Starting phenix.real_space_refine on Wed Mar 5 18:30:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gz8_34392/03_2025/8gz8_34392.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gz8_34392/03_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_34392/03_2025/8gz8_34392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gz8_34392/03_2025/8gz8_34392.map" model { file = "/net/cci-nas-00/data/ceres_data/8gz8_34392/03_2025/8gz8_34392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gz8_34392/03_2025/8gz8_34392.cif" } resolution = 2.35 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= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.96, per 1000 atoms: 0.89 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: 0.77 Conformation dependent library (CDL) restraints added in 405.6 milliseconds 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: 0.48 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: 0.65 Time building geometry restraints manager: 0.83 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.210 ------------------------------------------------------------------------------- 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= 0.376 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 : 6.32 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 (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: -0.71 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 436 *********************** 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 : 0.367 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: 1.1103 time to fit residues: 81.1682 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 : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.163277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.139705 restraints weight = 2741.688| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 1.54 r_work: 0.3938 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3288 Z= 0.213 Angle : 0.546 4.752 4364 Z= 0.253 Chirality : 0.059 0.126 592 Planarity : 0.002 0.011 512 Dihedral : 3.193 9.749 488 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 4.22 % Allowed : 15.26 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.38), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.34 (0.29), residues: 436 *********************** 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 81 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.335 Fit side-chains REVERT: s 6 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8149 (mt) REVERT: t 5 MET cc_start: 0.7444 (mtp) cc_final: 0.7120 (mtp) REVERT: c 5 MET cc_start: 0.9005 (mtt) cc_final: 0.8794 (mtm) REVERT: 1 6 LEU cc_start: 0.8625 (mt) cc_final: 0.8364 (tp) outliers start: 13 outliers final: 5 residues processed: 73 average time/residue: 1.0858 time to fit residues: 81.6158 Evaluate side-chains 73 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 8 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.158325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.134825 restraints weight = 2685.465| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 1.49 r_work: 0.3876 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3793 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.037 3288 Z= 0.520 Angle : 0.783 5.540 4364 Z= 0.356 Chirality : 0.064 0.142 592 Planarity : 0.003 0.022 512 Dihedral : 4.284 12.241 488 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 6.49 % Allowed : 14.61 % 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 (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: -0.87 (0.36), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.28), residues: 436 *********************** 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 91 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.384 Fit side-chains REVERT: s 6 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8279 (mt) REVERT: t 5 MET cc_start: 0.7492 (mtp) cc_final: 0.7218 (mtp) outliers start: 20 outliers final: 10 residues processed: 81 average time/residue: 1.0508 time to fit residues: 87.7695 Evaluate side-chains 80 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 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 7 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.160725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.137257 restraints weight = 2757.437| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 1.51 r_work: 0.3906 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3825 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3288 Z= 0.278 Angle : 0.604 5.444 4364 Z= 0.275 Chirality : 0.060 0.130 592 Planarity : 0.002 0.019 512 Dihedral : 3.681 10.745 488 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 5.52 % Allowed : 15.26 % 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 (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: -0.75 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.28), residues: 436 *********************** 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: 17 poor density : 68 time to evaluate : 0.359 Fit side-chains REVERT: t 5 MET cc_start: 0.7565 (mtp) cc_final: 0.7304 (mtp) REVERT: 1 6 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8372 (tp) outliers start: 17 outliers final: 10 residues processed: 75 average time/residue: 1.0874 time to fit residues: 83.9887 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 : 0.331 ------------------------------------------------------------------------------- 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 i residue 3 LEU 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 C residue 3 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 5 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.159937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.136366 restraints weight = 2746.088| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.51 r_work: 0.3896 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1247 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= 0.337 Angle : 0.651 5.692 4364 Z= 0.296 Chirality : 0.060 0.133 592 Planarity : 0.002 0.019 512 Dihedral : 3.896 11.357 488 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 6.49 % Allowed : 14.61 % 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 (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: -0.79 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.28), residues: 436 *********************** 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 88 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.368 Fit side-chains REVERT: t 5 MET cc_start: 0.7514 (mtp) cc_final: 0.7256 (mtp) outliers start: 20 outliers final: 12 residues processed: 75 average time/residue: 1.1001 time to fit residues: 84.8841 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 : 0.360 ------------------------------------------------------------------------------- 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 C residue 3 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 2 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- 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 = 0.4250 r_free = 0.4250 target = 0.158874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.135179 restraints weight = 2799.158| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 1.53 r_work: 0.3886 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1275 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= 0.451 Angle : 0.733 5.909 4364 Z= 0.333 Chirality : 0.062 0.135 592 Planarity : 0.003 0.022 512 Dihedral : 4.206 12.244 488 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 5.52 % Allowed : 15.58 % 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 (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: -0.87 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.65 (0.28), residues: 436 *********************** 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 84 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.410 Fit side-chains REVERT: t 5 MET cc_start: 0.7407 (mtp) cc_final: 0.7140 (mtp) outliers start: 17 outliers final: 13 residues processed: 73 average time/residue: 1.1130 time to fit residues: 83.7307 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 : 0.391 ------------------------------------------------------------------------------- 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 C residue 3 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 21 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.158968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.135319 restraints weight = 2735.829| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.51 r_work: 0.3889 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 3288 Z= 0.438 Angle : 0.725 5.925 4364 Z= 0.330 Chirality : 0.062 0.135 592 Planarity : 0.003 0.022 512 Dihedral : 4.213 12.275 488 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.22 % Allowed : 16.88 % 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 (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: -0.90 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.28), residues: 436 *********************** 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 80 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.313 Fit side-chains REVERT: t 5 MET cc_start: 0.7506 (mtp) cc_final: 0.7255 (mtp) outliers start: 13 outliers final: 12 residues processed: 71 average time/residue: 1.0813 time to fit residues: 79.0285 Evaluate side-chains 79 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 C residue 3 LEU 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 12 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.4282 r_free = 0.4282 target = 0.161589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.138124 restraints weight = 2769.154| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.53 r_work: 0.3922 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3288 Z= 0.223 Angle : 0.559 5.839 4364 Z= 0.256 Chirality : 0.059 0.126 592 Planarity : 0.002 0.019 512 Dihedral : 3.526 10.479 488 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.22 % Allowed : 17.21 % Favored : 78.57 % 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: -0.69 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.52 (0.28), residues: 436 *********************** 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 80 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.376 Fit side-chains REVERT: y 5 MET cc_start: 0.8733 (mtm) cc_final: 0.8488 (mtt) REVERT: 1 6 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8324 (tp) outliers start: 13 outliers final: 9 residues processed: 71 average time/residue: 1.0856 time to fit residues: 79.3550 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 : 0.343 ------------------------------------------------------------------------------- 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 F residue 5 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 11 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 0.0470 chunk 20 optimal weight: 0.0050 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 18 optimal weight: 10.0000 overall best weight: 1.0192 ------------------------------------------------------------------------------- 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 = 0.4346 r_free = 0.4346 target = 0.164881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.140607 restraints weight = 2812.430| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 1.65 r_work: 0.4001 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3915 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3288 Z= 0.119 Angle : 0.472 5.801 4364 Z= 0.218 Chirality : 0.058 0.119 592 Planarity : 0.002 0.017 512 Dihedral : 2.783 8.566 488 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.90 % Allowed : 17.21 % 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 (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: -0.41 (0.38), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.30 (0.29), residues: 436 *********************** 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 79 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.362 Fit side-chains REVERT: p 3 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8535 (tt) REVERT: t 5 MET cc_start: 0.7460 (mtp) cc_final: 0.7195 (mtp) REVERT: y 5 MET cc_start: 0.8692 (mtm) cc_final: 0.8451 (mtt) outliers start: 12 outliers final: 6 residues processed: 72 average time/residue: 1.1160 time to fit residues: 82.7625 Evaluate side-chains 73 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain p residue 3 LEU 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 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 3 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 18 optimal weight: 0.0370 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 overall best weight: 4.0064 ------------------------------------------------------------------------------- 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 = 0.4264 r_free = 0.4264 target = 0.160431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.137163 restraints weight = 2723.035| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 1.49 r_work: 0.3914 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3288 Z= 0.297 Angle : 0.613 6.365 4364 Z= 0.279 Chirality : 0.060 0.129 592 Planarity : 0.002 0.019 512 Dihedral : 3.674 10.914 488 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.27 % Allowed : 17.21 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.38), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.34 (0.29), residues: 436 ********************** 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 75 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.361 Fit side-chains REVERT: t 5 MET cc_start: 0.7336 (mtp) cc_final: 0.7080 (mtp) REVERT: y 5 MET cc_start: 0.8751 (mtm) cc_final: 0.8504 (mtt) outliers start: 7 outliers final: 5 residues processed: 70 average time/residue: 1.1292 time to fit residues: 81.2895 Evaluate side-chains 73 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.161461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.137962 restraints weight = 2731.356| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 1.51 r_work: 0.3923 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3288 Z= 0.259 Angle : 0.590 6.616 4364 Z= 0.268 Chirality : 0.059 0.127 592 Planarity : 0.002 0.018 512 Dihedral : 3.587 10.764 488 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.92 % Allowed : 16.88 % 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 (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: -0.48 (0.38), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.36 (0.29), residues: 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.67 seconds wall clock time: 54 minutes 47.96 seconds (3287.96 seconds total)