Starting phenix.real_space_refine on Sat Aug 23 09:21:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u2b_41844/08_2025/8u2b_41844.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u2b_41844/08_2025/8u2b_41844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=0.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u2b_41844/08_2025/8u2b_41844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u2b_41844/08_2025/8u2b_41844.map" model { file = "/net/cci-nas-00/data/ceres_data/8u2b_41844/08_2025/8u2b_41844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u2b_41844/08_2025/8u2b_41844.cif" } resolution = 0.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.027 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: 3 Type Number sf(0) Gaussians C 7400 2.51 5 N 1776 2.21 5 O 2220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11396 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "L" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "N" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "O" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "P" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "Q" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "R" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "S" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "T" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "U" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "V" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "W" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "X" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "Y" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "Z" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "a" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "c" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "d" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "e" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "f" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "g" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "h" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "i" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "j" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "k" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "l" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "m" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "n" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "o" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "p" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "q" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "r" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "s" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Time building chain proxies: 2.86, per 1000 atoms: 0.25 Number of scatterers: 11396 At special positions: 0 Unit cell: (59.34, 57.62, 249.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2220 8.00 N 1776 7.00 C 7400 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: 1.11 Conformation dependent library (CDL) restraints added in 611.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3034 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 0 sheets defined 95.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 15 through 27 Processing helix chain 'A' and resid 27 through 57 removed outlier: 4.979A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 27 through 57 removed outlier: 4.960A pdb=" N THR J 33 " --> pdb=" O VAL J 29 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA J 34 " --> pdb=" O VAL J 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 27 Processing helix chain 'K' and resid 27 through 58 removed outlier: 3.705A pdb=" N VAL K 32 " --> pdb=" O ALA K 28 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR K 33 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ALA K 34 " --> pdb=" O VAL K 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 27 Processing helix chain 'L' and resid 27 through 57 removed outlier: 3.673A pdb=" N VAL L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N THR L 33 " --> pdb=" O VAL L 29 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ALA L 34 " --> pdb=" O VAL L 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 27 through 57 removed outlier: 5.099A pdb=" N THR M 33 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA M 34 " --> pdb=" O VAL M 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 27 through 57 removed outlier: 3.603A pdb=" N VAL N 32 " --> pdb=" O ALA N 28 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR N 33 " --> pdb=" O VAL N 29 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ALA N 34 " --> pdb=" O VAL N 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 27 Processing helix chain 'O' and resid 27 through 57 removed outlier: 3.632A pdb=" N VAL O 32 " --> pdb=" O ALA O 28 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR O 33 " --> pdb=" O VAL O 29 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA O 34 " --> pdb=" O VAL O 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 27 through 57 removed outlier: 3.540A pdb=" N VAL P 32 " --> pdb=" O ALA P 28 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR P 33 " --> pdb=" O VAL P 29 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 27 through 57 removed outlier: 3.576A pdb=" N VAL Q 32 " --> pdb=" O ALA Q 28 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N THR Q 33 " --> pdb=" O VAL Q 29 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ALA Q 34 " --> pdb=" O VAL Q 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 27 through 57 removed outlier: 3.599A pdb=" N VAL R 32 " --> pdb=" O ALA R 28 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR R 33 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ALA R 34 " --> pdb=" O VAL R 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 27 Processing helix chain 'S' and resid 27 through 57 removed outlier: 3.686A pdb=" N VAL S 32 " --> pdb=" O ALA S 28 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N THR S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ALA S 34 " --> pdb=" O VAL S 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 27 Processing helix chain 'T' and resid 27 through 57 removed outlier: 3.522A pdb=" N VAL T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR T 33 " --> pdb=" O VAL T 29 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ALA T 34 " --> pdb=" O VAL T 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 27 Processing helix chain 'U' and resid 27 through 57 removed outlier: 3.598A pdb=" N VAL U 32 " --> pdb=" O ALA U 28 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR U 33 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA U 34 " --> pdb=" O VAL U 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 16 through 27 Processing helix chain 'V' and resid 27 through 57 removed outlier: 3.503A pdb=" N ILE V 31 " --> pdb=" O ILE V 27 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL V 32 " --> pdb=" O ALA V 28 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N THR V 33 " --> pdb=" O VAL V 29 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ALA V 34 " --> pdb=" O VAL V 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 27 Processing helix chain 'W' and resid 27 through 57 removed outlier: 3.612A pdb=" N VAL W 32 " --> pdb=" O ALA W 28 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N THR W 33 " --> pdb=" O VAL W 29 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 27 through 57 removed outlier: 3.572A pdb=" N VAL X 32 " --> pdb=" O ALA X 28 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N THR X 33 " --> pdb=" O VAL X 29 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N ALA X 34 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 27 through 57 removed outlier: 3.551A pdb=" N VAL Y 32 " --> pdb=" O ALA Y 28 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N THR Y 33 " --> pdb=" O VAL Y 29 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ALA Y 34 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 27 through 57 removed outlier: 3.521A pdb=" N ILE Z 31 " --> pdb=" O ILE Z 27 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL Z 32 " --> pdb=" O ALA Z 28 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N THR Z 33 " --> pdb=" O VAL Z 29 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA Z 34 " --> pdb=" O VAL Z 30 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 27 Processing helix chain 'a' and resid 27 through 57 removed outlier: 3.543A pdb=" N VAL a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N THR a 33 " --> pdb=" O VAL a 29 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA a 34 " --> pdb=" O VAL a 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 27 Processing helix chain 'b' and resid 27 through 57 removed outlier: 3.663A pdb=" N VAL b 32 " --> pdb=" O ALA b 28 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N THR b 33 " --> pdb=" O VAL b 29 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ALA b 34 " --> pdb=" O VAL b 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 27 Processing helix chain 'c' and resid 27 through 57 removed outlier: 3.613A pdb=" N VAL c 32 " --> pdb=" O ALA c 28 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR c 33 " --> pdb=" O VAL c 29 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N ALA c 34 " --> pdb=" O VAL c 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 Processing helix chain 'd' and resid 27 through 57 removed outlier: 3.630A pdb=" N VAL d 32 " --> pdb=" O ALA d 28 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N THR d 33 " --> pdb=" O VAL d 29 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA d 34 " --> pdb=" O VAL d 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 27 Processing helix chain 'e' and resid 27 through 57 removed outlier: 3.692A pdb=" N VAL e 32 " --> pdb=" O ALA e 28 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N THR e 33 " --> pdb=" O VAL e 29 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA e 34 " --> pdb=" O VAL e 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 16 through 27 Processing helix chain 'f' and resid 27 through 57 removed outlier: 3.641A pdb=" N VAL f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR f 33 " --> pdb=" O VAL f 29 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ALA f 34 " --> pdb=" O VAL f 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 27 Processing helix chain 'g' and resid 27 through 57 removed outlier: 3.541A pdb=" N VAL g 32 " --> pdb=" O ALA g 28 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N THR g 33 " --> pdb=" O VAL g 29 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ALA g 34 " --> pdb=" O VAL g 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 16 through 27 Processing helix chain 'h' and resid 27 through 57 removed outlier: 3.597A pdb=" N VAL h 32 " --> pdb=" O ALA h 28 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR h 33 " --> pdb=" O VAL h 29 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA h 34 " --> pdb=" O VAL h 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 16 through 27 Processing helix chain 'i' and resid 27 through 57 removed outlier: 3.637A pdb=" N VAL i 32 " --> pdb=" O ALA i 28 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR i 33 " --> pdb=" O VAL i 29 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ALA i 34 " --> pdb=" O VAL i 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 16 through 27 Processing helix chain 'j' and resid 27 through 57 removed outlier: 3.604A pdb=" N VAL j 32 " --> pdb=" O ALA j 28 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR j 33 " --> pdb=" O VAL j 29 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ALA j 34 " --> pdb=" O VAL j 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 27 Processing helix chain 'k' and resid 27 through 57 removed outlier: 3.604A pdb=" N VAL k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR k 33 " --> pdb=" O VAL k 29 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ALA k 34 " --> pdb=" O VAL k 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 16 through 27 Processing helix chain 'l' and resid 27 through 57 removed outlier: 3.578A pdb=" N VAL l 32 " --> pdb=" O ALA l 28 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N THR l 33 " --> pdb=" O VAL l 29 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA l 34 " --> pdb=" O VAL l 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 16 through 27 Processing helix chain 'm' and resid 27 through 57 removed outlier: 3.644A pdb=" N VAL m 32 " --> pdb=" O ALA m 28 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N THR m 33 " --> pdb=" O VAL m 29 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ALA m 34 " --> pdb=" O VAL m 30 " (cutoff:3.500A) Processing helix chain 'n' and resid 16 through 27 Processing helix chain 'n' and resid 27 through 57 removed outlier: 3.587A pdb=" N VAL n 32 " --> pdb=" O ALA n 28 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N THR n 33 " --> pdb=" O VAL n 29 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA n 34 " --> pdb=" O VAL n 30 " (cutoff:3.500A) Processing helix chain 'o' and resid 16 through 27 Processing helix chain 'o' and resid 27 through 57 removed outlier: 3.589A pdb=" N VAL o 32 " --> pdb=" O ALA o 28 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N THR o 33 " --> pdb=" O VAL o 29 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N ALA o 34 " --> pdb=" O VAL o 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 16 through 27 Processing helix chain 'p' and resid 27 through 57 removed outlier: 3.641A pdb=" N VAL p 32 " --> pdb=" O ALA p 28 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR p 33 " --> pdb=" O VAL p 29 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ALA p 34 " --> pdb=" O VAL p 30 " (cutoff:3.500A) Processing helix chain 'q' and resid 16 through 27 Processing helix chain 'q' and resid 27 through 57 removed outlier: 3.583A pdb=" N VAL q 32 " --> pdb=" O ALA q 28 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR q 33 " --> pdb=" O VAL q 29 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ALA q 34 " --> pdb=" O VAL q 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 16 through 27 Processing helix chain 'r' and resid 27 through 57 removed outlier: 5.119A pdb=" N THR r 33 " --> pdb=" O VAL r 29 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA r 34 " --> pdb=" O VAL r 30 " (cutoff:3.500A) Processing helix chain 's' and resid 16 through 27 Processing helix chain 's' and resid 27 through 57 removed outlier: 3.675A pdb=" N VAL s 32 " --> pdb=" O ALA s 28 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N THR s 33 " --> pdb=" O VAL s 29 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA s 34 " --> pdb=" O VAL s 30 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3564 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: 2.18 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1813 1.28 - 1.35: 1665 1.35 - 1.42: 851 1.42 - 1.48: 1658 1.48 - 1.55: 5446 Bond restraints: 11433 Sorted by residual: bond pdb=" CB THR L 59 " pdb=" OG1 THR L 59 " ideal model delta sigma weight residual 1.433 1.397 0.036 1.60e-02 3.91e+03 5.03e+00 bond pdb=" CB THR J 59 " pdb=" OG1 THR J 59 " ideal model delta sigma weight residual 1.433 1.397 0.036 1.60e-02 3.91e+03 4.97e+00 bond pdb=" CB THR K 59 " pdb=" OG1 THR K 59 " ideal model delta sigma weight residual 1.433 1.399 0.034 1.60e-02 3.91e+03 4.56e+00 bond pdb=" CB THR i 36 " pdb=" OG1 THR i 36 " ideal model delta sigma weight residual 1.433 1.399 0.034 1.60e-02 3.91e+03 4.49e+00 bond pdb=" CB THR e 36 " pdb=" OG1 THR e 36 " ideal model delta sigma weight residual 1.433 1.399 0.034 1.60e-02 3.91e+03 4.47e+00 ... (remaining 11428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 9365 1.35 - 2.71: 3892 2.71 - 4.06: 1962 4.06 - 5.41: 456 5.41 - 6.76: 50 Bond angle restraints: 15725 Sorted by residual: angle pdb=" N VAL M 32 " pdb=" CA VAL M 32 " pdb=" C VAL M 32 " ideal model delta sigma weight residual 110.62 114.59 -3.97 1.02e+00 9.61e-01 1.52e+01 angle pdb=" CA ILE P 27 " pdb=" C ILE P 27 " pdb=" N ALA P 28 " ideal model delta sigma weight residual 117.37 120.24 -2.87 7.40e-01 1.83e+00 1.50e+01 angle pdb=" N THR W 16 " pdb=" CA THR W 16 " pdb=" C THR W 16 " ideal model delta sigma weight residual 111.33 115.92 -4.59 1.21e+00 6.83e-01 1.44e+01 angle pdb=" N THR q 16 " pdb=" CA THR q 16 " pdb=" C THR q 16 " ideal model delta sigma weight residual 111.33 115.89 -4.56 1.21e+00 6.83e-01 1.42e+01 angle pdb=" N THR m 16 " pdb=" CA THR m 16 " pdb=" C THR m 16 " ideal model delta sigma weight residual 111.33 115.70 -4.37 1.21e+00 6.83e-01 1.30e+01 ... (remaining 15720 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 6498 16.07 - 32.14: 89 32.14 - 48.21: 1 48.21 - 64.29: 11 64.29 - 80.36: 24 Dihedral angle restraints: 6623 sinusoidal: 1924 harmonic: 4699 Sorted by residual: dihedral pdb=" C VAL U 29 " pdb=" N VAL U 29 " pdb=" CA VAL U 29 " pdb=" CB VAL U 29 " ideal model delta harmonic sigma weight residual -122.00 -130.27 8.27 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" N VAL U 29 " pdb=" C VAL U 29 " pdb=" CA VAL U 29 " pdb=" CB VAL U 29 " ideal model delta harmonic sigma weight residual 123.40 131.61 -8.21 0 2.50e+00 1.60e-01 1.08e+01 dihedral pdb=" C VAL f 29 " pdb=" N VAL f 29 " pdb=" CA VAL f 29 " pdb=" CB VAL f 29 " ideal model delta harmonic sigma weight residual -122.00 -130.19 8.19 0 2.50e+00 1.60e-01 1.07e+01 ... (remaining 6620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1107 0.048 - 0.096: 594 0.096 - 0.143: 587 0.143 - 0.191: 87 0.191 - 0.239: 30 Chirality restraints: 2405 Sorted by residual: chirality pdb=" CA VAL U 29 " pdb=" N VAL U 29 " pdb=" C VAL U 29 " pdb=" CB VAL U 29 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR A 16 " pdb=" CA THR A 16 " pdb=" OG1 THR A 16 " pdb=" CG2 THR A 16 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB THR M 16 " pdb=" CA THR M 16 " pdb=" OG1 THR M 16 " pdb=" CG2 THR M 16 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 2402 not shown) Planarity restraints: 1813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 20 " -0.044 2.00e-02 2.50e+03 2.52e-02 1.27e+01 pdb=" CG TYR K 20 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR K 20 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR K 20 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR K 20 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR K 20 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR K 20 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 20 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR b 20 " -0.043 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR b 20 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR b 20 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR b 20 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR b 20 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR b 20 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR b 20 " -0.020 2.00e-02 2.50e+03 pdb=" OH TYR b 20 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 20 " -0.040 2.00e-02 2.50e+03 2.16e-02 9.32e+00 pdb=" CG TYR O 20 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR O 20 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR O 20 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR O 20 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR O 20 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR O 20 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR O 20 " -0.013 2.00e-02 2.50e+03 ... (remaining 1810 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 5325 2.98 - 3.46: 13515 3.46 - 3.94: 19152 3.94 - 4.42: 20366 4.42 - 4.90: 35420 Nonbonded interactions: 93778 Sorted by model distance: nonbonded pdb=" OG SER J 54 " pdb=" OXT THR J 59 " model vdw 2.506 3.040 nonbonded pdb=" OG SER L 54 " pdb=" OXT THR L 59 " model vdw 2.516 3.040 nonbonded pdb=" OG SER Y 54 " pdb=" OXT THR Y 59 " model vdw 2.522 3.040 nonbonded pdb=" OG SER K 54 " pdb=" OXT THR K 59 " model vdw 2.522 3.040 nonbonded pdb=" OG SER g 54 " pdb=" OXT THR g 59 " model vdw 2.524 3.040 ... (remaining 93773 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 'A' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' } 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: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.430 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:9.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 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 : 0.011 0.036 11433 Z= 0.690 Angle : 1.832 6.764 15725 Z= 1.194 Chirality : 0.081 0.239 2405 Planarity : 0.011 0.025 1813 Dihedral : 9.629 80.358 3589 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 0.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.19), residues: 1591 helix: 0.20 (0.12), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.044 0.011 TYR K 20 PHE 0.031 0.012 PHE s 46 Details of bonding type rmsd covalent geometry : bond 0.01096 (11433) covalent geometry : angle 1.83244 (15725) hydrogen bonds : bond 0.17120 ( 1188) hydrogen bonds : angle 5.11900 ( 3564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.414 Fit side-chains REVERT: N 19 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7265 (mt-10) REVERT: Q 19 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7174 (mt-10) REVERT: a 19 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7319 (mt-10) REVERT: n 19 GLU cc_start: 0.7586 (mt-10) cc_final: 0.6997 (mt-10) REVERT: q 41 LYS cc_start: 0.8498 (mmtt) cc_final: 0.8273 (tttt) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.2654 time to fit residues: 128.9644 Evaluate side-chains 233 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4581 r_free = 0.4581 target = 0.048258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.037348 restraints weight = 31104.645| |-----------------------------------------------------------------------------| r_work (start): 0.4194 rms_B_bonded: 2.21 r_work: 0.4125 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9296 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11433 Z= 0.144 Angle : 0.537 5.899 15725 Z= 0.291 Chirality : 0.033 0.229 2405 Planarity : 0.002 0.008 1813 Dihedral : 8.781 84.534 1702 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.92 % Allowed : 16.39 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.17 (0.21), residues: 1591 helix: 2.72 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.001 TYR A 20 PHE 0.002 0.000 PHE O 46 Details of bonding type rmsd covalent geometry : bond 0.00309 (11433) covalent geometry : angle 0.53654 (15725) hydrogen bonds : bond 0.04720 ( 1188) hydrogen bonds : angle 2.98653 ( 3564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.437 Fit side-chains REVERT: o 19 GLU cc_start: 0.9519 (mt-10) cc_final: 0.9160 (mt-10) REVERT: q 19 GLU cc_start: 0.9302 (mt-10) cc_final: 0.9065 (mt-10) outliers start: 22 outliers final: 7 residues processed: 260 average time/residue: 0.2516 time to fit residues: 77.0699 Evaluate side-chains 205 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 198 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.047797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.036767 restraints weight = 31233.833| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.27 r_work: 0.4142 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11433 Z= 0.128 Angle : 0.496 6.744 15725 Z= 0.260 Chirality : 0.030 0.199 2405 Planarity : 0.002 0.009 1813 Dihedral : 8.051 89.672 1702 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.62 % Allowed : 20.49 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.97 (0.21), residues: 1591 helix: 3.21 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR T 20 PHE 0.003 0.000 PHE o 46 Details of bonding type rmsd covalent geometry : bond 0.00283 (11433) covalent geometry : angle 0.49636 (15725) hydrogen bonds : bond 0.04014 ( 1188) hydrogen bonds : angle 2.91226 ( 3564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 0.434 Fit side-chains REVERT: q 31 ILE cc_start: 0.9262 (mm) cc_final: 0.9055 (mp) REVERT: s 19 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8942 (mt-10) outliers start: 30 outliers final: 12 residues processed: 266 average time/residue: 0.2747 time to fit residues: 85.1317 Evaluate side-chains 215 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 140 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 146 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4605 r_free = 0.4605 target = 0.047946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.036914 restraints weight = 30878.862| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 2.27 r_work: 0.4156 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3927 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 11433 Z= 0.121 Angle : 0.484 6.351 15725 Z= 0.252 Chirality : 0.029 0.202 2405 Planarity : 0.002 0.010 1813 Dihedral : 7.567 89.724 1702 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.62 % Allowed : 22.32 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 5.03 (0.21), residues: 1591 helix: 3.25 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR o 20 PHE 0.003 0.000 PHE c 46 Details of bonding type rmsd covalent geometry : bond 0.00266 (11433) covalent geometry : angle 0.48398 (15725) hydrogen bonds : bond 0.03760 ( 1188) hydrogen bonds : angle 2.88811 ( 3564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 0.494 Fit side-chains REVERT: q 19 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9261 (mt-10) REVERT: q 31 ILE cc_start: 0.9270 (mm) cc_final: 0.9061 (mp) REVERT: s 19 GLU cc_start: 0.9194 (mt-10) cc_final: 0.8895 (mt-10) REVERT: s 41 LYS cc_start: 0.4417 (OUTLIER) cc_final: 0.2546 (mttt) outliers start: 30 outliers final: 15 residues processed: 247 average time/residue: 0.2408 time to fit residues: 69.7460 Evaluate side-chains 212 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 50 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.046636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.035500 restraints weight = 30824.497| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 2.26 r_work: 0.4120 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3898 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11433 Z= 0.154 Angle : 0.512 9.015 15725 Z= 0.262 Chirality : 0.030 0.204 2405 Planarity : 0.002 0.010 1813 Dihedral : 7.068 89.131 1702 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.84 % Allowed : 23.02 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.97 (0.21), residues: 1591 helix: 3.22 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 20 PHE 0.002 0.000 PHE l 46 Details of bonding type rmsd covalent geometry : bond 0.00369 (11433) covalent geometry : angle 0.51180 (15725) hydrogen bonds : bond 0.03944 ( 1188) hydrogen bonds : angle 2.97535 ( 3564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 200 time to evaluate : 0.414 Fit side-chains REVERT: q 19 GLU cc_start: 0.9449 (mt-10) cc_final: 0.9231 (mt-10) REVERT: s 19 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8894 (mt-10) REVERT: s 41 LYS cc_start: 0.4404 (OUTLIER) cc_final: 0.2797 (mttt) outliers start: 44 outliers final: 19 residues processed: 227 average time/residue: 0.2296 time to fit residues: 61.6194 Evaluate side-chains 205 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4650 r_free = 0.4650 target = 0.046943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.035578 restraints weight = 30986.078| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.02 r_work: 0.4162 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11433 Z= 0.121 Angle : 0.497 7.289 15725 Z= 0.254 Chirality : 0.030 0.190 2405 Planarity : 0.002 0.013 1813 Dihedral : 6.450 88.410 1702 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.57 % Allowed : 22.58 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.95 (0.21), residues: 1591 helix: 3.20 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.000 TYR o 20 PHE 0.002 0.000 PHE J 46 Details of bonding type rmsd covalent geometry : bond 0.00270 (11433) covalent geometry : angle 0.49664 (15725) hydrogen bonds : bond 0.03659 ( 1188) hydrogen bonds : angle 2.90103 ( 3564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.434 Fit side-chains REVERT: m 19 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8803 (pt0) REVERT: o 19 GLU cc_start: 0.9335 (mt-10) cc_final: 0.8994 (pt0) REVERT: p 19 GLU cc_start: 0.9378 (mt-10) cc_final: 0.8921 (pt0) REVERT: r 19 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8854 (pt0) REVERT: s 19 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8892 (mt-10) REVERT: s 23 ILE cc_start: 0.9639 (OUTLIER) cc_final: 0.9431 (mp) REVERT: s 41 LYS cc_start: 0.4494 (OUTLIER) cc_final: 0.3070 (mttt) outliers start: 41 outliers final: 22 residues processed: 245 average time/residue: 0.2765 time to fit residues: 79.3917 Evaluate side-chains 216 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain s residue 23 ILE Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 144 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 105 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 141 optimal weight: 0.1980 chunk 131 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4571 r_free = 0.4571 target = 0.046267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.035227 restraints weight = 31102.686| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 2.28 r_work: 0.4112 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3904 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11433 Z= 0.152 Angle : 0.514 6.867 15725 Z= 0.263 Chirality : 0.030 0.205 2405 Planarity : 0.002 0.011 1813 Dihedral : 5.892 80.692 1702 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.66 % Allowed : 23.28 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.87 (0.21), residues: 1591 helix: 3.15 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR J 20 PHE 0.002 0.000 PHE X 46 Details of bonding type rmsd covalent geometry : bond 0.00361 (11433) covalent geometry : angle 0.51394 (15725) hydrogen bonds : bond 0.03904 ( 1188) hydrogen bonds : angle 3.00600 ( 3564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.400 Fit side-chains REVERT: K 19 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8240 (mt-10) REVERT: K 23 ILE cc_start: 0.9344 (pp) cc_final: 0.9129 (mp) REVERT: m 19 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8723 (OUTLIER) REVERT: o 19 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9030 (pt0) REVERT: p 19 GLU cc_start: 0.9373 (mt-10) cc_final: 0.8971 (pt0) REVERT: q 26 LEU cc_start: 0.9478 (mt) cc_final: 0.9276 (mm) REVERT: r 19 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8808 (pt0) REVERT: s 19 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8889 (mt-10) REVERT: s 23 ILE cc_start: 0.9698 (OUTLIER) cc_final: 0.9473 (mp) REVERT: s 41 LYS cc_start: 0.4369 (OUTLIER) cc_final: 0.3036 (mttt) outliers start: 42 outliers final: 28 residues processed: 224 average time/residue: 0.2396 time to fit residues: 64.4017 Evaluate side-chains 215 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain U residue 23 ILE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain s residue 23 ILE Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 0.6980 chunk 140 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.045887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.034613 restraints weight = 30762.019| |-----------------------------------------------------------------------------| r_work (start): 0.4183 rms_B_bonded: 2.26 r_work: 0.4125 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3900 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11433 Z= 0.140 Angle : 0.509 6.512 15725 Z= 0.259 Chirality : 0.030 0.196 2405 Planarity : 0.002 0.011 1813 Dihedral : 5.433 71.416 1702 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.92 % Allowed : 22.93 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.79 (0.21), residues: 1591 helix: 3.10 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR o 20 PHE 0.002 0.000 PHE J 46 Details of bonding type rmsd covalent geometry : bond 0.00328 (11433) covalent geometry : angle 0.50937 (15725) hydrogen bonds : bond 0.03784 ( 1188) hydrogen bonds : angle 2.97264 ( 3564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 0.504 Fit side-chains REVERT: K 19 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8178 (mt-10) REVERT: K 23 ILE cc_start: 0.9300 (pp) cc_final: 0.9071 (mp) REVERT: m 19 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8714 (pt0) REVERT: o 19 GLU cc_start: 0.9374 (mt-10) cc_final: 0.9047 (pt0) REVERT: p 19 GLU cc_start: 0.9392 (mt-10) cc_final: 0.8995 (pt0) REVERT: q 31 ILE cc_start: 0.9287 (mm) cc_final: 0.9064 (mp) REVERT: r 19 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8838 (pt0) REVERT: s 19 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8915 (mt-10) REVERT: s 23 ILE cc_start: 0.9707 (OUTLIER) cc_final: 0.9483 (mp) REVERT: s 41 LYS cc_start: 0.4328 (OUTLIER) cc_final: 0.3017 (mttt) outliers start: 45 outliers final: 32 residues processed: 223 average time/residue: 0.2558 time to fit residues: 67.6349 Evaluate side-chains 220 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 23 ILE Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 26 LEU Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 23 ILE Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 12 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4657 r_free = 0.4657 target = 0.046696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.035309 restraints weight = 30813.302| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.34 r_work: 0.4147 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11433 Z= 0.121 Angle : 0.506 7.001 15725 Z= 0.257 Chirality : 0.030 0.200 2405 Planarity : 0.002 0.011 1813 Dihedral : 4.949 65.548 1702 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.57 % Allowed : 23.28 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.76 (0.21), residues: 1591 helix: 3.09 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.000 TYR m 20 PHE 0.002 0.000 PHE T 46 Details of bonding type rmsd covalent geometry : bond 0.00268 (11433) covalent geometry : angle 0.50630 (15725) hydrogen bonds : bond 0.03611 ( 1188) hydrogen bonds : angle 2.93592 ( 3564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 208 time to evaluate : 0.376 Fit side-chains REVERT: K 19 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8275 (mt-10) REVERT: K 23 ILE cc_start: 0.9366 (pp) cc_final: 0.9091 (mp) REVERT: m 19 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8816 (pt0) REVERT: o 19 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8991 (pt0) REVERT: p 19 GLU cc_start: 0.9361 (mt-10) cc_final: 0.8909 (pt0) REVERT: q 19 GLU cc_start: 0.9340 (mt-10) cc_final: 0.8703 (pt0) REVERT: q 26 LEU cc_start: 0.9357 (mt) cc_final: 0.9117 (mm) REVERT: q 31 ILE cc_start: 0.9271 (mm) cc_final: 0.9050 (mp) REVERT: r 19 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8831 (pt0) REVERT: s 19 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8971 (mt-10) REVERT: s 41 LYS cc_start: 0.4386 (OUTLIER) cc_final: 0.3809 (tttp) outliers start: 41 outliers final: 29 residues processed: 234 average time/residue: 0.2127 time to fit residues: 59.5987 Evaluate side-chains 227 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain l residue 19 GLU Chi-restraints excluded: chain m residue 42 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 126 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 45 optimal weight: 0.0030 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 = 0.4666 r_free = 0.4666 target = 0.046932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.035588 restraints weight = 30943.591| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.26 r_work: 0.4166 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3942 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11433 Z= 0.119 Angle : 0.514 7.391 15725 Z= 0.261 Chirality : 0.030 0.195 2405 Planarity : 0.002 0.011 1813 Dihedral : 4.625 63.155 1702 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.88 % Allowed : 24.15 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.76 (0.22), residues: 1591 helix: 3.08 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR o 20 PHE 0.001 0.000 PHE J 46 Details of bonding type rmsd covalent geometry : bond 0.00260 (11433) covalent geometry : angle 0.51427 (15725) hydrogen bonds : bond 0.03555 ( 1188) hydrogen bonds : angle 2.95068 ( 3564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3182 Ramachandran restraints generated. 1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.469 Fit side-chains REVERT: K 19 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8219 (mt-10) REVERT: K 23 ILE cc_start: 0.9339 (pp) cc_final: 0.9077 (mp) REVERT: m 19 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8701 (pt0) REVERT: o 19 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9015 (pt0) REVERT: p 19 GLU cc_start: 0.9364 (mt-10) cc_final: 0.8938 (pt0) REVERT: q 19 GLU cc_start: 0.9344 (mt-10) cc_final: 0.8765 (pt0) REVERT: q 31 ILE cc_start: 0.9277 (mm) cc_final: 0.9048 (mp) REVERT: r 19 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8838 (pt0) REVERT: s 19 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8946 (mt-10) REVERT: s 41 LYS cc_start: 0.4168 (OUTLIER) cc_final: 0.3655 (tttp) outliers start: 33 outliers final: 24 residues processed: 234 average time/residue: 0.2414 time to fit residues: 67.7889 Evaluate side-chains 219 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain U residue 30 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 30 VAL Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain h residue 29 VAL Chi-restraints excluded: chain i residue 30 VAL Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain o residue 29 VAL Chi-restraints excluded: chain p residue 29 VAL Chi-restraints excluded: chain q residue 29 VAL Chi-restraints excluded: chain r residue 29 VAL Chi-restraints excluded: chain s residue 41 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 5 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 = 0.4648 r_free = 0.4648 target = 0.047885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.036116 restraints weight = 30202.732| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 2.41 r_work: 0.4117 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9327 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11433 Z= 0.123 Angle : 0.523 8.751 15725 Z= 0.266 Chirality : 0.031 0.344 2405 Planarity : 0.002 0.011 1813 Dihedral : 4.447 61.361 1702 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.70 % Allowed : 24.76 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.71 (0.22), residues: 1591 helix: 3.05 (0.13), residues: 1591 sheet: None (None), residues: 0 loop : None (None), residues: 0 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR r 20 PHE 0.002 0.000 PHE M 46 Details of bonding type rmsd covalent geometry : bond 0.00277 (11433) covalent geometry : angle 0.52278 (15725) hydrogen bonds : bond 0.03561 ( 1188) hydrogen bonds : angle 2.99651 ( 3564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27342.15 seconds wall clock time: 460 minutes 57.73 seconds (27657.73 seconds total)