Starting phenix.real_space_refine on Sun Mar 10 19:07:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/03_2024/7yat_33719.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/03_2024/7yat_33719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/03_2024/7yat_33719.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/03_2024/7yat_33719.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/03_2024/7yat_33719.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yat_33719/03_2024/7yat_33719.pdb" } resolution = 2.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 2568 2.51 5 N 744 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4129 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "B" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "C" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "D" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "E" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "F" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "G" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "H" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "I" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "J" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "K" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "L" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "M" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "N" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "O" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "P" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "Q" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "R" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "S" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "T" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "U" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "V" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "X" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "Y" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 171 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 1, 'TRANS': 23} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.52, per 1000 atoms: 0.61 Number of scatterers: 4129 At special positions: 0 Unit cell: (77.19, 77.19, 47.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 721 8.00 N 744 7.00 C 2568 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 897.9 milliseconds 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 43.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 121 through 122 removed outlier: 6.521A pdb=" N VAL B 121 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 121 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 125 through 130 removed outlier: 6.629A pdb=" N GLY B 126 " --> pdb=" O GLY E 127 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N MET E 129 " --> pdb=" O GLY B 126 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR B 128 " --> pdb=" O MET E 129 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU B 125 " --> pdb=" O GLY C 126 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N TYR C 128 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY B 127 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU C 130 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET B 129 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU C 125 " --> pdb=" O GLY D 126 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR D 128 " --> pdb=" O LEU C 125 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLY C 127 " --> pdb=" O TYR D 128 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU D 130 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N MET C 129 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU A 125 " --> pdb=" O GLY F 126 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N TYR F 128 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY A 127 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU F 130 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N MET A 129 " --> pdb=" O LEU F 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 133 through 135 removed outlier: 6.347A pdb=" N ALA B 133 " --> pdb=" O MET E 134 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ALA A 133 " --> pdb=" O MET D 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 138 through 141 removed outlier: 6.366A pdb=" N MET B 138 " --> pdb=" O MET E 139 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE E 141 " --> pdb=" O MET B 138 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N HIS B 140 " --> pdb=" O PHE E 141 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET A 138 " --> pdb=" O MET D 139 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N PHE D 141 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N HIS A 140 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 121 through 122 removed outlier: 6.690A pdb=" N VAL G 121 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL H 121 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL I 121 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL J 121 " --> pdb=" O VAL K 122 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'K' and resid 125 through 130 removed outlier: 6.612A pdb=" N GLY I 126 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N MET J 129 " --> pdb=" O GLY I 126 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR I 128 " --> pdb=" O MET J 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 133 through 135 removed outlier: 6.402A pdb=" N ALA J 133 " --> pdb=" O MET K 134 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA I 133 " --> pdb=" O MET J 134 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA H 133 " --> pdb=" O MET I 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 138 through 141 removed outlier: 6.275A pdb=" N MET J 138 " --> pdb=" O MET K 139 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N PHE K 141 " --> pdb=" O MET J 138 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS J 140 " --> pdb=" O PHE K 141 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N MET I 138 " --> pdb=" O MET J 139 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE J 141 " --> pdb=" O MET I 138 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS I 140 " --> pdb=" O PHE J 141 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET H 138 " --> pdb=" O MET I 139 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE I 141 " --> pdb=" O MET H 138 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N HIS H 140 " --> pdb=" O PHE I 141 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N MET G 138 " --> pdb=" O MET H 139 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N PHE H 141 " --> pdb=" O MET G 138 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N HIS G 140 " --> pdb=" O PHE H 141 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 121 through 122 removed outlier: 6.698A pdb=" N VAL P 121 " --> pdb=" O VAL Q 122 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL O 121 " --> pdb=" O VAL P 122 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL N 121 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL M 121 " --> pdb=" O VAL N 122 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 125 through 130 removed outlier: 6.608A pdb=" N GLY M 126 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N MET N 129 " --> pdb=" O GLY M 126 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N TYR M 128 " --> pdb=" O MET N 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 133 through 135 removed outlier: 6.393A pdb=" N ALA P 133 " --> pdb=" O MET Q 134 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA O 133 " --> pdb=" O MET P 134 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ALA N 133 " --> pdb=" O MET O 134 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA M 133 " --> pdb=" O MET N 134 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 138 through 141 removed outlier: 6.237A pdb=" N MET P 138 " --> pdb=" O MET Q 139 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE Q 141 " --> pdb=" O MET P 138 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS P 140 " --> pdb=" O PHE Q 141 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N MET O 138 " --> pdb=" O MET P 139 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE P 141 " --> pdb=" O MET O 138 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS O 140 " --> pdb=" O PHE P 141 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET N 138 " --> pdb=" O MET O 139 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N PHE O 141 " --> pdb=" O MET N 138 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS N 140 " --> pdb=" O PHE O 141 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N MET M 138 " --> pdb=" O MET N 139 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE N 141 " --> pdb=" O MET M 138 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N HIS M 140 " --> pdb=" O PHE N 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'X' and resid 121 through 122 removed outlier: 6.713A pdb=" N VAL V 121 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL U 121 " --> pdb=" O VAL V 122 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL T 121 " --> pdb=" O VAL U 122 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL S 121 " --> pdb=" O VAL T 122 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'X' and resid 125 through 130 removed outlier: 6.550A pdb=" N GLY U 126 " --> pdb=" O GLY V 127 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N MET V 129 " --> pdb=" O GLY U 126 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR U 128 " --> pdb=" O MET V 129 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY S 126 " --> pdb=" O GLY T 127 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N MET T 129 " --> pdb=" O GLY S 126 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N TYR S 128 " --> pdb=" O MET T 129 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU S 125 " --> pdb=" O GLY Y 126 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N TYR Y 128 " --> pdb=" O LEU S 125 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY S 127 " --> pdb=" O TYR Y 128 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU Y 130 " --> pdb=" O GLY S 127 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N MET S 129 " --> pdb=" O LEU Y 130 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 133 through 135 removed outlier: 6.426A pdb=" N ALA V 133 " --> pdb=" O MET X 134 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA U 133 " --> pdb=" O MET V 134 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA T 133 " --> pdb=" O MET U 134 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA S 133 " --> pdb=" O MET T 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'X' and resid 138 through 141 removed outlier: 6.209A pdb=" N MET V 138 " --> pdb=" O MET X 139 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE X 141 " --> pdb=" O MET V 138 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N HIS V 140 " --> pdb=" O PHE X 141 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N MET U 138 " --> pdb=" O MET V 139 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N PHE V 141 " --> pdb=" O MET U 138 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N HIS U 140 " --> pdb=" O PHE V 141 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N MET T 138 " --> pdb=" O MET U 139 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N PHE U 141 " --> pdb=" O MET T 138 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS T 140 " --> pdb=" O PHE U 141 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N MET S 138 " --> pdb=" O MET T 139 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N PHE T 141 " --> pdb=" O MET S 138 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS S 140 " --> pdb=" O PHE T 141 " (cutoff:3.500A) 92 hydrogen bonds defined for protein. 276 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1312 1.33 - 1.45: 663 1.45 - 1.57: 2009 1.57 - 1.69: 0 1.69 - 1.80: 192 Bond restraints: 4176 Sorted by residual: bond pdb=" CB MET Y 129 " pdb=" CG MET Y 129 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.04e+00 bond pdb=" CB MET M 129 " pdb=" CG MET M 129 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" CB MET K 129 " pdb=" CG MET K 129 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CB MET H 129 " pdb=" CG MET H 129 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" CB MET D 129 " pdb=" CG MET D 129 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 4171 not shown) Histogram of bond angle deviations from ideal: 100.53 - 106.67: 192 106.67 - 112.81: 1825 112.81 - 118.95: 1127 118.95 - 125.09: 2280 125.09 - 131.22: 96 Bond angle restraints: 5520 Sorted by residual: angle pdb=" C GLY O 142 " pdb=" N ASN O 143 " pdb=" CA ASN O 143 " ideal model delta sigma weight residual 121.70 126.69 -4.99 1.80e+00 3.09e-01 7.67e+00 angle pdb=" C GLY U 142 " pdb=" N ASN U 143 " pdb=" CA ASN U 143 " ideal model delta sigma weight residual 121.70 126.68 -4.98 1.80e+00 3.09e-01 7.65e+00 angle pdb=" C GLY P 142 " pdb=" N ASN P 143 " pdb=" CA ASN P 143 " ideal model delta sigma weight residual 121.70 126.67 -4.97 1.80e+00 3.09e-01 7.62e+00 angle pdb=" C GLY Y 142 " pdb=" N ASN Y 143 " pdb=" CA ASN Y 143 " ideal model delta sigma weight residual 121.70 126.67 -4.97 1.80e+00 3.09e-01 7.61e+00 angle pdb=" C GLY M 142 " pdb=" N ASN M 143 " pdb=" CA ASN M 143 " ideal model delta sigma weight residual 121.70 126.66 -4.96 1.80e+00 3.09e-01 7.61e+00 ... (remaining 5515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.69: 1798 10.69 - 21.37: 314 21.37 - 32.06: 144 32.06 - 42.75: 24 42.75 - 53.43: 48 Dihedral angle restraints: 2328 sinusoidal: 864 harmonic: 1464 Sorted by residual: dihedral pdb=" CA MET C 139 " pdb=" CB MET C 139 " pdb=" CG MET C 139 " pdb=" SD MET C 139 " ideal model delta sinusoidal sigma weight residual 180.00 126.57 53.43 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA MET B 139 " pdb=" CB MET B 139 " pdb=" CG MET B 139 " pdb=" SD MET B 139 " ideal model delta sinusoidal sigma weight residual 180.00 126.57 53.43 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA MET T 139 " pdb=" CB MET T 139 " pdb=" CG MET T 139 " pdb=" SD MET T 139 " ideal model delta sinusoidal sigma weight residual 180.00 126.58 53.42 3 1.50e+01 4.44e-03 9.20e+00 ... (remaining 2325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 179 0.027 - 0.054: 221 0.054 - 0.080: 43 0.080 - 0.107: 37 0.107 - 0.134: 48 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ARG U 136 " pdb=" N ARG U 136 " pdb=" C ARG U 136 " pdb=" CB ARG U 136 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA ARG P 136 " pdb=" N ARG P 136 " pdb=" C ARG P 136 " pdb=" CB ARG P 136 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ARG C 136 " pdb=" N ARG C 136 " pdb=" C ARG C 136 " pdb=" CB ARG C 136 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 525 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA O 120 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C ALA O 120 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA O 120 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL O 121 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA T 120 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.83e+00 pdb=" C ALA T 120 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA T 120 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL T 121 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 120 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" C ALA Q 120 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA Q 120 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL Q 121 " -0.008 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 906 2.79 - 3.32: 3097 3.32 - 3.85: 7935 3.85 - 4.37: 9733 4.37 - 4.90: 16254 Nonbonded interactions: 37925 Sorted by model distance: nonbonded pdb=" O HOH M 201 " pdb=" O HOH S 201 " model vdw 2.267 2.440 nonbonded pdb=" O HOH N 201 " pdb=" O HOH T 201 " model vdw 2.272 2.440 nonbonded pdb=" O HOH K 202 " pdb=" O HOH Q 202 " model vdw 2.284 2.440 nonbonded pdb=" O HOH H 201 " pdb=" O HOH N 201 " model vdw 2.297 2.440 nonbonded pdb=" O HOH G 201 " pdb=" O HOH M 201 " model vdw 2.305 2.440 ... (remaining 37920 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 'X' selection = chain 'Y' } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.090 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.860 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 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 : 0.009 0.045 4176 Z= 0.677 Angle : 1.059 4.986 5520 Z= 0.572 Chirality : 0.056 0.134 528 Planarity : 0.004 0.014 720 Dihedral : 14.838 53.431 1464 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.79 (0.20), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS X 140 PHE 0.005 0.001 PHE I 141 TYR 0.002 0.001 TYR F 128 ARG 0.004 0.002 ARG X 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: C 136 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.7398 (mtt-85) REVERT: D 136 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7431 (mtt-85) REVERT: G 138 MET cc_start: 0.7241 (tmt) cc_final: 0.6728 (tmm) REVERT: I 136 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7353 (mtm180) REVERT: J 136 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7471 (mtt-85) REVERT: O 136 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7416 (mtt90) REVERT: R 138 MET cc_start: 0.7166 (tmt) cc_final: 0.6291 (tmm) REVERT: U 134 MET cc_start: 0.8962 (ttm) cc_final: 0.8664 (ttm) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 1.8831 time to fit residues: 242.3356 Evaluate side-chains 125 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 28 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 140 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4176 Z= 0.206 Angle : 0.737 5.464 5520 Z= 0.388 Chirality : 0.053 0.139 528 Planarity : 0.003 0.022 720 Dihedral : 5.262 13.849 624 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.08 % Allowed : 19.53 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.77 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS S 140 PHE 0.006 0.001 PHE D 141 TYR 0.009 0.002 TYR K 128 ARG 0.007 0.001 ARG V 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 139 MET cc_start: 0.8571 (mtm) cc_final: 0.8172 (mtm) REVERT: C 138 MET cc_start: 0.7115 (tmt) cc_final: 0.6610 (tmm) REVERT: D 136 ARG cc_start: 0.7645 (mtt-85) cc_final: 0.7406 (mtt-85) REVERT: I 136 ARG cc_start: 0.7624 (mtt-85) cc_final: 0.7343 (mtp85) REVERT: K 138 MET cc_start: 0.7177 (tmt) cc_final: 0.6681 (tmm) REVERT: L 138 MET cc_start: 0.7213 (OUTLIER) cc_final: 0.6145 (tmt) REVERT: N 138 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.7041 (tmt) REVERT: O 138 MET cc_start: 0.7330 (tmt) cc_final: 0.6872 (tmm) REVERT: S 138 MET cc_start: 0.7367 (tmt) cc_final: 0.7083 (tmt) REVERT: U 134 MET cc_start: 0.9276 (ttm) cc_final: 0.9031 (ttm) REVERT: X 138 MET cc_start: 0.7367 (tmt) cc_final: 0.6856 (tmt) outliers start: 8 outliers final: 0 residues processed: 125 average time/residue: 1.8161 time to fit residues: 231.7995 Evaluate side-chains 126 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 4176 Z= 0.498 Angle : 0.953 5.796 5520 Z= 0.513 Chirality : 0.055 0.164 528 Planarity : 0.004 0.033 720 Dihedral : 6.111 17.790 624 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.82 % Allowed : 20.31 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.83 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 140 PHE 0.007 0.002 PHE Y 141 TYR 0.007 0.001 TYR K 128 ARG 0.005 0.001 ARG V 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 132 time to evaluate : 0.486 Fit side-chains REVERT: A 138 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.6778 (tmt) REVERT: C 138 MET cc_start: 0.7209 (tmt) cc_final: 0.6675 (tmm) REVERT: D 136 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7429 (mtt-85) REVERT: F 138 MET cc_start: 0.7259 (OUTLIER) cc_final: 0.6733 (tmt) REVERT: H 136 ARG cc_start: 0.7783 (mtt-85) cc_final: 0.7539 (mtm180) REVERT: I 136 ARG cc_start: 0.7716 (mtt-85) cc_final: 0.7434 (mtp85) REVERT: I 138 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6489 (tmt) REVERT: L 138 MET cc_start: 0.7345 (OUTLIER) cc_final: 0.6338 (tmt) REVERT: M 136 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7506 (mtp85) REVERT: N 138 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6967 (tmt) REVERT: R 136 ARG cc_start: 0.7843 (mtp-110) cc_final: 0.7641 (mtp-110) REVERT: T 138 MET cc_start: 0.7262 (tmt) cc_final: 0.6917 (mtt) REVERT: X 138 MET cc_start: 0.7503 (tmt) cc_final: 0.6923 (tmt) outliers start: 7 outliers final: 1 residues processed: 132 average time/residue: 1.7968 time to fit residues: 242.3531 Evaluate side-chains 137 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain Y residue 139 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 26 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4176 Z= 0.297 Angle : 0.809 5.455 5520 Z= 0.431 Chirality : 0.053 0.148 528 Planarity : 0.003 0.028 720 Dihedral : 5.645 14.349 624 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.08 % Allowed : 20.05 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 140 PHE 0.007 0.001 PHE Y 141 TYR 0.009 0.001 TYR K 128 ARG 0.004 0.001 ARG T 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 127 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.6665 (tmt) REVERT: C 138 MET cc_start: 0.7212 (tmt) cc_final: 0.6631 (tmm) REVERT: D 136 ARG cc_start: 0.7600 (mtt-85) cc_final: 0.7389 (mtt-85) REVERT: H 138 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6845 (tmt) REVERT: I 136 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7443 (mtp85) REVERT: I 138 MET cc_start: 0.7523 (OUTLIER) cc_final: 0.6571 (tmt) REVERT: K 138 MET cc_start: 0.7267 (tmt) cc_final: 0.6711 (tmm) REVERT: L 138 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6420 (tmt) REVERT: N 138 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6982 (tmt) REVERT: R 136 ARG cc_start: 0.7879 (mtp-110) cc_final: 0.7629 (mtp-110) REVERT: S 138 MET cc_start: 0.7395 (tmt) cc_final: 0.6961 (tmt) REVERT: T 138 MET cc_start: 0.7271 (tmt) cc_final: 0.6974 (mtt) REVERT: X 138 MET cc_start: 0.7446 (tmt) cc_final: 0.6985 (tmt) outliers start: 8 outliers final: 0 residues processed: 127 average time/residue: 1.8222 time to fit residues: 236.3505 Evaluate side-chains 131 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 4176 Z= 0.495 Angle : 0.943 5.862 5520 Z= 0.507 Chirality : 0.056 0.164 528 Planarity : 0.004 0.033 720 Dihedral : 6.191 18.157 624 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.08 % Allowed : 19.27 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 140 PHE 0.007 0.002 PHE S 141 TYR 0.007 0.001 TYR K 128 ARG 0.003 0.001 ARG Q 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 131 time to evaluate : 0.497 Fit side-chains REVERT: A 138 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6768 (tmt) REVERT: C 138 MET cc_start: 0.7231 (tmt) cc_final: 0.6673 (tmm) REVERT: D 136 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.7393 (mtt-85) REVERT: F 138 MET cc_start: 0.7309 (OUTLIER) cc_final: 0.6637 (tmt) REVERT: H 136 ARG cc_start: 0.7727 (mtt-85) cc_final: 0.7419 (mtm180) REVERT: H 138 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6870 (tmt) REVERT: I 136 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.7446 (mtp85) REVERT: I 138 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.6554 (tmt) REVERT: L 138 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6344 (tmt) REVERT: M 136 ARG cc_start: 0.7801 (mtp-110) cc_final: 0.7564 (mtp85) REVERT: N 138 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6953 (tmt) REVERT: N 143 ASN cc_start: 0.7697 (m-40) cc_final: 0.7447 (m-40) REVERT: T 138 MET cc_start: 0.7323 (tmt) cc_final: 0.7080 (mtt) REVERT: X 138 MET cc_start: 0.7544 (tmt) cc_final: 0.6979 (tmt) outliers start: 8 outliers final: 0 residues processed: 131 average time/residue: 1.7577 time to fit residues: 235.3541 Evaluate side-chains 136 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 130 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.5980 chunk 46 optimal weight: 6.9990 chunk 38 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS H 143 ASN P 143 ASN Q 143 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4176 Z= 0.177 Angle : 0.701 5.776 5520 Z= 0.369 Chirality : 0.051 0.137 528 Planarity : 0.003 0.028 720 Dihedral : 5.266 12.948 624 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.60 % Allowed : 19.01 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.21), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.79 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS X 140 PHE 0.008 0.001 PHE F 141 TYR 0.010 0.002 TYR M 128 ARG 0.004 0.000 ARG U 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 138 MET cc_start: 0.7377 (OUTLIER) cc_final: 0.6622 (tmt) REVERT: C 138 MET cc_start: 0.7183 (tmt) cc_final: 0.6570 (tmm) REVERT: D 136 ARG cc_start: 0.7578 (mtt-85) cc_final: 0.7365 (mtt-85) REVERT: H 138 MET cc_start: 0.7335 (OUTLIER) cc_final: 0.6831 (tmt) REVERT: I 136 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7401 (mtp85) REVERT: I 138 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6505 (tmt) REVERT: K 138 MET cc_start: 0.7347 (tmt) cc_final: 0.6819 (tmm) REVERT: N 138 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6995 (tmt) REVERT: R 136 ARG cc_start: 0.7822 (mtp-110) cc_final: 0.7611 (mtp-110) REVERT: S 139 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8278 (mtm) REVERT: T 138 MET cc_start: 0.7253 (tmt) cc_final: 0.6921 (mtp) REVERT: X 138 MET cc_start: 0.7406 (tmt) cc_final: 0.6936 (tmt) outliers start: 10 outliers final: 0 residues processed: 130 average time/residue: 1.8256 time to fit residues: 242.3423 Evaluate side-chains 133 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain H residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 0.2980 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 0.0020 chunk 8 optimal weight: 0.0980 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4176 Z= 0.144 Angle : 0.657 5.885 5520 Z= 0.338 Chirality : 0.050 0.125 528 Planarity : 0.003 0.027 720 Dihedral : 4.723 14.153 624 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.56 % Allowed : 22.40 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS X 140 PHE 0.007 0.001 PHE F 141 TYR 0.009 0.001 TYR M 128 ARG 0.011 0.001 ARG U 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: C 138 MET cc_start: 0.7183 (tmt) cc_final: 0.6589 (tmm) REVERT: D 136 ARG cc_start: 0.7546 (mtt-85) cc_final: 0.7315 (mtt-85) REVERT: F 138 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6814 (tmm) REVERT: I 136 ARG cc_start: 0.7569 (mtt-85) cc_final: 0.7329 (mtp85) REVERT: I 138 MET cc_start: 0.7436 (OUTLIER) cc_final: 0.6520 (tmt) REVERT: K 138 MET cc_start: 0.7284 (tmt) cc_final: 0.6746 (tmm) REVERT: L 138 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6452 (tmt) REVERT: N 138 MET cc_start: 0.7203 (tmt) cc_final: 0.6995 (tmt) REVERT: R 138 MET cc_start: 0.7162 (OUTLIER) cc_final: 0.6482 (tmm) REVERT: S 139 MET cc_start: 0.8607 (OUTLIER) cc_final: 0.8184 (mtm) REVERT: T 138 MET cc_start: 0.7221 (tmt) cc_final: 0.6912 (mtp) REVERT: X 138 MET cc_start: 0.7331 (tmt) cc_final: 0.6861 (tmt) outliers start: 6 outliers final: 0 residues processed: 129 average time/residue: 1.8054 time to fit residues: 237.8631 Evaluate side-chains 131 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain R residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4176 Z= 0.270 Angle : 0.772 6.354 5520 Z= 0.402 Chirality : 0.051 0.140 528 Planarity : 0.004 0.047 720 Dihedral : 5.349 15.544 624 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.82 % Allowed : 23.44 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.16), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 140 PHE 0.007 0.001 PHE F 141 TYR 0.007 0.001 TYR K 128 ARG 0.009 0.001 ARG U 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: C 138 MET cc_start: 0.7210 (tmt) cc_final: 0.6615 (tmm) REVERT: D 136 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.7382 (mtt-85) REVERT: I 136 ARG cc_start: 0.7668 (mtt-85) cc_final: 0.7421 (mtp85) REVERT: I 138 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6579 (tmt) REVERT: K 138 MET cc_start: 0.7332 (tmt) cc_final: 0.6795 (tmm) REVERT: L 138 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6358 (tmt) REVERT: M 136 ARG cc_start: 0.7699 (mtp-110) cc_final: 0.7483 (mtp85) REVERT: N 138 MET cc_start: 0.7251 (tmt) cc_final: 0.7025 (tmt) REVERT: R 138 MET cc_start: 0.7188 (OUTLIER) cc_final: 0.6634 (tmm) REVERT: S 139 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8245 (mtm) REVERT: T 138 MET cc_start: 0.7278 (tmt) cc_final: 0.6853 (mtt) REVERT: X 138 MET cc_start: 0.7422 (tmt) cc_final: 0.6951 (tmt) outliers start: 7 outliers final: 0 residues processed: 130 average time/residue: 1.8572 time to fit residues: 246.4983 Evaluate side-chains 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain R residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4176 Z= 0.222 Angle : 0.742 6.720 5520 Z= 0.383 Chirality : 0.051 0.145 528 Planarity : 0.004 0.056 720 Dihedral : 5.256 15.433 624 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.56 % Allowed : 24.48 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 140 PHE 0.008 0.001 PHE F 141 TYR 0.008 0.001 TYR M 128 ARG 0.010 0.001 ARG U 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 129 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: C 138 MET cc_start: 0.7204 (tmt) cc_final: 0.6598 (tmm) REVERT: D 136 ARG cc_start: 0.7596 (mtt-85) cc_final: 0.7375 (mtt-85) REVERT: F 138 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.6814 (tmm) REVERT: I 136 ARG cc_start: 0.7651 (mtt-85) cc_final: 0.7404 (mtp85) REVERT: I 138 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.6397 (tmt) REVERT: J 138 MET cc_start: 0.7225 (tmt) cc_final: 0.7008 (tmm) REVERT: K 138 MET cc_start: 0.7328 (tmt) cc_final: 0.6919 (tmm) REVERT: L 138 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6299 (tmt) REVERT: N 138 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7013 (tmt) REVERT: S 139 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: T 138 MET cc_start: 0.7269 (tmt) cc_final: 0.6849 (mtt) REVERT: X 138 MET cc_start: 0.7411 (tmt) cc_final: 0.6939 (tmt) outliers start: 6 outliers final: 0 residues processed: 129 average time/residue: 1.8632 time to fit residues: 245.4104 Evaluate side-chains 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain L residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 0.1980 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.0870 chunk 30 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.0040 overall best weight: 0.3570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 143 ASN H 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4176 Z= 0.142 Angle : 0.664 7.215 5520 Z= 0.335 Chirality : 0.049 0.142 528 Planarity : 0.004 0.044 720 Dihedral : 4.703 15.381 624 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.30 % Allowed : 23.96 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.85 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 140 PHE 0.008 0.001 PHE F 141 TYR 0.010 0.002 TYR M 128 ARG 0.009 0.001 ARG U 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1104 Ramachandran restraints generated. 552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: C 138 MET cc_start: 0.7205 (tmt) cc_final: 0.6576 (tmm) REVERT: D 136 ARG cc_start: 0.7557 (mtt-85) cc_final: 0.7356 (mtt-85) REVERT: F 138 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6795 (tmm) REVERT: G 138 MET cc_start: 0.7131 (tmt) cc_final: 0.6782 (tmm) REVERT: I 136 ARG cc_start: 0.7561 (mtt-85) cc_final: 0.7320 (mtp85) REVERT: I 138 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.6361 (tmt) REVERT: J 138 MET cc_start: 0.7256 (tmt) cc_final: 0.7055 (tmm) REVERT: K 138 MET cc_start: 0.7182 (tmt) cc_final: 0.6741 (tmm) REVERT: N 138 MET cc_start: 0.7299 (OUTLIER) cc_final: 0.7076 (tmt) REVERT: S 139 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8159 (mtm) REVERT: T 138 MET cc_start: 0.7241 (tmt) cc_final: 0.6925 (mtp) REVERT: X 138 MET cc_start: 0.7303 (tmt) cc_final: 0.6826 (tmt) outliers start: 5 outliers final: 0 residues processed: 129 average time/residue: 1.8676 time to fit residues: 246.0591 Evaluate side-chains 130 residues out of total 384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 126 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 138 MET Chi-restraints excluded: chain I residue 138 MET Chi-restraints excluded: chain N residue 138 MET Chi-restraints excluded: chain S residue 139 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.114875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096701 restraints weight = 2782.187| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.35 r_work: 0.3246 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work: 0.2878 rms_B_bonded: 4.89 restraints_weight: 0.1250 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4176 Z= 0.367 Angle : 0.873 7.476 5520 Z= 0.456 Chirality : 0.053 0.199 528 Planarity : 0.005 0.061 720 Dihedral : 5.808 16.438 624 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.56 % Allowed : 23.18 % Favored : 75.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.89 (0.22), residues: 552 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.17), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 140 PHE 0.008 0.002 PHE F 141 TYR 0.005 0.001 TYR T 128 ARG 0.017 0.002 ARG U 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3609.50 seconds wall clock time: 63 minutes 41.41 seconds (3821.41 seconds total)