Starting phenix.real_space_refine on Fri Aug 22 13:23:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz8_34392/08_2025/8gz8_34392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz8_34392/08_2025/8gz8_34392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gz8_34392/08_2025/8gz8_34392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz8_34392/08_2025/8gz8_34392.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz8_34392/08_2025/8gz8_34392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz8_34392/08_2025/8gz8_34392.cif" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.004 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 52 5.16 5 C 2184 2.51 5 N 540 2.21 5 O 560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3336 Number of models: 1 Model: "" Number of chains: 71 Chain: "e" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "p" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "o" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "q" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "s" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "r" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "t" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "u" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "w" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "v" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "y" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "x" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "O" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "S" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "Q" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "U" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "Y" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "W" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "a" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "c" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "i" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "g" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "l" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "k" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "1" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "0" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "K" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "T" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "X" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "b" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "Z" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "d" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "f" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "j" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "h" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "z" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "n" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "C" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "E" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "F" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "H" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "M" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "P" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "N" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 55 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "e" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "w" 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: "S" 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: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 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: 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: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.02, per 1000 atoms: 0.31 Number of scatterers: 3336 At special positions: 0 Unit cell: (117.03, 138.61, 30.71, 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 52 16.00 O 560 8.00 N 540 7.00 C 2184 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 - 3.00 Amino acid : True - 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: 0.25 Conformation dependent library (CDL) restraints added in 139.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 28 sheets defined 0.0% alpha, 64.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'e' and resid 3 through 11 removed outlier: 6.968A pdb=" N GLY K 4 " --> pdb=" O LEU e 3 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET e 5 " --> pdb=" O GLY K 4 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU K 6 " --> pdb=" O MET e 5 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY e 7 " --> pdb=" O LEU K 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'p' and resid 3 through 11 removed outlier: 7.017A pdb=" N GLY V 4 " --> pdb=" O LEU p 3 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N MET p 5 " --> pdb=" O GLY V 4 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU V 6 " --> pdb=" O MET p 5 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY p 7 " --> pdb=" O LEU V 6 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'o' and resid 5 through 11 removed outlier: 6.993A pdb=" N LEU T 6 " --> pdb=" O MET o 5 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY o 7 " --> pdb=" O LEU T 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'q' and resid 3 through 11 removed outlier: 6.950A pdb=" N GLY X 4 " --> pdb=" O LEU q 3 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N MET q 5 " --> pdb=" O GLY X 4 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU X 6 " --> pdb=" O MET q 5 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N GLY q 7 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 's' and resid 3 through 6 removed outlier: 6.302A pdb=" N LEU s 3 " --> pdb=" O GLY b 4 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU b 6 " --> pdb=" O LEU s 3 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N MET s 5 " --> pdb=" O LEU b 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 's' and resid 9 through 11 removed outlier: 6.581A pdb=" N VAL s 10 " --> pdb=" O ILE b 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'r' and resid 5 through 11 removed outlier: 6.721A pdb=" N GLY r 8 " --> pdb=" O GLY Z 7 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL Z 9 " --> pdb=" O GLY r 8 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL r 10 " --> pdb=" O VAL Z 9 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE Z 11 " --> pdb=" O VAL r 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 't' and resid 5 through 11 removed outlier: 6.942A pdb=" N LEU t 6 " --> pdb=" O MET d 5 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY d 7 " --> pdb=" O LEU t 6 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLY t 8 " --> pdb=" O GLY d 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'u' and resid 5 through 11 removed outlier: 6.726A pdb=" N GLY u 8 " --> pdb=" O GLY f 7 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL f 9 " --> pdb=" O GLY u 8 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL u 10 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE f 11 " --> pdb=" O VAL u 10 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'w' and resid 3 through 11 removed outlier: 6.947A pdb=" N GLY j 4 " --> pdb=" O LEU w 3 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N MET w 5 " --> pdb=" O GLY j 4 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU j 6 " --> pdb=" O MET w 5 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY w 7 " --> pdb=" O LEU j 6 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'v' and resid 5 through 11 removed outlier: 7.004A pdb=" N LEU h 6 " --> pdb=" O MET v 5 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY v 7 " --> pdb=" O LEU h 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'y' and resid 3 through 11 removed outlier: 6.771A pdb=" N GLY y 8 " --> pdb=" O GLY z 7 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL z 9 " --> pdb=" O GLY y 8 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL y 10 " --> pdb=" O VAL z 9 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE z 11 " --> pdb=" O VAL y 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'x' and resid 5 through 11 removed outlier: 6.979A pdb=" N LEU n 6 " --> pdb=" O MET x 5 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY x 7 " --> pdb=" O LEU n 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'O' and resid 3 through 11 removed outlier: 6.954A pdb=" N GLY C 4 " --> pdb=" O LEU O 3 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET O 5 " --> pdb=" O GLY C 4 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU C 6 " --> pdb=" O MET O 5 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY O 7 " --> pdb=" O LEU C 6 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 3 through 11 removed outlier: 7.005A pdb=" N GLY E 4 " --> pdb=" O LEU S 3 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET S 5 " --> pdb=" O GLY E 4 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU E 6 " --> pdb=" O MET S 5 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY S 7 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 5 through 11 removed outlier: 6.727A pdb=" N GLY Q 8 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL D 9 " --> pdb=" O GLY Q 8 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL Q 10 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE D 11 " --> pdb=" O VAL Q 10 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'U' and resid 3 through 11 removed outlier: 6.732A pdb=" N GLY U 8 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL F 9 " --> pdb=" O GLY U 8 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL U 10 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE F 11 " --> pdb=" O VAL U 10 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 3 through 6 removed outlier: 6.340A pdb=" N LEU Y 3 " --> pdb=" O GLY H 4 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU H 6 " --> pdb=" O LEU Y 3 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N MET Y 5 " --> pdb=" O LEU H 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'Y' and resid 9 through 11 removed outlier: 6.807A pdb=" N VAL Y 10 " --> pdb=" O ILE H 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'W' and resid 5 through 11 removed outlier: 6.701A pdb=" N GLY W 8 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL G 9 " --> pdb=" O GLY W 8 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL W 10 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE G 11 " --> pdb=" O VAL W 10 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 5 through 11 removed outlier: 6.918A pdb=" N LEU a 6 " --> pdb=" O MET I 5 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY I 7 " --> pdb=" O LEU a 6 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY a 8 " --> pdb=" O GLY I 7 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'c' and resid 5 through 11 removed outlier: 6.718A pdb=" N GLY c 8 " --> pdb=" O GLY J 7 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL J 9 " --> pdb=" O GLY c 8 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL c 10 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE J 11 " --> pdb=" O VAL c 10 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'i' and resid 3 through 11 removed outlier: 6.974A pdb=" N GLY M 4 " --> pdb=" O LEU i 3 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N MET i 5 " --> pdb=" O GLY M 4 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU M 6 " --> pdb=" O MET i 5 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY i 7 " --> pdb=" O LEU M 6 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 5 through 11 removed outlier: 6.990A pdb=" N LEU L 6 " --> pdb=" O MET g 5 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY g 7 " --> pdb=" O LEU L 6 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'l' and resid 3 through 11 removed outlier: 6.975A pdb=" N GLY P 4 " --> pdb=" O LEU l 3 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET l 5 " --> pdb=" O GLY P 4 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU P 6 " --> pdb=" O MET l 5 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N GLY l 7 " --> pdb=" O LEU P 6 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'k' and resid 5 through 11 removed outlier: 6.952A pdb=" N LEU N 6 " --> pdb=" O MET k 5 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLY k 7 " --> pdb=" O LEU N 6 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '1' and resid 5 through 11 removed outlier: 9.384A pdb=" N MET 1 5 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLY B 8 " --> pdb=" O MET 1 5 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLY 1 7 " --> pdb=" O GLY B 8 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL B 10 " --> pdb=" O GLY 1 7 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL 1 9 " --> pdb=" O VAL B 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain '0' and resid 5 through 11 removed outlier: 9.457A pdb=" N MET 0 5 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N GLY A 8 " --> pdb=" O MET 0 5 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N GLY 0 7 " --> pdb=" O GLY A 8 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL A 10 " --> pdb=" O GLY 0 7 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL 0 9 " --> pdb=" O VAL A 10 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 76 hydrogen bonds defined for protein. 228 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: 0.28 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1028 1.34 - 1.46: 281 1.46 - 1.57: 1875 1.57 - 1.69: 0 1.69 - 1.80: 104 Bond restraints: 3288 Sorted by residual: bond pdb=" N LEU V 3 " pdb=" CA LEU V 3 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.22e-02 6.72e+03 6.07e+00 bond pdb=" N LEU p 3 " pdb=" CA LEU p 3 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.22e-02 6.72e+03 5.88e+00 bond pdb=" N LEU S 3 " pdb=" CA LEU S 3 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.69e+00 bond pdb=" N LEU E 3 " pdb=" CA LEU E 3 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.62e+00 bond pdb=" N ALA I 12 " pdb=" CA ALA I 12 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.90e-02 2.77e+03 1.67e+00 ... (remaining 3283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 4055 1.25 - 2.51: 215 2.51 - 3.76: 85 3.76 - 5.01: 7 5.01 - 6.26: 2 Bond angle restraints: 4364 Sorted by residual: angle pdb=" CA ALA x 12 " pdb=" C ALA x 12 " pdb=" O ALA x 12 " ideal model delta sigma weight residual 120.80 117.04 3.76 1.70e+00 3.46e-01 4.89e+00 angle pdb=" CA ALA n 12 " pdb=" C ALA n 12 " pdb=" O ALA n 12 " ideal model delta sigma weight residual 120.80 117.04 3.76 1.70e+00 3.46e-01 4.88e+00 angle pdb=" CA ALA D 12 " pdb=" C ALA D 12 " pdb=" O ALA D 12 " ideal model delta sigma weight residual 120.80 117.05 3.75 1.70e+00 3.46e-01 4.88e+00 angle pdb=" CA ALA f 12 " pdb=" C ALA f 12 " pdb=" O ALA f 12 " ideal model delta sigma weight residual 120.80 117.06 3.74 1.70e+00 3.46e-01 4.84e+00 angle pdb=" CA ALA Q 12 " pdb=" C ALA Q 12 " pdb=" O ALA Q 12 " ideal model delta sigma weight residual 120.80 117.07 3.73 1.70e+00 3.46e-01 4.82e+00 ... (remaining 4359 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.70: 1518 11.70 - 23.39: 148 23.39 - 35.09: 85 35.09 - 46.79: 31 46.79 - 58.49: 14 Dihedral angle restraints: 1796 sinusoidal: 588 harmonic: 1208 Sorted by residual: dihedral pdb=" N LEU Y 6 " pdb=" CA LEU Y 6 " pdb=" CB LEU Y 6 " pdb=" CG LEU Y 6 " ideal model delta sinusoidal sigma weight residual -60.00 -118.49 58.49 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU H 6 " pdb=" CA LEU H 6 " pdb=" CB LEU H 6 " pdb=" CG LEU H 6 " ideal model delta sinusoidal sigma weight residual -60.00 -118.47 58.47 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N MET y 5 " pdb=" CA MET y 5 " pdb=" CB MET y 5 " pdb=" CG MET y 5 " ideal model delta sinusoidal sigma weight residual -60.00 -114.57 54.57 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 1793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 290 0.034 - 0.067: 136 0.067 - 0.101: 52 0.101 - 0.134: 110 0.134 - 0.168: 4 Chirality restraints: 592 Sorted by residual: chirality pdb=" CA LEU p 3 " pdb=" N LEU p 3 " pdb=" C LEU p 3 " pdb=" CB LEU p 3 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.02e-01 chirality pdb=" CA LEU V 3 " pdb=" N LEU V 3 " pdb=" C LEU V 3 " pdb=" CB LEU V 3 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CA LEU E 3 " pdb=" N LEU E 3 " pdb=" C LEU E 3 " pdb=" CB LEU E 3 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.69e-01 ... (remaining 589 not shown) Planarity restraints: 512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO p 2 " 0.003 2.00e-02 2.50e+03 5.13e-03 2.64e-01 pdb=" C PRO p 2 " -0.009 2.00e-02 2.50e+03 pdb=" O PRO p 2 " 0.003 2.00e-02 2.50e+03 pdb=" N LEU p 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO V 2 " 0.003 2.00e-02 2.50e+03 5.09e-03 2.59e-01 pdb=" C PRO V 2 " -0.009 2.00e-02 2.50e+03 pdb=" O PRO V 2 " 0.003 2.00e-02 2.50e+03 pdb=" N LEU V 3 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY P 1 " -0.008 5.00e-02 4.00e+02 1.23e-02 2.40e-01 pdb=" N PRO P 2 " 0.021 5.00e-02 4.00e+02 pdb=" CA PRO P 2 " -0.006 5.00e-02 4.00e+02 pdb=" CD PRO P 2 " -0.007 5.00e-02 4.00e+02 ... (remaining 509 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1361 2.98 - 3.46: 2527 3.46 - 3.94: 4893 3.94 - 4.42: 4801 4.42 - 4.90: 9648 Nonbonded interactions: 23230 Sorted by model distance: nonbonded pdb=" N GLY U 1 " pdb=" O ALA f 12 " model vdw 2.500 3.120 nonbonded pdb=" N GLY X 1 " pdb=" O ALA J 12 " model vdw 2.547 3.120 nonbonded pdb=" N GLY q 1 " pdb=" O ALA c 12 " model vdw 2.548 3.120 nonbonded pdb=" O ILE k 11 " pdb=" N ALA N 12 " model vdw 2.649 3.120 nonbonded pdb=" N GLY l 8 " pdb=" O GLY l 8 " model vdw 2.656 2.496 ... (remaining 23225 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'A' selection = chain 'B' selection = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'Q' selection = chain 'T' selection = chain 'W' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'k' selection = chain 'n' selection = chain 'o' selection = chain 'r' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'x' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'b' selection = chain 'e' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'p' selection = chain 'q' selection = chain 's' selection = chain 'w' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 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: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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: 0.020 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 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 : 0.005 0.032 3288 Z= 0.274 Angle : 0.730 6.265 4364 Z= 0.354 Chirality : 0.062 0.168 592 Planarity : 0.002 0.012 512 Dihedral : 14.149 58.486 1076 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 0.00 % Allowed : 16.88 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 3288) covalent geometry : angle 0.72975 ( 4364) hydrogen bonds : bond 0.22946 ( 76) hydrogen bonds : angle 11.51070 ( 228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.131 Fit side-chains REVERT: t 5 MET cc_start: 0.7301 (mtp) cc_final: 0.6993 (mtp) REVERT: c 5 MET cc_start: 0.9070 (mtt) cc_final: 0.8856 (mtm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.4761 time to fit residues: 34.7966 Evaluate side-chains 67 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.162956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.139211 restraints weight = 2766.807| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.55 r_work: 0.3931 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3845 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3288 Z= 0.156 Angle : 0.555 4.844 4364 Z= 0.255 Chirality : 0.059 0.126 592 Planarity : 0.002 0.012 512 Dihedral : 3.235 9.891 488 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.22 % Allowed : 15.58 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.38), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3288) covalent geometry : angle 0.55523 ( 4364) hydrogen bonds : bond 0.03654 ( 76) hydrogen bonds : angle 9.36868 ( 228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.098 Fit side-chains REVERT: s 6 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8144 (mt) REVERT: t 5 MET cc_start: 0.7441 (mtp) cc_final: 0.7114 (mtp) REVERT: c 5 MET cc_start: 0.9014 (mtt) cc_final: 0.8790 (mtm) REVERT: 1 6 LEU cc_start: 0.8625 (mt) cc_final: 0.8357 (tp) outliers start: 13 outliers final: 5 residues processed: 72 average time/residue: 0.4187 time to fit residues: 31.0636 Evaluate side-chains 72 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 6 LEU Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain X residue 3 LEU Chi-restraints excluded: chain X residue 5 MET Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 22 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 12 optimal weight: 0.4980 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 overall best weight: 4.3184 ------------------------------------------------------------------------------- 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 = 0.4272 r_free = 0.4272 target = 0.160171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.136591 restraints weight = 2767.338| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.52 r_work: 0.3904 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3823 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3288 Z= 0.213 Angle : 0.628 5.252 4364 Z= 0.287 Chirality : 0.060 0.134 592 Planarity : 0.002 0.017 512 Dihedral : 3.696 10.452 488 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 6.49 % Allowed : 13.96 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.48 (0.28), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 3288) covalent geometry : angle 0.62773 ( 4364) hydrogen bonds : bond 0.03885 ( 76) hydrogen bonds : angle 9.17354 ( 228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.124 Fit side-chains REVERT: t 5 MET cc_start: 0.7515 (mtp) cc_final: 0.7247 (mtp) outliers start: 20 outliers final: 10 residues processed: 78 average time/residue: 0.4235 time to fit residues: 34.0755 Evaluate side-chains 77 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 5 MET Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain X residue 3 LEU Chi-restraints excluded: chain X residue 5 MET Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 21 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 overall best weight: 3.5586 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.161182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.137821 restraints weight = 2745.790| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.51 r_work: 0.3916 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3288 Z= 0.182 Angle : 0.584 5.288 4364 Z= 0.268 Chirality : 0.060 0.129 592 Planarity : 0.002 0.016 512 Dihedral : 3.533 10.352 488 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 5.84 % Allowed : 14.29 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.44 (0.28), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00394 ( 3288) covalent geometry : angle 0.58403 ( 4364) hydrogen bonds : bond 0.03417 ( 76) hydrogen bonds : angle 8.95365 ( 228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.090 Fit side-chains REVERT: t 5 MET cc_start: 0.7505 (mtp) cc_final: 0.7244 (mtp) REVERT: 1 6 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8417 (tp) outliers start: 18 outliers final: 7 residues processed: 75 average time/residue: 0.4349 time to fit residues: 33.5871 Evaluate side-chains 75 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 5 MET Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain X residue 3 LEU Chi-restraints excluded: chain X residue 5 MET Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 overall best weight: 4.6388 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.160090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.136545 restraints weight = 2755.015| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.51 r_work: 0.3904 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3288 Z= 0.227 Angle : 0.644 5.621 4364 Z= 0.293 Chirality : 0.060 0.132 592 Planarity : 0.002 0.019 512 Dihedral : 3.830 11.175 488 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.87 % Allowed : 15.26 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.28), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 3288) covalent geometry : angle 0.64374 ( 4364) hydrogen bonds : bond 0.03763 ( 76) hydrogen bonds : angle 9.02926 ( 228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.097 Fit side-chains REVERT: t 5 MET cc_start: 0.7483 (mtp) cc_final: 0.7230 (mtp) outliers start: 15 outliers final: 9 residues processed: 74 average time/residue: 0.4968 time to fit residues: 37.8691 Evaluate side-chains 77 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 5 MET Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain X residue 3 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.4251 r_free = 0.4251 target = 0.158781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.135234 restraints weight = 2732.215| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 1.51 r_work: 0.3889 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3803 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 3288 Z= 0.297 Angle : 0.737 5.943 4364 Z= 0.334 Chirality : 0.062 0.136 592 Planarity : 0.003 0.022 512 Dihedral : 4.230 12.330 488 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 5.19 % Allowed : 15.91 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.28), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00661 ( 3288) covalent geometry : angle 0.73655 ( 4364) hydrogen bonds : bond 0.04291 ( 76) hydrogen bonds : angle 9.20995 ( 228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.129 Fit side-chains REVERT: s 6 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8219 (mt) REVERT: t 5 MET cc_start: 0.7405 (mtp) cc_final: 0.7147 (mtp) outliers start: 16 outliers final: 12 residues processed: 75 average time/residue: 0.4712 time to fit residues: 36.4271 Evaluate side-chains 82 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 5 MET Chi-restraints excluded: chain s residue 6 LEU Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain X residue 3 LEU Chi-restraints excluded: chain X residue 5 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain F residue 5 MET Chi-restraints excluded: chain A residue 6 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 5 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.160254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.136563 restraints weight = 2794.287| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.53 r_work: 0.3907 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3820 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.022 3288 Z= 0.212 Angle : 0.631 6.228 4364 Z= 0.287 Chirality : 0.060 0.130 592 Planarity : 0.002 0.020 512 Dihedral : 3.823 11.194 488 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 5.19 % Allowed : 15.91 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.28), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3288) covalent geometry : angle 0.63111 ( 4364) hydrogen bonds : bond 0.03619 ( 76) hydrogen bonds : angle 9.04161 ( 228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.128 Fit side-chains REVERT: 1 6 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8368 (tp) outliers start: 16 outliers final: 11 residues processed: 73 average time/residue: 0.4642 time to fit residues: 34.8684 Evaluate side-chains 80 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 5 MET Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain Y residue 6 LEU Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain X residue 3 LEU Chi-restraints excluded: chain X residue 5 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain j residue 5 MET Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 0.3980 chunk 1 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.160622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.137013 restraints weight = 2791.308| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.53 r_work: 0.3909 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3836 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3288 Z= 0.197 Angle : 0.610 6.173 4364 Z= 0.278 Chirality : 0.060 0.129 592 Planarity : 0.002 0.018 512 Dihedral : 3.749 11.068 488 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 4.22 % Allowed : 16.56 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.73 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.55 (0.28), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 3288) covalent geometry : angle 0.61001 ( 4364) hydrogen bonds : bond 0.03514 ( 76) hydrogen bonds : angle 8.95406 ( 228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.083 Fit side-chains REVERT: 1 6 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8345 (tp) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.4836 time to fit residues: 35.8006 Evaluate side-chains 79 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 5 MET Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain X residue 3 LEU Chi-restraints excluded: chain X residue 5 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain j residue 5 MET Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 0.0040 chunk 11 optimal weight: 6.9990 chunk 13 optimal weight: 0.0970 chunk 1 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 3.1794 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.160971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.137670 restraints weight = 2798.702| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.52 r_work: 0.3920 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3288 Z= 0.168 Angle : 0.573 6.351 4364 Z= 0.262 Chirality : 0.059 0.126 592 Planarity : 0.002 0.018 512 Dihedral : 3.555 10.585 488 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 4.87 % Allowed : 15.91 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.28), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3288) covalent geometry : angle 0.57300 ( 4364) hydrogen bonds : bond 0.03230 ( 76) hydrogen bonds : angle 8.83035 ( 228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.141 Fit side-chains REVERT: t 5 MET cc_start: 0.7449 (mtp) cc_final: 0.7204 (mtp) REVERT: 1 6 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8298 (tp) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.4533 time to fit residues: 34.0663 Evaluate side-chains 79 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 5 MET Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain g residue 5 MET Chi-restraints excluded: chain 1 residue 6 LEU Chi-restraints excluded: chain X residue 3 LEU Chi-restraints excluded: chain X residue 5 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain j residue 5 MET Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 0.0870 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 23 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 overall best weight: 1.3762 ------------------------------------------------------------------------------- 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 = 0.4340 r_free = 0.4340 target = 0.165076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.141629 restraints weight = 2822.388| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.57 r_work: 0.3988 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3288 Z= 0.096 Angle : 0.491 6.313 4364 Z= 0.226 Chirality : 0.058 0.122 592 Planarity : 0.002 0.016 512 Dihedral : 2.983 8.992 488 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 3.25 % Allowed : 17.21 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.38), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.30 (0.29), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 3288) covalent geometry : angle 0.49122 ( 4364) hydrogen bonds : bond 0.02569 ( 76) hydrogen bonds : angle 8.44581 ( 228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.136 Fit side-chains REVERT: t 5 MET cc_start: 0.7401 (mtp) cc_final: 0.7134 (mtp) REVERT: y 5 MET cc_start: 0.8702 (mtm) cc_final: 0.8457 (mtt) outliers start: 10 outliers final: 5 residues processed: 70 average time/residue: 0.4878 time to fit residues: 35.1080 Evaluate side-chains 72 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain q residue 5 MET Chi-restraints excluded: chain U residue 5 MET Chi-restraints excluded: chain X residue 5 MET Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain F residue 5 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.0870 chunk 12 optimal weight: 7.9990 overall best weight: 4.5764 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.160324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.136683 restraints weight = 2802.790| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.53 r_work: 0.3895 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3288 Z= 0.224 Angle : 0.651 6.770 4364 Z= 0.294 Chirality : 0.060 0.130 592 Planarity : 0.002 0.018 512 Dihedral : 3.805 11.188 488 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.27 % Allowed : 17.86 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.38 (0.29), residues: 436 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3288) covalent geometry : angle 0.65104 ( 4364) hydrogen bonds : bond 0.03634 ( 76) hydrogen bonds : angle 8.84915 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1540.43 seconds wall clock time: 26 minutes 48.98 seconds (1608.98 seconds total)