug_29458/02_2024/8fug_29458_trim_updated.pdb" } resolution = 2.7 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= 0.003 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: 6 Type Number sf(0) Gaussians S 23 5.16 5 C 8464 2.51 5 N 2415 2.21 5 O 2392 1.98 5 F 23 1.80 5 H 13317 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 26634 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "K" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "L" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "M" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "N" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "O" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "P" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "Q" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "R" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "S" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "T" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "U" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "V" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "W" Number of atoms: 1136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1136 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'Y9H': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.84, per 1000 atoms: 0.41 Number of scatterers: 26634 At special positions: 0 Unit cell: (115.926, 129.27, 75.894, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 23 16.00 F 23 9.00 O 2392 8.00 N 2415 7.00 C 8464 6.00 H 13317 1.00 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: 21.67 Conformation dependent library (CDL) restraints added in 2.7 seconds 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... No hydrogen bonds 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: 0.01 Time building geometry restraints manager: 22.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13294 1.03 - 1.22: 23 1.22 - 1.42: 5428 1.42 - 1.61: 8142 1.61 - 1.81: 23 Bond restraints: 26910 Sorted by residual: bond pdb=" C7 Y9H M 401 " pdb=" N1 Y9H M 401 " ideal model delta sigma weight residual 1.452 1.385 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C7 Y9H J 401 " pdb=" N1 Y9H J 401 " ideal model delta sigma weight residual 1.452 1.385 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C7 Y9H I 401 " pdb=" N1 Y9H I 401 " ideal model delta sigma weight residual 1.452 1.385 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C7 Y9H G 401 " pdb=" N1 Y9H G 401 " ideal model delta sigma weight residual 1.452 1.386 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" C7 Y9H W 401 " pdb=" N1 Y9H W 401 " ideal model delta sigma weight residual 1.452 1.386 0.066 2.00e-02 2.50e+03 1.10e+01 ... (remaining 26905 not shown) Histogram of bond angle deviations from ideal: 102.58 - 108.60: 9428 108.60 - 114.61: 26912 114.61 - 120.62: 5093 120.62 - 126.64: 7189 126.64 - 132.65: 253 Bond angle restraints: 48875 Sorted by residual: angle pdb=" C16 Y9H C 401 " pdb=" C7 Y9H C 401 " pdb=" N1 Y9H C 401 " ideal model delta sigma weight residual 139.26 121.69 17.57 3.00e+00 1.11e-01 3.43e+01 angle pdb=" C16 Y9H R 401 " pdb=" C7 Y9H R 401 " pdb=" N1 Y9H R 401 " ideal model delta sigma weight residual 139.26 121.69 17.57 3.00e+00 1.11e-01 3.43e+01 angle pdb=" C16 Y9H U 401 " pdb=" C7 Y9H U 401 " pdb=" N1 Y9H U 401 " ideal model delta sigma weight residual 139.26 121.70 17.56 3.00e+00 1.11e-01 3.43e+01 angle pdb=" C16 Y9H L 401 " pdb=" C7 Y9H L 401 " pdb=" N1 Y9H L 401 " ideal model delta sigma weight residual 139.26 121.70 17.56 3.00e+00 1.11e-01 3.42e+01 angle pdb=" C16 Y9H A 401 " pdb=" C7 Y9H A 401 " pdb=" N1 Y9H A 401 " ideal model delta sigma weight residual 139.26 121.71 17.55 3.00e+00 1.11e-01 3.42e+01 ... (remaining 48870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 11937 35.90 - 71.79: 230 71.79 - 107.69: 46 107.69 - 143.58: 92 143.58 - 179.48: 23 Dihedral angle restraints: 12328 sinusoidal: 7107 harmonic: 5221 Sorted by residual: dihedral pdb=" C17 Y9H V 401 " pdb=" C1 Y9H V 401 " pdb=" C2 Y9H V 401 " pdb=" C5 Y9H V 401 " ideal model delta sinusoidal sigma weight residual 243.77 64.29 179.48 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C17 Y9H J 401 " pdb=" C1 Y9H J 401 " pdb=" C2 Y9H J 401 " pdb=" C5 Y9H J 401 " ideal model delta sinusoidal sigma weight residual 243.77 64.31 179.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C17 Y9H S 401 " pdb=" C1 Y9H S 401 " pdb=" C2 Y9H S 401 " pdb=" C5 Y9H S 401 " ideal model delta sinusoidal sigma weight residual 243.77 64.32 179.45 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 12325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.057: 1978 1.057 - 2.115: 0 2.115 - 3.172: 0 3.172 - 4.229: 0 4.229 - 5.287: 23 Chirality restraints: 2001 Sorted by residual: chirality pdb=" C2 Y9H U 401 " pdb=" C1 Y9H U 401 " pdb=" C3 Y9H U 401 " pdb=" C5 Y9H U 401 " both_signs ideal model delta sigma weight residual False -2.69 2.60 -5.29 2.00e-01 2.50e+01 6.99e+02 chirality pdb=" C2 Y9H E 401 " pdb=" C1 Y9H E 401 " pdb=" C3 Y9H E 401 " pdb=" C5 Y9H E 401 " both_signs ideal model delta sigma weight residual False -2.69 2.60 -5.28 2.00e-01 2.50e+01 6.98e+02 chirality pdb=" C2 Y9H M 401 " pdb=" C1 Y9H M 401 " pdb=" C3 Y9H M 401 " pdb=" C5 Y9H M 401 " both_signs ideal model delta sigma weight residual False -2.69 2.60 -5.28 2.00e-01 2.50e+01 6.98e+02 ... (remaining 1998 not shown) Planarity restraints: 3818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS L 331 " 0.016 5.00e-02 4.00e+02 2.34e-02 8.80e-01 pdb=" N PRO L 332 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO L 332 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 332 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS I 331 " 0.015 5.00e-02 4.00e+02 2.34e-02 8.78e-01 pdb=" N PRO I 332 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO I 332 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO I 332 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS T 331 " 0.015 5.00e-02 4.00e+02 2.34e-02 8.76e-01 pdb=" N PRO T 332 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO T 332 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO T 332 " 0.013 5.00e-02 4.00e+02 ... (remaining 3815 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 11119 2.35 - 2.91: 63104 2.91 - 3.48: 66030 3.48 - 4.04: 104505 4.04 - 4.60: 143596 Nonbonded interactions: 388354 Sorted by model distance: nonbonded pdb=" OG SER U 320 " pdb="HD22 ASN U 368 " model vdw 1.790 1.850 nonbonded pdb=" OG SER E 320 " pdb="HD22 ASN E 368 " model vdw 1.790 1.850 nonbonded pdb=" OG SER W 320 " pdb="HD22 ASN W 368 " model vdw 1.791 1.850 nonbonded pdb=" OG SER M 320 " pdb="HD22 ASN M 368 " model vdw 1.791 1.850 nonbonded pdb=" OG SER A 320 " pdb="HD22 ASN A 368 " model vdw 1.791 1.850 ... (remaining 388349 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' } 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: 1.330 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: 0.400 Extract box with map and model: 6.230 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 73.670 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.290 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 13593 Z= 0.357 Angle : 1.333 17.567 18239 Z= 0.489 Chirality : 0.568 5.287 2001 Planarity : 0.003 0.023 2231 Dihedral : 23.659 179.477 5175 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % Rotamer: Outliers : 3.12 % Allowed : 3.12 % Favored : 93.75 % 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: -3.91 (0.16), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.98 (0.12), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS P 330 PHE 0.004 0.001 PHE S 346 TYR 0.004 0.001 TYR J 310 ARG 0.002 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 407 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 320 SER cc_start: 0.8214 (m) cc_final: 0.7824 (t) REVERT: D 321 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8079 (mtmt) REVERT: E 321 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7831 (mttp) REVERT: F 321 LYS cc_start: 0.8253 (mtpt) cc_final: 0.8017 (mttp) REVERT: G 320 SER cc_start: 0.8118 (m) cc_final: 0.7740 (t) REVERT: G 321 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7977 (mttt) REVERT: I 340 LYS cc_start: 0.8204 (ttmm) cc_final: 0.7956 (mtpt) REVERT: I 369 LYS cc_start: 0.8095 (ptpt) cc_final: 0.7870 (ptpt) REVERT: J 369 LYS cc_start: 0.8137 (ptpt) cc_final: 0.7669 (ptmt) REVERT: J 370 LYS cc_start: 0.7875 (tttm) cc_final: 0.7602 (ttpt) REVERT: J 377 THR cc_start: 0.8034 (m) cc_final: 0.7632 (p) REVERT: K 331 LYS cc_start: 0.8696 (mttp) cc_final: 0.8474 (mtpm) REVERT: K 369 LYS cc_start: 0.8037 (ptpt) cc_final: 0.7748 (ptpt) REVERT: L 331 LYS cc_start: 0.8697 (mttp) cc_final: 0.8435 (mtpm) REVERT: L 340 LYS cc_start: 0.8138 (ttmm) cc_final: 0.7702 (mttt) REVERT: L 350 VAL cc_start: 0.7867 (OUTLIER) cc_final: 0.7341 (p) REVERT: L 369 LYS cc_start: 0.8201 (ptpt) cc_final: 0.7800 (ptmt) REVERT: L 370 LYS cc_start: 0.7965 (tttm) cc_final: 0.7647 (ttpt) REVERT: L 378 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6628 (m-80) REVERT: M 319 THR cc_start: 0.7741 (m) cc_final: 0.7348 (p) REVERT: M 331 LYS cc_start: 0.8767 (mttp) cc_final: 0.8470 (mtmt) REVERT: M 340 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7859 (mtmm) REVERT: M 350 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7335 (p) REVERT: M 369 LYS cc_start: 0.8067 (ptpt) cc_final: 0.7716 (ptmt) REVERT: N 321 LYS cc_start: 0.7874 (mtpt) cc_final: 0.7643 (mttp) REVERT: N 331 LYS cc_start: 0.8777 (mttp) cc_final: 0.8439 (mtpm) REVERT: N 340 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8019 (mtmm) REVERT: N 369 LYS cc_start: 0.8231 (ptpt) cc_final: 0.7728 (ptmt) REVERT: N 377 THR cc_start: 0.7979 (m) cc_final: 0.7765 (p) REVERT: N 378 PHE cc_start: 0.6713 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: O 331 LYS cc_start: 0.8807 (mttp) cc_final: 0.8411 (mtpm) REVERT: O 340 LYS cc_start: 0.8303 (ttmm) cc_final: 0.8033 (mtmm) REVERT: P 370 LYS cc_start: 0.8116 (tttm) cc_final: 0.7884 (ttpt) REVERT: Q 317 LYS cc_start: 0.6377 (ptmt) cc_final: 0.6097 (ptmt) REVERT: Q 319 THR cc_start: 0.8051 (m) cc_final: 0.7671 (p) REVERT: Q 321 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7651 (tttp) REVERT: Q 373 THR cc_start: 0.8606 (m) cc_final: 0.8137 (p) REVERT: R 331 LYS cc_start: 0.8783 (mttp) cc_final: 0.8490 (mtmt) REVERT: R 378 PHE cc_start: 0.6593 (OUTLIER) cc_final: 0.5941 (m-80) REVERT: S 319 THR cc_start: 0.7742 (m) cc_final: 0.7510 (p) REVERT: S 331 LYS cc_start: 0.8681 (mttp) cc_final: 0.8415 (mtmt) REVERT: S 345 ASP cc_start: 0.7965 (m-30) cc_final: 0.7586 (t0) REVERT: S 373 THR cc_start: 0.8494 (m) cc_final: 0.8058 (p) REVERT: S 375 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7801 (ttpp) REVERT: S 378 PHE cc_start: 0.6479 (OUTLIER) cc_final: 0.6043 (m-80) REVERT: T 331 LYS cc_start: 0.8632 (mttp) cc_final: 0.8423 (mtmt) REVERT: U 319 THR cc_start: 0.7743 (m) cc_final: 0.7338 (p) REVERT: U 331 LYS cc_start: 0.8761 (mttp) cc_final: 0.8402 (mtpt) REVERT: U 373 THR cc_start: 0.8636 (m) cc_final: 0.8245 (p) REVERT: U 378 PHE cc_start: 0.6553 (OUTLIER) cc_final: 0.5817 (m-80) REVERT: V 331 LYS cc_start: 0.8760 (mttp) cc_final: 0.8450 (mtpt) REVERT: V 378 PHE cc_start: 0.6595 (OUTLIER) cc_final: 0.5677 (p90) REVERT: W 338 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7354 (tm-30) REVERT: W 373 THR cc_start: 0.8653 (m) cc_final: 0.8155 (p) outliers start: 46 outliers final: 22 residues processed: 440 average time/residue: 2.9041 time to fit residues: 1389.2539 Evaluate side-chains 328 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 298 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 378 PHE Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 378 PHE Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 135 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 359 ASN C 359 ASN D 359 ASN E 359 ASN F 359 ASN G 359 ASN H 359 ASN I 359 ASN J 359 ASN K 359 ASN L 359 ASN M 359 ASN N 359 ASN O 359 ASN P 359 ASN Q 359 ASN R 359 ASN S 359 ASN T 359 ASN U 359 ASN V 359 ASN W 359 ASN ** W 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13593 Z= 0.146 Angle : 0.669 7.736 18239 Z= 0.292 Chirality : 0.052 0.204 2001 Planarity : 0.003 0.027 2231 Dihedral : 11.088 59.987 1946 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 4.76 % Allowed : 15.08 % Favored : 80.16 % 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: -3.63 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS W 329 PHE 0.010 0.001 PHE B 378 TYR 0.010 0.002 TYR Q 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 317 time to evaluate : 2.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7903 (p) REVERT: B 320 SER cc_start: 0.8224 (m) cc_final: 0.7975 (t) REVERT: D 321 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8090 (mtmt) REVERT: E 321 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7822 (mttp) REVERT: E 370 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.7694 (ttpp) REVERT: F 321 LYS cc_start: 0.8251 (mtpt) cc_final: 0.7955 (mttp) REVERT: G 320 SER cc_start: 0.8358 (m) cc_final: 0.8089 (t) REVERT: G 321 LYS cc_start: 0.8186 (mtpt) cc_final: 0.7930 (mttt) REVERT: H 377 THR cc_start: 0.8045 (m) cc_final: 0.7620 (p) REVERT: I 320 SER cc_start: 0.8270 (m) cc_final: 0.8043 (t) REVERT: I 340 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7953 (mtpt) REVERT: I 369 LYS cc_start: 0.8186 (ptpt) cc_final: 0.7966 (ptpt) REVERT: J 369 LYS cc_start: 0.8260 (ptpt) cc_final: 0.7663 (ptmt) REVERT: J 370 LYS cc_start: 0.8228 (tttm) cc_final: 0.7772 (ttpt) REVERT: K 331 LYS cc_start: 0.8722 (mttp) cc_final: 0.8425 (mtpm) REVERT: K 369 LYS cc_start: 0.8171 (ptpt) cc_final: 0.7897 (ptpt) REVERT: L 331 LYS cc_start: 0.8789 (mttp) cc_final: 0.8587 (mtpm) REVERT: L 350 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7471 (p) REVERT: L 369 LYS cc_start: 0.8192 (ptpt) cc_final: 0.7774 (ptmt) REVERT: L 370 LYS cc_start: 0.8200 (tttm) cc_final: 0.7811 (ttpt) REVERT: L 378 PHE cc_start: 0.6987 (OUTLIER) cc_final: 0.6663 (m-80) REVERT: M 331 LYS cc_start: 0.8863 (mttp) cc_final: 0.8595 (mtpm) REVERT: M 336 GLN cc_start: 0.9245 (tt0) cc_final: 0.9019 (tt0) REVERT: M 340 LYS cc_start: 0.8268 (ttmm) cc_final: 0.7913 (mtmm) REVERT: M 350 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7546 (p) REVERT: M 369 LYS cc_start: 0.8206 (ptpt) cc_final: 0.7835 (ptmt) REVERT: M 370 LYS cc_start: 0.8136 (tttm) cc_final: 0.7858 (ttpt) REVERT: N 311 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8228 (tmtt) REVERT: N 321 LYS cc_start: 0.8026 (mtpt) cc_final: 0.7736 (mttp) REVERT: N 331 LYS cc_start: 0.8891 (mttp) cc_final: 0.8479 (mtpm) REVERT: N 340 LYS cc_start: 0.8366 (ttmm) cc_final: 0.8108 (mtmm) REVERT: N 369 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7913 (ptmt) REVERT: N 370 LYS cc_start: 0.8252 (tttm) cc_final: 0.7885 (ttpt) REVERT: N 378 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6093 (m-80) REVERT: O 317 LYS cc_start: 0.6597 (ptmt) cc_final: 0.6218 (pttt) REVERT: O 331 LYS cc_start: 0.8812 (mttp) cc_final: 0.8575 (mtpt) REVERT: O 340 LYS cc_start: 0.8275 (ttmm) cc_final: 0.8003 (mttt) REVERT: P 340 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7918 (mtmm) REVERT: P 370 LYS cc_start: 0.8281 (tttm) cc_final: 0.8039 (ttpt) REVERT: Q 317 LYS cc_start: 0.6551 (ptmt) cc_final: 0.6261 (ptmt) REVERT: Q 378 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.5994 (m-80) REVERT: R 331 LYS cc_start: 0.8863 (mttp) cc_final: 0.8617 (mtmt) REVERT: R 345 ASP cc_start: 0.8053 (m-30) cc_final: 0.7657 (t0) REVERT: R 378 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5917 (m-80) REVERT: S 319 THR cc_start: 0.7869 (m) cc_final: 0.7615 (p) REVERT: S 331 LYS cc_start: 0.8761 (mttp) cc_final: 0.8526 (mtmt) REVERT: S 338 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7636 (tm-30) REVERT: S 345 ASP cc_start: 0.8071 (m-30) cc_final: 0.7699 (t0) REVERT: S 375 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7838 (ttpp) REVERT: S 378 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.6142 (m-80) REVERT: T 345 ASP cc_start: 0.7963 (m-30) cc_final: 0.7639 (t0) REVERT: U 319 THR cc_start: 0.7966 (m) cc_final: 0.7576 (p) REVERT: U 345 ASP cc_start: 0.7767 (m-30) cc_final: 0.7509 (t0) REVERT: U 378 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5933 (m-80) REVERT: V 331 LYS cc_start: 0.8874 (mttp) cc_final: 0.8560 (mtpt) REVERT: V 345 ASP cc_start: 0.7720 (m-30) cc_final: 0.7351 (t0) REVERT: V 378 PHE cc_start: 0.6583 (OUTLIER) cc_final: 0.5639 (p90) REVERT: W 338 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7680 (tm-30) outliers start: 70 outliers final: 42 residues processed: 362 average time/residue: 2.7314 time to fit residues: 1079.7431 Evaluate side-chains 347 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 293 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 378 PHE Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain N residue 311 LYS Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 360 ILE Chi-restraints excluded: chain N residue 378 PHE Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 378 PHE Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain S residue 360 ILE Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 81 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13593 Z= 0.224 Angle : 0.697 6.365 18239 Z= 0.324 Chirality : 0.048 0.134 2001 Planarity : 0.003 0.025 2231 Dihedral : 8.065 59.523 1944 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.59 % Favored : 86.41 % Rotamer: Outliers : 5.84 % Allowed : 14.81 % Favored : 79.35 % 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: -3.45 (0.17), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.13), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 330 PHE 0.007 0.001 PHE U 346 TYR 0.018 0.003 TYR R 310 ARG 0.002 0.000 ARG N 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 330 time to evaluate : 2.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.7991 (p) REVERT: B 338 GLU cc_start: 0.8279 (tm-30) cc_final: 0.7888 (tm-30) REVERT: D 321 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8028 (mttt) REVERT: E 321 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7927 (mttp) REVERT: F 317 LYS cc_start: 0.7529 (ptmt) cc_final: 0.7286 (ptmt) REVERT: F 321 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7973 (mttp) REVERT: G 321 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7967 (mttt) REVERT: I 340 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7886 (mtpt) REVERT: J 369 LYS cc_start: 0.8430 (ptpt) cc_final: 0.7777 (ptmt) REVERT: K 331 LYS cc_start: 0.8875 (mttp) cc_final: 0.8650 (mtpm) REVERT: K 369 LYS cc_start: 0.8384 (ptpt) cc_final: 0.8016 (ptpt) REVERT: L 331 LYS cc_start: 0.8879 (mttp) cc_final: 0.8622 (mtpm) REVERT: L 350 VAL cc_start: 0.8151 (OUTLIER) cc_final: 0.7613 (p) REVERT: L 369 LYS cc_start: 0.8280 (ptpt) cc_final: 0.7850 (ptmt) REVERT: L 370 LYS cc_start: 0.8336 (tttm) cc_final: 0.8014 (ttpt) REVERT: M 331 LYS cc_start: 0.8881 (mttp) cc_final: 0.8635 (mtpm) REVERT: M 340 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7896 (mtmm) REVERT: M 350 VAL cc_start: 0.8208 (OUTLIER) cc_final: 0.7714 (p) REVERT: M 369 LYS cc_start: 0.8357 (ptpt) cc_final: 0.8012 (ptmt) REVERT: M 370 LYS cc_start: 0.8238 (tttm) cc_final: 0.8030 (ttpt) REVERT: N 311 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8261 (tmtt) REVERT: N 321 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7885 (mttp) REVERT: N 331 LYS cc_start: 0.8946 (mttp) cc_final: 0.8708 (mttt) REVERT: N 340 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8075 (mtmm) REVERT: N 369 LYS cc_start: 0.8433 (ptpt) cc_final: 0.7972 (ptmt) REVERT: N 370 LYS cc_start: 0.8413 (tttm) cc_final: 0.8059 (ttpt) REVERT: N 378 PHE cc_start: 0.6905 (OUTLIER) cc_final: 0.6093 (m-80) REVERT: O 317 LYS cc_start: 0.6760 (ptmt) cc_final: 0.6483 (ptmt) REVERT: O 331 LYS cc_start: 0.8829 (mttp) cc_final: 0.8549 (mtpm) REVERT: O 340 LYS cc_start: 0.8353 (ttmm) cc_final: 0.8019 (mttt) REVERT: O 378 PHE cc_start: 0.6927 (OUTLIER) cc_final: 0.5938 (m-80) REVERT: P 317 LYS cc_start: 0.6741 (ptmt) cc_final: 0.6405 (ptmt) REVERT: P 370 LYS cc_start: 0.8365 (tttm) cc_final: 0.8135 (ttpt) REVERT: Q 370 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8309 (ttmp) REVERT: Q 378 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6100 (m-80) REVERT: R 331 LYS cc_start: 0.8919 (mttp) cc_final: 0.8697 (mtmt) REVERT: R 338 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: R 345 ASP cc_start: 0.8180 (m-30) cc_final: 0.7818 (t0) REVERT: R 370 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8397 (ttmm) REVERT: R 372 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7617 (mm-30) REVERT: S 319 THR cc_start: 0.8176 (m) cc_final: 0.7909 (p) REVERT: S 331 LYS cc_start: 0.8836 (mttp) cc_final: 0.8612 (mtmt) REVERT: S 345 ASP cc_start: 0.8126 (m-30) cc_final: 0.7845 (t0) REVERT: S 375 LYS cc_start: 0.8165 (ttmm) cc_final: 0.7858 (ttpp) REVERT: S 378 PHE cc_start: 0.6659 (OUTLIER) cc_final: 0.6149 (m-80) REVERT: U 319 THR cc_start: 0.8217 (m) cc_final: 0.7776 (p) REVERT: U 378 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5971 (m-80) REVERT: V 331 LYS cc_start: 0.8938 (mttp) cc_final: 0.8554 (mtpt) REVERT: V 345 ASP cc_start: 0.7855 (m-30) cc_final: 0.7474 (t0) REVERT: V 378 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.5720 (p90) outliers start: 86 outliers final: 52 residues processed: 381 average time/residue: 2.8950 time to fit residues: 1209.9662 Evaluate side-chains 368 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 303 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 319 THR Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 341 SER Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 360 ILE Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain N residue 311 LYS Chi-restraints excluded: chain N residue 319 THR Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 372 GLU Chi-restraints excluded: chain N residue 378 PHE Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 THR Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain P residue 369 LYS Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 338 GLU Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13593 Z= 0.166 Angle : 0.630 5.312 18239 Z= 0.295 Chirality : 0.049 0.142 2001 Planarity : 0.003 0.027 2231 Dihedral : 7.965 58.101 1940 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 5.57 % Allowed : 16.64 % Favored : 77.79 % 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: -3.37 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 362 PHE 0.005 0.001 PHE U 346 TYR 0.011 0.002 TYR R 310 ARG 0.002 0.000 ARG G 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 313 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.7915 (p) REVERT: B 338 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7877 (tm-30) REVERT: D 321 LYS cc_start: 0.8455 (mtpt) cc_final: 0.8036 (mttt) REVERT: E 321 LYS cc_start: 0.8336 (mtpt) cc_final: 0.7906 (mttp) REVERT: F 317 LYS cc_start: 0.7588 (ptmt) cc_final: 0.7295 (ptmt) REVERT: F 321 LYS cc_start: 0.8295 (mtpt) cc_final: 0.7969 (mttp) REVERT: G 321 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7985 (mttt) REVERT: I 340 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7882 (mtpt) REVERT: J 369 LYS cc_start: 0.8363 (ptpt) cc_final: 0.7728 (ptmt) REVERT: K 331 LYS cc_start: 0.8871 (mttp) cc_final: 0.8656 (mtpm) REVERT: K 343 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7983 (mtpm) REVERT: K 369 LYS cc_start: 0.8283 (ptpt) cc_final: 0.7911 (ptpt) REVERT: K 378 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.6342 (m-80) REVERT: L 331 LYS cc_start: 0.8885 (mttp) cc_final: 0.8633 (mtpm) REVERT: L 350 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7546 (p) REVERT: L 369 LYS cc_start: 0.8225 (ptpt) cc_final: 0.7809 (ptmt) REVERT: L 370 LYS cc_start: 0.8288 (tttm) cc_final: 0.7990 (ttpt) REVERT: M 331 LYS cc_start: 0.8887 (mttp) cc_final: 0.8629 (mtpm) REVERT: M 340 LYS cc_start: 0.8349 (ttmm) cc_final: 0.7891 (mtmm) REVERT: M 350 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7656 (p) REVERT: M 369 LYS cc_start: 0.8294 (ptpt) cc_final: 0.7875 (ptmt) REVERT: M 378 PHE cc_start: 0.7013 (OUTLIER) cc_final: 0.6317 (m-80) REVERT: N 311 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8267 (tmtt) REVERT: N 321 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7892 (mttp) REVERT: N 331 LYS cc_start: 0.8930 (mttp) cc_final: 0.8702 (mttt) REVERT: N 340 LYS cc_start: 0.8397 (ttmm) cc_final: 0.7992 (mtmm) REVERT: N 369 LYS cc_start: 0.8413 (ptpt) cc_final: 0.7948 (ptmt) REVERT: N 370 LYS cc_start: 0.8358 (tttm) cc_final: 0.7971 (ttpt) REVERT: O 317 LYS cc_start: 0.6966 (ptmt) cc_final: 0.6653 (ptmt) REVERT: O 331 LYS cc_start: 0.8852 (mttp) cc_final: 0.8629 (mtpt) REVERT: O 340 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8035 (mttt) REVERT: O 378 PHE cc_start: 0.6925 (OUTLIER) cc_final: 0.5988 (m-80) REVERT: P 317 LYS cc_start: 0.6800 (ptmt) cc_final: 0.6585 (ptmt) REVERT: P 370 LYS cc_start: 0.8327 (tttm) cc_final: 0.8101 (ttpt) REVERT: P 378 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.5817 (m-10) REVERT: Q 370 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8251 (ttmp) REVERT: Q 378 PHE cc_start: 0.6708 (OUTLIER) cc_final: 0.6089 (m-80) REVERT: R 345 ASP cc_start: 0.8171 (m-30) cc_final: 0.7805 (t0) REVERT: R 370 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8426 (ttmm) REVERT: R 372 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7654 (mm-30) REVERT: S 317 LYS cc_start: 0.6971 (ptmt) cc_final: 0.6499 (ptmt) REVERT: S 319 THR cc_start: 0.8137 (m) cc_final: 0.7768 (p) REVERT: S 331 LYS cc_start: 0.8831 (mttp) cc_final: 0.8601 (mtmt) REVERT: S 345 ASP cc_start: 0.8095 (m-30) cc_final: 0.7842 (t0) REVERT: S 375 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7788 (ttpp) REVERT: S 378 PHE cc_start: 0.6485 (OUTLIER) cc_final: 0.6177 (m-80) REVERT: U 378 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.6083 (m-80) REVERT: V 331 LYS cc_start: 0.8959 (mttp) cc_final: 0.8576 (mtpt) REVERT: V 345 ASP cc_start: 0.7791 (m-30) cc_final: 0.7503 (t0) REVERT: V 378 PHE cc_start: 0.6486 (OUTLIER) cc_final: 0.5619 (p90) outliers start: 82 outliers final: 50 residues processed: 359 average time/residue: 2.8626 time to fit residues: 1118.8092 Evaluate side-chains 365 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 300 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 360 ILE Chi-restraints excluded: chain J residue 372 GLU Chi-restraints excluded: chain K residue 343 LYS Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain K residue 378 PHE Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 311 LYS Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain P residue 378 PHE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 370 LYS Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain S residue 370 LYS Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 88 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 0 optimal weight: 40.0000 chunk 79 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 368 ASN T 362 HIS T 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13593 Z= 0.198 Angle : 0.656 5.227 18239 Z= 0.309 Chirality : 0.048 0.149 2001 Planarity : 0.003 0.039 2231 Dihedral : 8.084 57.962 1938 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.92 % Favored : 87.08 % Rotamer: Outliers : 5.77 % Allowed : 17.05 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.006 0.001 PHE U 346 TYR 0.015 0.003 TYR V 310 ARG 0.004 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 316 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8321 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 338 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 369 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8315 (mttm) REVERT: C 317 LYS cc_start: 0.7483 (ptmt) cc_final: 0.7023 (ptpp) REVERT: D 321 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8039 (mttt) REVERT: E 321 LYS cc_start: 0.8328 (mtpt) cc_final: 0.7909 (mttp) REVERT: F 317 LYS cc_start: 0.7846 (ptmt) cc_final: 0.7613 (ptmt) REVERT: F 321 LYS cc_start: 0.8323 (mtpt) cc_final: 0.7973 (mttp) REVERT: G 321 LYS cc_start: 0.8279 (mtpt) cc_final: 0.7989 (mttt) REVERT: I 340 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7941 (mtpt) REVERT: I 343 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7915 (mppt) REVERT: J 369 LYS cc_start: 0.8471 (ptpt) cc_final: 0.7820 (ptmt) REVERT: K 331 LYS cc_start: 0.8860 (mttp) cc_final: 0.8573 (mtpm) REVERT: K 338 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: K 369 LYS cc_start: 0.8325 (ptpt) cc_final: 0.7953 (ptpt) REVERT: K 372 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7855 (mt-10) REVERT: L 331 LYS cc_start: 0.8890 (mttp) cc_final: 0.8681 (mtpm) REVERT: L 350 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7561 (p) REVERT: L 369 LYS cc_start: 0.8244 (ptpt) cc_final: 0.7763 (ptmt) REVERT: L 370 LYS cc_start: 0.8335 (tttm) cc_final: 0.8045 (ttpt) REVERT: M 331 LYS cc_start: 0.8897 (mttp) cc_final: 0.8640 (mtpm) REVERT: M 340 LYS cc_start: 0.8393 (ttmm) cc_final: 0.7954 (mtmm) REVERT: M 350 VAL cc_start: 0.8216 (OUTLIER) cc_final: 0.7724 (p) REVERT: M 369 LYS cc_start: 0.8404 (ptpt) cc_final: 0.7948 (ptmt) REVERT: M 378 PHE cc_start: 0.7012 (OUTLIER) cc_final: 0.6308 (m-80) REVERT: N 321 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7936 (mttp) REVERT: N 331 LYS cc_start: 0.8936 (mttp) cc_final: 0.8717 (mttt) REVERT: N 340 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8006 (mtmm) REVERT: N 369 LYS cc_start: 0.8516 (ptpt) cc_final: 0.7962 (ptmt) REVERT: N 370 LYS cc_start: 0.8368 (tttm) cc_final: 0.8008 (ttpt) REVERT: O 317 LYS cc_start: 0.7262 (ptmt) cc_final: 0.6895 (ptmt) REVERT: O 331 LYS cc_start: 0.8848 (mttp) cc_final: 0.8579 (mtpm) REVERT: O 340 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8056 (mttt) REVERT: O 378 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5954 (m-80) REVERT: P 370 LYS cc_start: 0.8371 (tttm) cc_final: 0.8139 (ttpt) REVERT: Q 370 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8260 (ttmp) REVERT: Q 378 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: R 317 LYS cc_start: 0.6891 (ptmt) cc_final: 0.6473 (ptmt) REVERT: R 338 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: R 345 ASP cc_start: 0.8161 (m-30) cc_final: 0.7846 (t0) REVERT: S 317 LYS cc_start: 0.7092 (ptmt) cc_final: 0.6655 (ptmt) REVERT: S 319 THR cc_start: 0.8205 (m) cc_final: 0.7870 (p) REVERT: S 331 LYS cc_start: 0.8833 (mttp) cc_final: 0.8603 (mtmt) REVERT: S 375 LYS cc_start: 0.8186 (ttmm) cc_final: 0.7857 (ttpp) REVERT: S 378 PHE cc_start: 0.6497 (OUTLIER) cc_final: 0.6064 (m-80) REVERT: U 378 PHE cc_start: 0.6653 (OUTLIER) cc_final: 0.6054 (m-80) REVERT: V 331 LYS cc_start: 0.8974 (mttp) cc_final: 0.8593 (mtpt) REVERT: V 345 ASP cc_start: 0.7809 (m-30) cc_final: 0.7513 (t0) REVERT: V 378 PHE cc_start: 0.6521 (OUTLIER) cc_final: 0.5693 (p90) outliers start: 85 outliers final: 55 residues processed: 365 average time/residue: 2.8481 time to fit residues: 1133.7267 Evaluate side-chains 370 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 301 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 352 SER Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 338 GLU Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 THR Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 338 GLU Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain S residue 370 LYS Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 319 THR Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 369 LYS Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Chi-restraints excluded: chain W residue 369 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 140 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 150 optimal weight: 0.0970 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 368 ASN ** S 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13593 Z= 0.124 Angle : 0.601 4.839 18239 Z= 0.280 Chirality : 0.049 0.126 2001 Planarity : 0.003 0.026 2231 Dihedral : 7.572 58.374 1938 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 4.76 % Allowed : 18.82 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS V 362 PHE 0.003 0.001 PHE K 378 TYR 0.009 0.002 TYR T 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 311 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.6457 (tm-30) REVERT: A 350 VAL cc_start: 0.8243 (OUTLIER) cc_final: 0.7880 (p) REVERT: C 317 LYS cc_start: 0.7573 (ptmt) cc_final: 0.7097 (ptpp) REVERT: D 321 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8061 (mttt) REVERT: E 321 LYS cc_start: 0.8344 (mtpt) cc_final: 0.7920 (mttp) REVERT: F 317 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7580 (ptmt) REVERT: F 321 LYS cc_start: 0.8320 (mtpt) cc_final: 0.7970 (mttp) REVERT: G 321 LYS cc_start: 0.8274 (mtpt) cc_final: 0.8002 (mttt) REVERT: I 340 LYS cc_start: 0.8255 (ttmm) cc_final: 0.7931 (mtpt) REVERT: I 343 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7902 (mppt) REVERT: J 369 LYS cc_start: 0.8419 (ptpt) cc_final: 0.7785 (ptmt) REVERT: K 369 LYS cc_start: 0.8212 (ptpt) cc_final: 0.7841 (ptpt) REVERT: K 372 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7858 (mt-10) REVERT: L 331 LYS cc_start: 0.8869 (mttp) cc_final: 0.8667 (mtpm) REVERT: L 350 VAL cc_start: 0.8048 (OUTLIER) cc_final: 0.7499 (p) REVERT: L 369 LYS cc_start: 0.8213 (ptpt) cc_final: 0.7768 (ptmt) REVERT: L 370 LYS cc_start: 0.8259 (tttm) cc_final: 0.7985 (ttpt) REVERT: L 375 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7697 (ttmp) REVERT: M 331 LYS cc_start: 0.8896 (mttp) cc_final: 0.8635 (mtpm) REVERT: M 336 GLN cc_start: 0.9267 (tt0) cc_final: 0.9031 (tt0) REVERT: M 340 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7913 (mtmm) REVERT: M 350 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7669 (p) REVERT: M 369 LYS cc_start: 0.8283 (ptpt) cc_final: 0.7858 (ptmt) REVERT: M 378 PHE cc_start: 0.7037 (OUTLIER) cc_final: 0.6279 (m-80) REVERT: N 311 LYS cc_start: 0.8211 (tttt) cc_final: 0.7850 (tmtt) REVERT: N 321 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7934 (mttp) REVERT: N 331 LYS cc_start: 0.8924 (mttp) cc_final: 0.8639 (mttt) REVERT: N 340 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8036 (mtmm) REVERT: N 369 LYS cc_start: 0.8451 (ptpt) cc_final: 0.7906 (ptmt) REVERT: N 370 LYS cc_start: 0.8307 (tttm) cc_final: 0.7972 (ttpt) REVERT: O 317 LYS cc_start: 0.7339 (ptmt) cc_final: 0.6982 (ptmt) REVERT: O 331 LYS cc_start: 0.8829 (mttp) cc_final: 0.8617 (mtpt) REVERT: O 340 LYS cc_start: 0.8374 (ttmm) cc_final: 0.8007 (mttt) REVERT: O 378 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.5940 (m-80) REVERT: P 370 LYS cc_start: 0.8309 (tttm) cc_final: 0.8042 (ttpt) REVERT: Q 370 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8194 (ttmp) REVERT: Q 378 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: R 317 LYS cc_start: 0.6923 (ptmt) cc_final: 0.6524 (ptmt) REVERT: R 345 ASP cc_start: 0.8152 (m-30) cc_final: 0.7796 (t0) REVERT: S 317 LYS cc_start: 0.7008 (ptmt) cc_final: 0.6593 (ptmt) REVERT: S 319 THR cc_start: 0.8092 (m) cc_final: 0.7748 (p) REVERT: S 331 LYS cc_start: 0.8811 (mttp) cc_final: 0.8585 (mtmt) REVERT: S 340 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8057 (ttmm) REVERT: S 375 LYS cc_start: 0.8166 (ttmm) cc_final: 0.7837 (ttpp) REVERT: S 378 PHE cc_start: 0.6445 (OUTLIER) cc_final: 0.6177 (m-80) REVERT: U 331 LYS cc_start: 0.8928 (mttp) cc_final: 0.8551 (mtmt) REVERT: U 343 LYS cc_start: 0.8261 (mptt) cc_final: 0.7979 (mtpm) REVERT: U 378 PHE cc_start: 0.6493 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: V 331 LYS cc_start: 0.8956 (mttp) cc_final: 0.8577 (mtpt) REVERT: V 345 ASP cc_start: 0.7758 (m-30) cc_final: 0.7487 (t0) REVERT: V 378 PHE cc_start: 0.6523 (OUTLIER) cc_final: 0.5533 (p90) outliers start: 70 outliers final: 47 residues processed: 354 average time/residue: 2.7350 time to fit residues: 1066.8236 Evaluate side-chains 357 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 298 time to evaluate : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain S residue 370 LYS Chi-restraints excluded: chain S residue 378 PHE Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 352 SER Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 352 SER Chi-restraints excluded: chain V residue 376 LEU Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 17 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13593 Z= 0.123 Angle : 0.582 4.868 18239 Z= 0.272 Chirality : 0.048 0.132 2001 Planarity : 0.003 0.030 2231 Dihedral : 7.374 58.581 1938 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % Rotamer: Outliers : 4.76 % Allowed : 18.95 % Favored : 76.29 % 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: -3.24 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS V 362 PHE 0.002 0.001 PHE R 346 TYR 0.009 0.002 TYR T 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 310 time to evaluate : 2.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8195 (OUTLIER) cc_final: 0.7834 (p) REVERT: C 317 LYS cc_start: 0.7571 (ptmt) cc_final: 0.7080 (ptpp) REVERT: D 321 LYS cc_start: 0.8492 (mtpt) cc_final: 0.7990 (mtmm) REVERT: E 321 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7914 (mttp) REVERT: E 373 THR cc_start: 0.8371 (m) cc_final: 0.7878 (p) REVERT: F 317 LYS cc_start: 0.7857 (ptmt) cc_final: 0.7626 (ptmt) REVERT: F 321 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7989 (mttp) REVERT: G 321 LYS cc_start: 0.8268 (mtpt) cc_final: 0.7992 (mttt) REVERT: G 378 PHE cc_start: 0.6748 (OUTLIER) cc_final: 0.6116 (m-80) REVERT: H 352 SER cc_start: 0.8442 (OUTLIER) cc_final: 0.8148 (p) REVERT: I 340 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7938 (mtpt) REVERT: I 343 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7908 (mppt) REVERT: I 378 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6272 (m-80) REVERT: J 369 LYS cc_start: 0.8444 (ptpt) cc_final: 0.7806 (ptmt) REVERT: K 372 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7839 (mt-10) REVERT: L 350 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7521 (p) REVERT: L 369 LYS cc_start: 0.8215 (ptpt) cc_final: 0.7781 (ptmt) REVERT: L 370 LYS cc_start: 0.8275 (tttm) cc_final: 0.7998 (ttpt) REVERT: L 375 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7686 (ttmp) REVERT: L 378 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6446 (m-80) REVERT: M 331 LYS cc_start: 0.8900 (mttp) cc_final: 0.8628 (mtpm) REVERT: M 336 GLN cc_start: 0.9266 (tt0) cc_final: 0.9041 (tt0) REVERT: M 340 LYS cc_start: 0.8412 (ttmm) cc_final: 0.7973 (mtmm) REVERT: M 350 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7682 (p) REVERT: M 369 LYS cc_start: 0.8266 (ptpt) cc_final: 0.7858 (ptmt) REVERT: M 378 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6248 (m-80) REVERT: N 321 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7942 (mttp) REVERT: N 331 LYS cc_start: 0.8935 (mttp) cc_final: 0.8594 (mtpm) REVERT: N 340 LYS cc_start: 0.8419 (ttmm) cc_final: 0.8058 (mtmm) REVERT: N 369 LYS cc_start: 0.8457 (ptpt) cc_final: 0.7907 (ptmt) REVERT: N 370 LYS cc_start: 0.8313 (tttm) cc_final: 0.7989 (ttpt) REVERT: O 321 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7709 (mtmp) REVERT: O 331 LYS cc_start: 0.8854 (mttp) cc_final: 0.8635 (mtpt) REVERT: O 340 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8021 (mttt) REVERT: O 378 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.5915 (m-80) REVERT: P 370 LYS cc_start: 0.8298 (tttm) cc_final: 0.8083 (ttpt) REVERT: Q 378 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6136 (m-80) REVERT: R 317 LYS cc_start: 0.6923 (ptmt) cc_final: 0.6545 (ptmt) REVERT: R 345 ASP cc_start: 0.8148 (m-30) cc_final: 0.7775 (t0) REVERT: S 317 LYS cc_start: 0.7014 (ptmt) cc_final: 0.6598 (ptmt) REVERT: S 319 THR cc_start: 0.8051 (m) cc_final: 0.7746 (p) REVERT: S 331 LYS cc_start: 0.8809 (mttp) cc_final: 0.8584 (mtmt) REVERT: S 340 LYS cc_start: 0.8388 (ttmm) cc_final: 0.8050 (ttmm) REVERT: S 375 LYS cc_start: 0.8176 (ttmm) cc_final: 0.7839 (ttpp) REVERT: U 331 LYS cc_start: 0.8950 (mttp) cc_final: 0.8522 (mtpt) REVERT: U 343 LYS cc_start: 0.8268 (mptt) cc_final: 0.7977 (mtpm) REVERT: U 378 PHE cc_start: 0.6550 (OUTLIER) cc_final: 0.5974 (m-80) REVERT: V 331 LYS cc_start: 0.8962 (mttp) cc_final: 0.8583 (mtpt) REVERT: V 345 ASP cc_start: 0.7761 (m-30) cc_final: 0.7504 (t0) REVERT: V 378 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.5515 (p90) REVERT: W 321 LYS cc_start: 0.8036 (tttm) cc_final: 0.7816 (tmtt) outliers start: 70 outliers final: 48 residues processed: 354 average time/residue: 2.7301 time to fit residues: 1057.8193 Evaluate side-chains 364 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 302 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 378 PHE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 378 PHE Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 360 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain Q residue 378 PHE Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 376 LEU Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 92 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 135 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13593 Z= 0.128 Angle : 0.584 5.389 18239 Z= 0.273 Chirality : 0.048 0.129 2001 Planarity : 0.003 0.029 2231 Dihedral : 7.216 58.402 1936 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.39 % Favored : 88.61 % Rotamer: Outliers : 4.76 % Allowed : 19.36 % Favored : 75.88 % 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: -3.23 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS V 362 PHE 0.003 0.001 PHE Q 378 TYR 0.009 0.002 TYR T 310 ARG 0.002 0.000 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 308 time to evaluate : 2.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7782 (p) REVERT: A 370 LYS cc_start: 0.7677 (tttm) cc_final: 0.7243 (tttm) REVERT: C 317 LYS cc_start: 0.7584 (ptmt) cc_final: 0.7085 (ptpp) REVERT: D 321 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8113 (mttt) REVERT: E 321 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7913 (mttp) REVERT: E 373 THR cc_start: 0.8378 (m) cc_final: 0.7873 (p) REVERT: F 317 LYS cc_start: 0.7864 (ptmt) cc_final: 0.7623 (ptmt) REVERT: F 321 LYS cc_start: 0.8324 (mtpt) cc_final: 0.8010 (mttp) REVERT: G 321 LYS cc_start: 0.8266 (mtpt) cc_final: 0.7988 (mttt) REVERT: H 352 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.8152 (p) REVERT: H 378 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.5963 (m-80) REVERT: I 340 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7954 (mtpt) REVERT: I 343 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7905 (mppt) REVERT: I 378 PHE cc_start: 0.7030 (OUTLIER) cc_final: 0.6282 (m-80) REVERT: J 369 LYS cc_start: 0.8443 (ptpt) cc_final: 0.7814 (ptmt) REVERT: K 372 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7830 (mt-10) REVERT: L 350 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7520 (p) REVERT: L 369 LYS cc_start: 0.8182 (ptpt) cc_final: 0.7783 (ptmt) REVERT: L 370 LYS cc_start: 0.8276 (tttm) cc_final: 0.8000 (ttpt) REVERT: L 375 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7660 (ttmp) REVERT: L 378 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6452 (m-80) REVERT: M 331 LYS cc_start: 0.8890 (mttp) cc_final: 0.8620 (mtpm) REVERT: M 336 GLN cc_start: 0.9284 (tt0) cc_final: 0.9060 (tt0) REVERT: M 340 LYS cc_start: 0.8418 (ttmm) cc_final: 0.7978 (mtmm) REVERT: M 350 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7682 (p) REVERT: M 369 LYS cc_start: 0.8322 (ptpt) cc_final: 0.7897 (ptmt) REVERT: M 378 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6198 (m-80) REVERT: N 321 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7930 (mttp) REVERT: N 331 LYS cc_start: 0.8927 (mttp) cc_final: 0.8642 (mttt) REVERT: N 340 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8046 (mtmm) REVERT: N 369 LYS cc_start: 0.8435 (ptpt) cc_final: 0.7896 (ptmt) REVERT: N 370 LYS cc_start: 0.8302 (tttm) cc_final: 0.7992 (ttpt) REVERT: O 331 LYS cc_start: 0.8854 (mttp) cc_final: 0.8637 (mtpt) REVERT: O 340 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8015 (mttt) REVERT: O 378 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.5891 (m-80) REVERT: P 370 LYS cc_start: 0.8300 (tttm) cc_final: 0.8087 (ttpt) REVERT: R 317 LYS cc_start: 0.6918 (ptmt) cc_final: 0.6541 (ptmt) REVERT: R 340 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7984 (mtmp) REVERT: R 345 ASP cc_start: 0.8145 (m-30) cc_final: 0.7784 (t0) REVERT: S 317 LYS cc_start: 0.7129 (ptmt) cc_final: 0.6718 (ptmt) REVERT: S 319 THR cc_start: 0.8088 (m) cc_final: 0.7779 (p) REVERT: S 331 LYS cc_start: 0.8808 (mttp) cc_final: 0.8578 (mtmt) REVERT: S 340 LYS cc_start: 0.8394 (ttmm) cc_final: 0.8057 (ttmm) REVERT: S 375 LYS cc_start: 0.8180 (ttmm) cc_final: 0.7836 (ttpp) REVERT: U 331 LYS cc_start: 0.8936 (mttp) cc_final: 0.8527 (mtmt) REVERT: U 378 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.5917 (m-80) REVERT: V 331 LYS cc_start: 0.8963 (mttp) cc_final: 0.8586 (mtpt) REVERT: V 345 ASP cc_start: 0.7767 (m-30) cc_final: 0.7497 (t0) REVERT: V 378 PHE cc_start: 0.6538 (OUTLIER) cc_final: 0.5591 (p90) REVERT: W 321 LYS cc_start: 0.8037 (tttm) cc_final: 0.7813 (tmtt) outliers start: 70 outliers final: 50 residues processed: 353 average time/residue: 2.6043 time to fit residues: 1009.1439 Evaluate side-chains 363 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 300 time to evaluate : 2.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 360 ILE Chi-restraints excluded: chain G residue 378 PHE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 360 ILE Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 338 GLU Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 378 PHE Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 360 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 THR Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain P residue 360 ILE Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 352 SER Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 376 LEU Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 144 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 130 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 152 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13593 Z= 0.112 Angle : 0.574 5.754 18239 Z= 0.268 Chirality : 0.048 0.128 2001 Planarity : 0.003 0.030 2231 Dihedral : 6.971 58.239 1936 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 4.35 % Allowed : 19.90 % Favored : 75.75 % 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: -3.22 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS V 362 PHE 0.003 0.001 PHE Q 378 TYR 0.008 0.002 TYR T 310 ARG 0.002 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 309 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8108 (OUTLIER) cc_final: 0.7757 (p) REVERT: C 317 LYS cc_start: 0.7570 (ptmt) cc_final: 0.7080 (ptpp) REVERT: D 321 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8112 (mttt) REVERT: E 321 LYS cc_start: 0.8331 (mtpt) cc_final: 0.7903 (mttp) REVERT: E 373 THR cc_start: 0.8370 (m) cc_final: 0.7862 (p) REVERT: F 317 LYS cc_start: 0.7849 (ptmt) cc_final: 0.7623 (ptmt) REVERT: F 321 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8026 (mttp) REVERT: G 321 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7976 (mttt) REVERT: G 378 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: H 352 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8153 (p) REVERT: H 378 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5964 (m-80) REVERT: I 340 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7963 (mtpt) REVERT: I 343 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7933 (mppt) REVERT: I 378 PHE cc_start: 0.6954 (OUTLIER) cc_final: 0.6226 (m-80) REVERT: J 369 LYS cc_start: 0.8433 (ptpt) cc_final: 0.7814 (ptmt) REVERT: J 370 LYS cc_start: 0.8385 (tttm) cc_final: 0.7908 (ttpt) REVERT: K 372 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7798 (mt-10) REVERT: L 350 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7503 (p) REVERT: L 369 LYS cc_start: 0.8179 (ptpt) cc_final: 0.7782 (ptmt) REVERT: L 370 LYS cc_start: 0.8259 (tttm) cc_final: 0.7989 (ttpt) REVERT: L 375 LYS cc_start: 0.7956 (ttmt) cc_final: 0.7669 (ttmp) REVERT: M 331 LYS cc_start: 0.8873 (mttp) cc_final: 0.8608 (mtpm) REVERT: M 336 GLN cc_start: 0.9268 (tt0) cc_final: 0.9053 (tt0) REVERT: M 340 LYS cc_start: 0.8420 (ttmm) cc_final: 0.7980 (mtmm) REVERT: M 350 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7686 (p) REVERT: M 369 LYS cc_start: 0.8306 (ptpt) cc_final: 0.7884 (ptmt) REVERT: M 378 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6196 (m-80) REVERT: N 321 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7932 (mttp) REVERT: N 331 LYS cc_start: 0.8918 (mttp) cc_final: 0.8585 (mtpm) REVERT: N 340 LYS cc_start: 0.8389 (ttmm) cc_final: 0.8041 (mtmm) REVERT: N 369 LYS cc_start: 0.8430 (ptpt) cc_final: 0.7910 (ptmt) REVERT: N 370 LYS cc_start: 0.8275 (tttm) cc_final: 0.7975 (ttpt) REVERT: O 321 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7768 (mtmp) REVERT: O 331 LYS cc_start: 0.8845 (mttp) cc_final: 0.8637 (mtpt) REVERT: O 340 LYS cc_start: 0.8387 (ttmm) cc_final: 0.7995 (mttt) REVERT: O 378 PHE cc_start: 0.6759 (OUTLIER) cc_final: 0.5874 (m-80) REVERT: R 317 LYS cc_start: 0.6926 (ptmt) cc_final: 0.6555 (ptmt) REVERT: R 345 ASP cc_start: 0.8138 (m-30) cc_final: 0.7773 (t0) REVERT: S 317 LYS cc_start: 0.7225 (ptmt) cc_final: 0.6803 (ptmt) REVERT: S 319 THR cc_start: 0.8074 (m) cc_final: 0.7784 (p) REVERT: S 331 LYS cc_start: 0.8799 (mttp) cc_final: 0.8564 (mtmt) REVERT: S 340 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8073 (ttmm) REVERT: S 375 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7818 (ttpp) REVERT: U 331 LYS cc_start: 0.8934 (mttp) cc_final: 0.8522 (mtmt) REVERT: U 378 PHE cc_start: 0.6427 (OUTLIER) cc_final: 0.5902 (m-80) REVERT: V 331 LYS cc_start: 0.8952 (mttp) cc_final: 0.8580 (mtpt) REVERT: V 345 ASP cc_start: 0.7769 (m-30) cc_final: 0.7502 (t0) REVERT: V 378 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.5576 (p90) REVERT: W 321 LYS cc_start: 0.8064 (tttm) cc_final: 0.7828 (tmtt) outliers start: 64 outliers final: 48 residues processed: 348 average time/residue: 2.7315 time to fit residues: 1046.7243 Evaluate side-chains 364 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 303 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 378 PHE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain H residue 378 PHE Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 378 PHE Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 360 ILE Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 377 THR Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 352 SER Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 360 ILE Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 376 LEU Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 72 optimal weight: 0.5980 chunk 106 optimal weight: 0.0570 chunk 160 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 13593 Z= 0.198 Angle : 0.638 6.066 18239 Z= 0.301 Chirality : 0.048 0.130 2001 Planarity : 0.003 0.029 2231 Dihedral : 7.746 57.799 1936 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 4.08 % Allowed : 20.31 % Favored : 75.61 % 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: -3.22 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 330 PHE 0.005 0.001 PHE S 346 TYR 0.015 0.003 TYR M 310 ARG 0.002 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3266 Ramachandran restraints generated. 1633 Oldfield, 0 Emsley, 1633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 320 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8223 (OUTLIER) cc_final: 0.7867 (p) REVERT: C 317 LYS cc_start: 0.7605 (ptmt) cc_final: 0.7115 (ptpp) REVERT: D 321 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8004 (mtmm) REVERT: E 321 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7942 (mttp) REVERT: E 373 THR cc_start: 0.8441 (m) cc_final: 0.7929 (p) REVERT: F 321 LYS cc_start: 0.8321 (mtpt) cc_final: 0.8013 (mttp) REVERT: G 321 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8024 (mttt) REVERT: G 378 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: I 340 LYS cc_start: 0.8314 (ttmm) cc_final: 0.7963 (mtpt) REVERT: I 343 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7916 (mppt) REVERT: I 378 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: J 369 LYS cc_start: 0.8499 (ptpt) cc_final: 0.7869 (ptmt) REVERT: K 372 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7785 (mt-10) REVERT: L 350 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7594 (p) REVERT: L 369 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7811 (ptmt) REVERT: L 370 LYS cc_start: 0.8312 (tttm) cc_final: 0.8043 (ttpt) REVERT: L 375 LYS cc_start: 0.7968 (ttmt) cc_final: 0.7686 (ttmp) REVERT: L 378 PHE cc_start: 0.6977 (OUTLIER) cc_final: 0.6435 (m-80) REVERT: M 331 LYS cc_start: 0.8893 (mttp) cc_final: 0.8629 (mtpm) REVERT: M 336 GLN cc_start: 0.9310 (tt0) cc_final: 0.9065 (tt0) REVERT: M 340 LYS cc_start: 0.8451 (ttmm) cc_final: 0.7991 (mtmm) REVERT: M 350 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.7748 (p) REVERT: M 369 LYS cc_start: 0.8401 (ptpt) cc_final: 0.8065 (ptmt) REVERT: M 378 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6211 (m-80) REVERT: N 321 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7949 (mttp) REVERT: N 331 LYS cc_start: 0.8937 (mttp) cc_final: 0.8650 (mttt) REVERT: N 340 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8050 (mtmm) REVERT: N 369 LYS cc_start: 0.8525 (ptpt) cc_final: 0.7933 (ptmt) REVERT: N 370 LYS cc_start: 0.8340 (tttm) cc_final: 0.8031 (ttpt) REVERT: O 321 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7843 (mttp) REVERT: O 331 LYS cc_start: 0.8851 (mttp) cc_final: 0.8620 (mtpt) REVERT: O 340 LYS cc_start: 0.8433 (ttmm) cc_final: 0.8009 (mttt) REVERT: O 378 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.5877 (m-80) REVERT: R 317 LYS cc_start: 0.7165 (ptmt) cc_final: 0.6861 (ptmt) REVERT: R 340 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8027 (mtmp) REVERT: R 345 ASP cc_start: 0.8141 (m-30) cc_final: 0.7865 (t0) REVERT: S 317 LYS cc_start: 0.7274 (ptmt) cc_final: 0.6838 (ptmt) REVERT: S 319 THR cc_start: 0.8155 (m) cc_final: 0.7863 (p) REVERT: S 331 LYS cc_start: 0.8826 (mttp) cc_final: 0.8596 (mtmt) REVERT: S 340 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8079 (ttmm) REVERT: S 375 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7850 (ttpp) REVERT: U 331 LYS cc_start: 0.8963 (mttp) cc_final: 0.8553 (mtmt) REVERT: U 378 PHE cc_start: 0.6437 (OUTLIER) cc_final: 0.5906 (m-80) REVERT: V 331 LYS cc_start: 0.8953 (mttp) cc_final: 0.8575 (mtpt) REVERT: V 345 ASP cc_start: 0.7767 (m-30) cc_final: 0.7537 (t0) REVERT: V 378 PHE cc_start: 0.6604 (OUTLIER) cc_final: 0.5627 (p90) REVERT: W 321 LYS cc_start: 0.8069 (tttm) cc_final: 0.7824 (tmtt) outliers start: 60 outliers final: 45 residues processed: 359 average time/residue: 2.5357 time to fit residues: 1000.8426 Evaluate side-chains 366 residues out of total 1472 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 308 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 352 SER Chi-restraints excluded: chain G residue 378 PHE Chi-restraints excluded: chain H residue 338 GLU Chi-restraints excluded: chain H residue 350 VAL Chi-restraints excluded: chain H residue 352 SER Chi-restraints excluded: chain I residue 343 LYS Chi-restraints excluded: chain I residue 350 VAL Chi-restraints excluded: chain I residue 378 PHE Chi-restraints excluded: chain J residue 350 VAL Chi-restraints excluded: chain J residue 352 SER Chi-restraints excluded: chain K residue 350 VAL Chi-restraints excluded: chain L residue 350 VAL Chi-restraints excluded: chain L residue 378 PHE Chi-restraints excluded: chain M residue 350 VAL Chi-restraints excluded: chain M residue 378 PHE Chi-restraints excluded: chain N residue 350 VAL Chi-restraints excluded: chain N residue 352 SER Chi-restraints excluded: chain N residue 360 ILE Chi-restraints excluded: chain O residue 321 LYS Chi-restraints excluded: chain O residue 350 VAL Chi-restraints excluded: chain O residue 360 ILE Chi-restraints excluded: chain O residue 369 LYS Chi-restraints excluded: chain O residue 378 PHE Chi-restraints excluded: chain P residue 338 GLU Chi-restraints excluded: chain P residue 350 VAL Chi-restraints excluded: chain P residue 352 SER Chi-restraints excluded: chain Q residue 338 GLU Chi-restraints excluded: chain Q residue 350 VAL Chi-restraints excluded: chain Q residue 370 LYS Chi-restraints excluded: chain R residue 340 LYS Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain S residue 350 VAL Chi-restraints excluded: chain S residue 352 SER Chi-restraints excluded: chain T residue 350 VAL Chi-restraints excluded: chain T residue 360 ILE Chi-restraints excluded: chain U residue 350 VAL Chi-restraints excluded: chain U residue 378 PHE Chi-restraints excluded: chain V residue 350 VAL Chi-restraints excluded: chain V residue 376 LEU Chi-restraints excluded: chain V residue 378 PHE Chi-restraints excluded: chain W residue 350 VAL Chi-restraints excluded: chain W residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 117 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 368 ASN ** 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 = 0.4470 r_free = 0.4470 target = 0.199725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.154767 restraints weight = 42251.378| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.18 r_work: 0.3892 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3777 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13593 Z= 0.135 Angle : 0.606 6.472 18239 Z= 0.284 Chirality : 0.048 0.124 2001 Planarity : 0.003 0.030 2231 Dihedral : 7.438 57.864 1936 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 4.14 % Allowed : 20.65 % Favored : 75.20 % 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: -3.24 (0.18), residues: 1633 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS W 362 PHE 0.003 0.001 PHE F 378 TYR 0.011 0.002 TYR V 310 ARG 0.003 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15533.95 seconds wall clock time: 274 minutes 17.46 seconds (16457.46 seconds total)