Starting phenix.real_space_refine on Fri Mar 15 22:28:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo0_32637/03_2024/7wo0_32637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo0_32637/03_2024/7wo0_32637.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo0_32637/03_2024/7wo0_32637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo0_32637/03_2024/7wo0_32637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo0_32637/03_2024/7wo0_32637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wo0_32637/03_2024/7wo0_32637.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= 0.002 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 C 3948 2.51 5 N 1092 2.21 5 O 1302 1.98 5 H 6622 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 35": "OE1" <-> "OE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "E GLU 35": "OE1" <-> "OE2" Residue "F GLU 35": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "O GLU 35": "OE1" <-> "OE2" Residue "P GLU 35": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "R GLU 35": "OE1" <-> "OE2" Residue "S GLU 35": "OE1" <-> "OE2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "U GLU 35": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12964 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "A" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "B" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "D" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "E" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "F" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "G" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "O" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "P" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "Q" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "R" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "S" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "T" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Chain: "U" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 926 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'TRANS': 64} Time building chain proxies: 5.97, per 1000 atoms: 0.46 Number of scatterers: 12964 At special positions: 0 Unit cell: (100.43, 110.39, 54.78, 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) O 1302 8.00 N 1092 7.00 C 3948 6.00 H 6622 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: 10.52 Conformation dependent library (CDL) restraints added in 1.3 seconds 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 49.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 37 through 44 removed outlier: 6.382A pdb=" N LEU A 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY B 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 40 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LYS B 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N SER A 42 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU D 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLY E 41 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL D 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LYS E 43 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N SER D 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU E 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY F 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL E 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N LYS F 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER E 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU F 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY G 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL F 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS G 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER F 42 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 57 removed outlier: 6.834A pdb=" N VAL A 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS A 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY B 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N GLY C 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 10.349A pdb=" N HIS B 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.779A pdb=" N VAL C 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N VAL B 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY C 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR B 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR C 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ALA B 56 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL C 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL D 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS C 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY D 51 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL D 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL E 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N HIS D 50 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY E 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL E 48 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL F 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N HIS E 50 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY F 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL F 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL G 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS F 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY G 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66 removed outlier: 6.338A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR E 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR F 64 " --> pdb=" O ASN G 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 72 removed outlier: 6.456A pdb=" N VAL C 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 77 through 78 removed outlier: 6.547A pdb=" N VAL A 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL E 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL F 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.243A pdb=" N VAL C 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 89 removed outlier: 6.854A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE E 88 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE F 88 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 98 removed outlier: 6.793A pdb=" N GLY A 93 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N THR C 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL B 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE C 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N LYS B 97 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LYS C 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY C 93 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY D 93 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY E 93 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY F 93 " --> pdb=" O THR G 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 37 through 44 removed outlier: 6.381A pdb=" N LEU O 38 " --> pdb=" O TYR P 39 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY P 41 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL O 40 " --> pdb=" O GLY P 41 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LYS P 43 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N SER O 42 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU P 38 " --> pdb=" O TYR Q 39 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY Q 41 " --> pdb=" O LEU P 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL P 40 " --> pdb=" O GLY Q 41 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LYS Q 43 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER P 42 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU Q 38 " --> pdb=" O TYR R 39 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N GLY R 41 " --> pdb=" O LEU Q 38 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL Q 40 " --> pdb=" O GLY R 41 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LYS R 43 " --> pdb=" O VAL Q 40 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N SER Q 42 " --> pdb=" O LYS R 43 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU R 38 " --> pdb=" O TYR S 39 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N GLY S 41 " --> pdb=" O LEU R 38 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL R 40 " --> pdb=" O GLY S 41 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS S 43 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER R 42 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU S 38 " --> pdb=" O TYR T 39 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLY T 41 " --> pdb=" O LEU S 38 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL S 40 " --> pdb=" O GLY T 41 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N LYS T 43 " --> pdb=" O VAL S 40 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N SER S 42 " --> pdb=" O LYS T 43 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU T 38 " --> pdb=" O TYR U 39 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N GLY U 41 " --> pdb=" O LEU T 38 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL T 40 " --> pdb=" O GLY U 41 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LYS U 43 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER T 42 " --> pdb=" O LYS U 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'O' and resid 47 through 57 removed outlier: 6.835A pdb=" N VAL O 48 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL P 49 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N HIS O 50 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY P 51 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL P 48 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL Q 49 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS P 50 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY Q 51 " --> pdb=" O HIS P 50 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N VAL Q 48 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N GLY R 51 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS Q 50 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N THR R 53 " --> pdb=" O HIS Q 50 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL Q 52 " --> pdb=" O THR R 53 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N VAL R 55 " --> pdb=" O VAL Q 52 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR Q 54 " --> pdb=" O VAL R 55 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N GLU R 57 " --> pdb=" O THR Q 54 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA Q 56 " --> pdb=" O GLU R 57 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL R 48 " --> pdb=" O GLY S 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL S 49 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N HIS R 50 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY S 51 " --> pdb=" O HIS R 50 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL S 48 " --> pdb=" O GLY T 47 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL T 49 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N HIS S 50 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY T 51 " --> pdb=" O HIS S 50 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL T 48 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL U 49 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N HIS T 50 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLY U 51 " --> pdb=" O HIS T 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'O' and resid 63 through 66 removed outlier: 6.337A pdb=" N THR O 64 " --> pdb=" O ASN P 65 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR P 64 " --> pdb=" O ASN Q 65 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR Q 64 " --> pdb=" O ASN R 65 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N THR R 64 " --> pdb=" O ASN S 65 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR S 64 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR T 64 " --> pdb=" O ASN U 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'O' and resid 70 through 72 Processing sheet with id=AB4, first strand: chain 'O' and resid 77 through 78 removed outlier: 6.547A pdb=" N VAL O 77 " --> pdb=" O ALA P 78 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL P 77 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL Q 77 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL R 77 " --> pdb=" O ALA S 78 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL S 77 " --> pdb=" O ALA T 78 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL T 77 " --> pdb=" O ALA U 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'O' and resid 81 through 83 Processing sheet with id=AB6, first strand: chain 'O' and resid 88 through 89 removed outlier: 6.854A pdb=" N ILE O 88 " --> pdb=" O ALA P 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE P 88 " --> pdb=" O ALA Q 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE Q 88 " --> pdb=" O ALA R 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE R 88 " --> pdb=" O ALA S 89 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE S 88 " --> pdb=" O ALA T 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE T 88 " --> pdb=" O ALA U 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'O' and resid 92 through 98 removed outlier: 6.793A pdb=" N GLY O 93 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY P 93 " --> pdb=" O THR Q 92 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY Q 93 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLY R 93 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY S 93 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY T 93 " --> pdb=" O THR U 92 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 531 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: 4.68 Time building geometry restraints manager: 10.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.87 - 1.00: 392 1.00 - 1.14: 6230 1.14 - 1.28: 1134 1.28 - 1.41: 1204 1.41 - 1.55: 4032 Bond restraints: 12992 Sorted by residual: bond pdb=" N GLU D 61 " pdb=" H GLU D 61 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" ND2 ASN F 65 " pdb="HD22 ASN F 65 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLU P 61 " pdb=" H GLU P 61 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR P 81 " pdb=" H THR P 81 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N THR Q 54 " pdb=" H THR Q 54 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 12987 not shown) Histogram of bond angle deviations from ideal: 105.19 - 110.41: 14500 110.41 - 115.63: 2623 115.63 - 120.85: 4169 120.85 - 126.07: 2298 126.07 - 131.29: 42 Bond angle restraints: 23632 Sorted by residual: angle pdb=" C ASP Q 98 " pdb=" CA ASP Q 98 " pdb=" CB ASP Q 98 " ideal model delta sigma weight residual 110.42 118.66 -8.24 1.99e+00 2.53e-01 1.71e+01 angle pdb=" C ASP U 98 " pdb=" CA ASP U 98 " pdb=" CB ASP U 98 " ideal model delta sigma weight residual 110.42 118.63 -8.21 1.99e+00 2.53e-01 1.70e+01 angle pdb=" C ASP O 98 " pdb=" CA ASP O 98 " pdb=" CB ASP O 98 " ideal model delta sigma weight residual 110.42 118.62 -8.20 1.99e+00 2.53e-01 1.70e+01 angle pdb=" C ASP S 98 " pdb=" CA ASP S 98 " pdb=" CB ASP S 98 " ideal model delta sigma weight residual 110.42 118.62 -8.20 1.99e+00 2.53e-01 1.70e+01 angle pdb=" C ASP C 98 " pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " ideal model delta sigma weight residual 110.42 118.61 -8.19 1.99e+00 2.53e-01 1.69e+01 ... (remaining 23627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4956 17.77 - 35.53: 322 35.53 - 53.30: 252 53.30 - 71.06: 392 71.06 - 88.83: 14 Dihedral angle restraints: 5936 sinusoidal: 3318 harmonic: 2618 Sorted by residual: dihedral pdb=" CA LYS A 45 " pdb=" CB LYS A 45 " pdb=" CG LYS A 45 " pdb=" CD LYS A 45 " ideal model delta sinusoidal sigma weight residual -60.00 -117.75 57.75 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA LYS D 45 " pdb=" CB LYS D 45 " pdb=" CG LYS D 45 " pdb=" CD LYS D 45 " ideal model delta sinusoidal sigma weight residual -60.00 -117.75 57.75 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CA LYS P 45 " pdb=" CB LYS P 45 " pdb=" CG LYS P 45 " pdb=" CD LYS P 45 " ideal model delta sinusoidal sigma weight residual -60.00 -117.74 57.74 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 5933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 444 0.027 - 0.053: 320 0.053 - 0.080: 100 0.080 - 0.107: 179 0.107 - 0.133: 77 Chirality restraints: 1120 Sorted by residual: chirality pdb=" CA VAL P 95 " pdb=" N VAL P 95 " pdb=" C VAL P 95 " pdb=" CB VAL P 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CA VAL S 95 " pdb=" N VAL S 95 " pdb=" C VAL S 95 " pdb=" CB VAL S 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 chirality pdb=" CA VAL F 95 " pdb=" N VAL F 95 " pdb=" C VAL F 95 " pdb=" CB VAL F 95 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1117 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 99 " 0.030 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN A 99 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN A 99 " -0.023 2.00e-02 2.50e+03 pdb=" NE2 GLN A 99 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN A 99 " -0.760 2.00e-02 2.50e+03 pdb="HE22 GLN A 99 " 0.771 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN S 99 " -0.029 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN S 99 " 0.016 2.00e-02 2.50e+03 pdb=" OE1 GLN S 99 " 0.023 2.00e-02 2.50e+03 pdb=" NE2 GLN S 99 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN S 99 " 0.760 2.00e-02 2.50e+03 pdb="HE22 GLN S 99 " -0.771 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 99 " 0.030 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CD GLN B 99 " -0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN B 99 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 GLN B 99 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN B 99 " -0.759 2.00e-02 2.50e+03 pdb="HE22 GLN B 99 " 0.770 2.00e-02 2.50e+03 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.20: 1616 2.20 - 2.77: 24667 2.77 - 3.35: 32275 3.35 - 3.92: 48036 3.92 - 4.50: 65038 Nonbonded interactions: 171632 Sorted by model distance: nonbonded pdb=" OE1 GLU D 35 " pdb=" H3 GLU D 35 " model vdw 1.619 1.850 nonbonded pdb=" OE1 GLU R 35 " pdb=" H3 GLU R 35 " model vdw 1.619 1.850 nonbonded pdb=" OE1 GLU E 35 " pdb=" H3 GLU E 35 " model vdw 1.619 1.850 nonbonded pdb=" OE1 GLU G 35 " pdb=" H3 GLU G 35 " model vdw 1.620 1.850 nonbonded pdb=" OE1 GLU Q 35 " pdb=" H3 GLU Q 35 " model vdw 1.620 1.850 ... (remaining 171627 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 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 1.710 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: 0.210 Extract box with map and model: 5.050 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 43.950 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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:17.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 0.050 6370 Z= 0.499 Angle : 0.905 8.238 8610 Z= 0.530 Chirality : 0.056 0.133 1120 Planarity : 0.005 0.026 1078 Dihedral : 15.451 69.877 2184 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % 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: -3.84 (0.18), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.14), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.022 0.006 PHE A 94 TYR 0.033 0.009 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7955 (tttp) REVERT: T 60 LYS cc_start: 0.8171 (mttt) cc_final: 0.7864 (mtpt) REVERT: T 61 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8060 (mt-10) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 3.4718 time to fit residues: 285.3179 Evaluate side-chains 65 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 6370 Z= 0.162 Angle : 0.466 4.456 8610 Z= 0.268 Chirality : 0.054 0.124 1120 Planarity : 0.002 0.010 1078 Dihedral : 4.501 13.449 910 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 10.49 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.22), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS O 50 PHE 0.016 0.004 PHE P 94 TYR 0.003 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.001 Fit side-chains REVERT: C 45 LYS cc_start: 0.8302 (tmtt) cc_final: 0.7889 (tmtm) REVERT: F 60 LYS cc_start: 0.8096 (mttt) cc_final: 0.7815 (mtpt) REVERT: G 60 LYS cc_start: 0.8070 (mttt) cc_final: 0.7779 (mtpt) REVERT: T 60 LYS cc_start: 0.8046 (mttt) cc_final: 0.7692 (mtpt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 4.0819 time to fit residues: 282.8155 Evaluate side-chains 59 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 6370 Z= 0.307 Angle : 0.526 4.623 8610 Z= 0.300 Chirality : 0.054 0.129 1120 Planarity : 0.002 0.009 1078 Dihedral : 5.028 14.175 910 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.30 % Allowed : 12.46 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.23), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.020 0.005 PHE D 94 TYR 0.002 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: C 45 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7920 (tmtm) REVERT: F 60 LYS cc_start: 0.8150 (mttt) cc_final: 0.7889 (mtpt) REVERT: G 60 LYS cc_start: 0.8196 (mttt) cc_final: 0.7841 (mtpt) REVERT: R 60 LYS cc_start: 0.8128 (mttt) cc_final: 0.7908 (mtpt) REVERT: S 45 LYS cc_start: 0.8299 (tmtt) cc_final: 0.7967 (tttp) REVERT: T 60 LYS cc_start: 0.8155 (mttt) cc_final: 0.7803 (mtpt) REVERT: U 60 LYS cc_start: 0.8105 (mttt) cc_final: 0.7717 (mtpt) outliers start: 2 outliers final: 0 residues processed: 65 average time/residue: 4.0292 time to fit residues: 270.9643 Evaluate side-chains 62 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 6370 Z= 0.246 Angle : 0.472 4.660 8610 Z= 0.272 Chirality : 0.054 0.126 1120 Planarity : 0.002 0.008 1078 Dihedral : 4.762 14.324 910 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.15 % Allowed : 13.07 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.22), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS T 50 PHE 0.018 0.004 PHE D 94 TYR 0.002 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.892 Fit side-chains REVERT: C 45 LYS cc_start: 0.8255 (tmtt) cc_final: 0.7857 (tmtm) REVERT: G 60 LYS cc_start: 0.8240 (mttt) cc_final: 0.7865 (mtpt) REVERT: T 60 LYS cc_start: 0.8164 (mttt) cc_final: 0.7808 (mtpt) REVERT: U 60 LYS cc_start: 0.8080 (mttt) cc_final: 0.7724 (mtpt) outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 4.0915 time to fit residues: 258.1632 Evaluate side-chains 60 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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: 0.8111 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 6370 Z= 0.386 Angle : 0.550 5.149 8610 Z= 0.315 Chirality : 0.055 0.130 1120 Planarity : 0.002 0.010 1078 Dihedral : 5.223 15.393 910 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.30 % Allowed : 13.22 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.23), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.022 0.006 PHE D 94 TYR 0.002 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.950 Fit side-chains REVERT: C 45 LYS cc_start: 0.8303 (tmtt) cc_final: 0.7926 (tmtm) REVERT: F 60 LYS cc_start: 0.8180 (mttt) cc_final: 0.7909 (mtpt) REVERT: G 60 LYS cc_start: 0.8259 (mttt) cc_final: 0.7896 (mtpt) REVERT: S 45 LYS cc_start: 0.8256 (tmtt) cc_final: 0.8002 (tttp) REVERT: T 60 LYS cc_start: 0.8240 (mttt) cc_final: 0.7833 (mtpt) REVERT: U 60 LYS cc_start: 0.8152 (mttt) cc_final: 0.7773 (mtpt) outliers start: 2 outliers final: 1 residues processed: 61 average time/residue: 3.9949 time to fit residues: 252.4472 Evaluate side-chains 60 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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: 0.8079 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 6370 Z= 0.250 Angle : 0.468 4.161 8610 Z= 0.270 Chirality : 0.054 0.124 1120 Planarity : 0.002 0.008 1078 Dihedral : 4.829 14.708 910 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.61 % Allowed : 12.46 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.23), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS T 50 PHE 0.018 0.004 PHE D 94 TYR 0.002 0.000 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 60 time to evaluate : 1.015 Fit side-chains REVERT: C 45 LYS cc_start: 0.8261 (tmtt) cc_final: 0.7860 (tmtm) REVERT: F 60 LYS cc_start: 0.8150 (mttt) cc_final: 0.7892 (mtpt) REVERT: G 60 LYS cc_start: 0.8257 (mttt) cc_final: 0.7908 (mtpt) REVERT: T 60 LYS cc_start: 0.8183 (mttt) cc_final: 0.7826 (mtpt) REVERT: U 60 LYS cc_start: 0.8116 (mttt) cc_final: 0.7746 (mtpt) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 4.1591 time to fit residues: 262.3742 Evaluate side-chains 61 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 0.0970 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 6370 Z= 0.185 Angle : 0.436 4.052 8610 Z= 0.253 Chirality : 0.054 0.124 1120 Planarity : 0.002 0.008 1078 Dihedral : 4.547 14.230 910 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.46 % Allowed : 12.92 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.23), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 50 PHE 0.018 0.004 PHE D 94 TYR 0.002 0.000 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.994 Fit side-chains REVERT: C 45 LYS cc_start: 0.8259 (tmtt) cc_final: 0.7865 (tmtm) REVERT: G 60 LYS cc_start: 0.8243 (mttt) cc_final: 0.7866 (mtpt) REVERT: T 60 LYS cc_start: 0.8167 (mttt) cc_final: 0.7815 (mtpt) REVERT: U 60 LYS cc_start: 0.8102 (mttt) cc_final: 0.7735 (mtpt) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 4.0804 time to fit residues: 249.6041 Evaluate side-chains 62 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8108 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 6370 Z= 0.388 Angle : 0.537 5.055 8610 Z= 0.309 Chirality : 0.055 0.128 1120 Planarity : 0.002 0.010 1078 Dihedral : 5.085 15.425 910 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.61 % Allowed : 13.37 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.24), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 50 PHE 0.023 0.006 PHE S 94 TYR 0.002 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 0.895 Fit side-chains REVERT: C 45 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7863 (tmtm) REVERT: F 60 LYS cc_start: 0.8178 (mttt) cc_final: 0.7909 (mtpt) REVERT: G 60 LYS cc_start: 0.8282 (mttt) cc_final: 0.7907 (mtpt) REVERT: T 60 LYS cc_start: 0.8199 (mttt) cc_final: 0.7820 (mtpt) REVERT: U 60 LYS cc_start: 0.8174 (mttt) cc_final: 0.7782 (mtpt) outliers start: 4 outliers final: 4 residues processed: 64 average time/residue: 3.9000 time to fit residues: 258.5641 Evaluate side-chains 67 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6370 Z= 0.360 Angle : 0.523 4.911 8610 Z= 0.300 Chirality : 0.055 0.126 1120 Planarity : 0.002 0.010 1078 Dihedral : 5.087 15.343 910 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.76 % Allowed : 13.68 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.022 0.005 PHE D 94 TYR 0.002 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 1.045 Fit side-chains REVERT: F 60 LYS cc_start: 0.8176 (mttt) cc_final: 0.7902 (mtpt) REVERT: G 60 LYS cc_start: 0.8282 (mttt) cc_final: 0.7912 (mtpt) REVERT: T 60 LYS cc_start: 0.8220 (mttt) cc_final: 0.7833 (mtpt) REVERT: U 60 LYS cc_start: 0.8172 (mttt) cc_final: 0.7787 (mtpt) outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 3.7999 time to fit residues: 244.3445 Evaluate side-chains 66 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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: 0.8090 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 6370 Z= 0.285 Angle : 0.485 4.313 8610 Z= 0.280 Chirality : 0.054 0.125 1120 Planarity : 0.002 0.009 1078 Dihedral : 4.898 15.163 910 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.76 % Allowed : 13.83 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.24), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS T 50 PHE 0.021 0.005 PHE D 94 TYR 0.002 0.000 TYR E 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1764 Ramachandran restraints generated. 882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.129 Fit side-chains REVERT: F 60 LYS cc_start: 0.8155 (mttt) cc_final: 0.7886 (mtpt) REVERT: G 60 LYS cc_start: 0.8274 (mttt) cc_final: 0.7906 (mtpt) REVERT: T 60 LYS cc_start: 0.8217 (mttt) cc_final: 0.7827 (mtpt) REVERT: U 60 LYS cc_start: 0.8162 (mttt) cc_final: 0.7782 (mtpt) outliers start: 5 outliers final: 5 residues processed: 60 average time/residue: 3.8352 time to fit residues: 238.4971 Evaluate side-chains 64 residues out of total 658 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain R residue 75 THR Chi-restraints excluded: chain R residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.4561 r_free = 0.4561 target = 0.163029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.119061 restraints weight = 19635.974| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.53 r_work: 0.3762 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3617 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 6370 Z= 0.362 Angle : 0.526 4.738 8610 Z= 0.303 Chirality : 0.055 0.127 1120 Planarity : 0.002 0.010 1078 Dihedral : 5.102 15.829 910 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.61 % Allowed : 13.98 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.24), residues: 882 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.021 0.005 PHE D 94 TYR 0.002 0.001 TYR Q 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5633.80 seconds wall clock time: 99 minutes 13.41 seconds (5953.41 seconds total)