Starting phenix.real_space_refine on Thu Dec 7 18:11:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz8_34392/12_2023/8gz8_34392.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz8_34392/12_2023/8gz8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz8_34392/12_2023/8gz8_34392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz8_34392/12_2023/8gz8_34392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz8_34392/12_2023/8gz8_34392.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz8_34392/12_2023/8gz8_34392.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 1.92, per 1000 atoms: 0.58 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 596.0 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: 0.59 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: 0.82 Time building geometry restraints manager: 1.18 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: 99.49 - 105.26: 120 105.26 - 111.02: 1312 111.02 - 116.79: 1264 116.79 - 122.55: 978 122.55 - 128.32: 690 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 2.520 nonbonded pdb=" N GLY X 1 " pdb=" O ALA J 12 " model vdw 2.547 2.520 nonbonded pdb=" N GLY q 1 " pdb=" O ALA c 12 " model vdw 2.548 2.520 nonbonded pdb=" O ILE k 11 " pdb=" N ALA N 12 " model vdw 2.649 2.520 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 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: 2.110 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: 9.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.030 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 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:10.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.670 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 1.0526 time to fit residues: 76.9679 Evaluate side-chains 67 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.302 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3496 ------------------------------------------------------------------------------- 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: 6.9990 chunk 18 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 : 0.002 0.014 3288 Z= 0.154 Angle : 0.494 4.531 4364 Z= 0.231 Chirality : 0.058 0.122 592 Planarity : 0.002 0.010 512 Dihedral : 2.876 9.013 488 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Rotamer: Outliers : 4.55 % Allowed : 14.94 % 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: -0.32 (0.38), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.23 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 82 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.367 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 73 average time/residue: 1.0218 time to fit residues: 76.9065 Evaluate side-chains 73 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.309 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 2 residues processed: 4 average time/residue: 0.7741 time to fit residues: 3.5793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1103 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= 0.412 Angle : 0.701 5.923 4364 Z= 0.319 Chirality : 0.062 0.138 592 Planarity : 0.003 0.019 512 Dihedral : 3.923 11.108 488 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 5.19 % Allowed : 14.94 % 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 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.349 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 79 average time/residue: 0.9822 time to fit residues: 80.1095 Evaluate side-chains 76 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.8946 time to fit residues: 5.0150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 3288 Z= 0.392 Angle : 0.692 5.027 4364 Z= 0.314 Chirality : 0.061 0.136 592 Planarity : 0.003 0.021 512 Dihedral : 3.981 11.562 488 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 5.84 % Allowed : 14.61 % 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 (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: -0.81 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.61 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 86 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.904 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 77 average time/residue: 0.9644 time to fit residues: 76.7687 Evaluate side-chains 77 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 4 residues processed: 5 average time/residue: 0.6502 time to fit residues: 3.7886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 overall best weight: 6.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1243 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= 0.430 Angle : 0.720 5.286 4364 Z= 0.327 Chirality : 0.062 0.136 592 Planarity : 0.003 0.023 512 Dihedral : 4.144 12.151 488 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.22 % Allowed : 16.23 % 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 (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: -0.86 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 81 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.372 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 74 average time/residue: 0.9946 time to fit residues: 75.9796 Evaluate side-chains 77 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.7008 time to fit residues: 4.7694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 13 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 9 optimal weight: 0.0050 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3288 Z= 0.185 Angle : 0.528 5.150 4364 Z= 0.242 Chirality : 0.059 0.125 592 Planarity : 0.002 0.019 512 Dihedral : 3.353 9.677 488 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -0.59 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.44 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 81 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.341 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 74 average time/residue: 1.0257 time to fit residues: 78.2428 Evaluate side-chains 75 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 68 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.5446 time to fit residues: 2.6515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 0.0060 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 9 optimal weight: 0.0030 overall best weight: 3.1810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 3288 Z= 0.244 Angle : 0.569 5.330 4364 Z= 0.261 Chirality : 0.059 0.127 592 Planarity : 0.002 0.017 512 Dihedral : 3.570 10.338 488 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.90 % Allowed : 16.88 % 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: -0.56 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.42 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.367 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 74 average time/residue: 0.9986 time to fit residues: 76.2350 Evaluate side-chains 77 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 3 residues processed: 6 average time/residue: 0.6914 time to fit residues: 4.6928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 0.2980 chunk 13 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 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 0.028 3288 Z= 0.388 Angle : 0.683 5.737 4364 Z= 0.311 Chirality : 0.061 0.133 592 Planarity : 0.003 0.020 512 Dihedral : 4.087 11.616 488 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.25 % Allowed : 17.53 % 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: -0.71 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.53 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 77 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.364 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 73 average time/residue: 0.9905 time to fit residues: 74.5480 Evaluate side-chains 74 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 1.1701 time to fit residues: 2.8035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1346 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= 0.245 Angle : 0.575 5.943 4364 Z= 0.263 Chirality : 0.059 0.128 592 Planarity : 0.002 0.018 512 Dihedral : 3.610 10.804 488 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.27 % Allowed : 18.18 % 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 (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: -0.63 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.47 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile *********************** 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 74 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.299 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 72 average time/residue: 1.0347 time to fit residues: 76.7776 Evaluate side-chains 74 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.5719 time to fit residues: 1.6123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 16 optimal weight: 0.0060 chunk 1 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 overall best weight: 3.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3288 Z= 0.284 Angle : 0.603 6.066 4364 Z= 0.275 Chirality : 0.059 0.129 592 Planarity : 0.002 0.018 512 Dihedral : 3.738 11.186 488 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: -0.60 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.44 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ********************** 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 fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.397 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 1.0589 time to fit residues: 78.5719 Evaluate side-chains 73 residues out of total 308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.365 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 1.2020 time to fit residues: 2.8813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 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 = 0.4247 r_free = 0.4247 target = 0.156390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.131137 restraints weight = 2758.153| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 1.65 r_work: 0.3874 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3288 Z= 0.448 Angle : 0.740 7.097 4364 Z= 0.334 Chirality : 0.062 0.134 592 Planarity : 0.003 0.021 512 Dihedral : 4.264 12.084 488 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.36 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 (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: -0.76 (0.37), residues: 436 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.57 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1811.45 seconds wall clock time: 32 minutes 38.95 seconds (1958.95 seconds total)