Starting phenix.real_space_refine on Mon Oct 14 15:34:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub3_42075/10_2024/8ub3_42075.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub3_42075/10_2024/8ub3_42075.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub3_42075/10_2024/8ub3_42075.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub3_42075/10_2024/8ub3_42075.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub3_42075/10_2024/8ub3_42075.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ub3_42075/10_2024/8ub3_42075.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.403 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: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 21640 2.51 5 N 6120 2.21 5 O 6680 1.98 5 H 36780 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 71260 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "B" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "C" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "D" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "E" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "F" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "G" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "H" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "J" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "K" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "L" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "M" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "Q" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "U" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "c" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "k" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "s" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "w" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "4" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Chain: "Z" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3563 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 3, 'TRANS': 220} Time building chain proxies: 24.05, per 1000 atoms: 0.34 Number of scatterers: 71260 At special positions: 0 Unit cell: (143.85, 141.75, 165.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 6680 8.00 N 6120 7.00 C 21640 6.00 H 36780 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 14.60 Conformation dependent library (CDL) restraints added in 4.3 seconds 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8840 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 0 sheets defined 95.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 1 through 35 removed outlier: 3.507A pdb=" N GLU A 5 " --> pdb=" O GLY A 1 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 76 removed outlier: 3.764A pdb=" N LEU A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 112 Processing helix chain 'A' and resid 114 through 150 Processing helix chain 'A' and resid 154 through 188 Processing helix chain 'A' and resid 190 through 224 Processing helix chain 'B' and resid 2 through 35 removed outlier: 3.675A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 76 removed outlier: 3.771A pdb=" N LEU B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 112 Processing helix chain 'B' and resid 114 through 150 Processing helix chain 'B' and resid 154 through 188 Processing helix chain 'B' and resid 190 through 224 Processing helix chain 'C' and resid 2 through 35 removed outlier: 3.724A pdb=" N LEU C 7 " --> pdb=" O GLU C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 76 removed outlier: 3.747A pdb=" N LEU C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 112 Processing helix chain 'C' and resid 114 through 150 Processing helix chain 'C' and resid 154 through 188 Processing helix chain 'C' and resid 190 through 224 Processing helix chain 'D' and resid 2 through 35 removed outlier: 3.722A pdb=" N LEU D 7 " --> pdb=" O GLU D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 76 removed outlier: 3.762A pdb=" N LEU D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 112 Processing helix chain 'D' and resid 114 through 150 Processing helix chain 'D' and resid 154 through 188 Processing helix chain 'D' and resid 190 through 224 Processing helix chain 'E' and resid 2 through 35 removed outlier: 3.721A pdb=" N LEU E 7 " --> pdb=" O GLU E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 76 removed outlier: 3.765A pdb=" N LEU E 70 " --> pdb=" O ALA E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 112 Processing helix chain 'E' and resid 114 through 150 Processing helix chain 'E' and resid 154 through 188 Processing helix chain 'E' and resid 190 through 224 Processing helix chain 'F' and resid 2 through 35 removed outlier: 3.722A pdb=" N LEU F 7 " --> pdb=" O GLU F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 76 removed outlier: 3.746A pdb=" N LEU F 70 " --> pdb=" O ALA F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 112 Processing helix chain 'F' and resid 114 through 150 Processing helix chain 'F' and resid 154 through 188 Processing helix chain 'F' and resid 190 through 224 Processing helix chain 'G' and resid 2 through 35 removed outlier: 3.727A pdb=" N LEU G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 76 removed outlier: 3.750A pdb=" N LEU G 70 " --> pdb=" O ALA G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 112 Processing helix chain 'G' and resid 114 through 150 Processing helix chain 'G' and resid 154 through 188 Processing helix chain 'G' and resid 190 through 224 Processing helix chain 'H' and resid 2 through 35 removed outlier: 3.719A pdb=" N LEU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 76 removed outlier: 3.764A pdb=" N LEU H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 112 Processing helix chain 'H' and resid 114 through 150 Processing helix chain 'H' and resid 154 through 188 Processing helix chain 'H' and resid 190 through 224 Processing helix chain 'J' and resid 2 through 35 removed outlier: 3.720A pdb=" N LEU J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 76 removed outlier: 3.764A pdb=" N LEU J 70 " --> pdb=" O ALA J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 112 Processing helix chain 'J' and resid 114 through 150 Processing helix chain 'J' and resid 154 through 188 Processing helix chain 'J' and resid 190 through 224 Processing helix chain 'K' and resid 2 through 35 removed outlier: 3.727A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 76 removed outlier: 3.746A pdb=" N LEU K 70 " --> pdb=" O ALA K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 112 Processing helix chain 'K' and resid 114 through 150 Processing helix chain 'K' and resid 154 through 188 Processing helix chain 'K' and resid 190 through 224 Processing helix chain 'L' and resid 2 through 35 removed outlier: 3.676A pdb=" N LEU L 7 " --> pdb=" O GLU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 76 removed outlier: 3.770A pdb=" N LEU L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 112 Processing helix chain 'L' and resid 114 through 150 Processing helix chain 'L' and resid 154 through 188 Processing helix chain 'L' and resid 190 through 224 Processing helix chain 'M' and resid 2 through 35 removed outlier: 3.679A pdb=" N LEU M 7 " --> pdb=" O GLU M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 40 through 76 removed outlier: 3.768A pdb=" N LEU M 70 " --> pdb=" O ALA M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 112 Processing helix chain 'M' and resid 114 through 150 Processing helix chain 'M' and resid 154 through 188 Processing helix chain 'M' and resid 190 through 224 Processing helix chain 'Q' and resid 2 through 35 removed outlier: 3.642A pdb=" N LEU Q 7 " --> pdb=" O GLU Q 3 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 76 removed outlier: 3.766A pdb=" N LEU Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 112 Processing helix chain 'Q' and resid 114 through 150 Processing helix chain 'Q' and resid 154 through 188 Processing helix chain 'Q' and resid 190 through 224 Processing helix chain 'U' and resid 2 through 35 removed outlier: 3.702A pdb=" N LEU U 7 " --> pdb=" O GLU U 3 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 76 removed outlier: 3.748A pdb=" N LEU U 70 " --> pdb=" O ALA U 66 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 112 Processing helix chain 'U' and resid 114 through 150 Processing helix chain 'U' and resid 154 through 188 Processing helix chain 'U' and resid 190 through 224 Processing helix chain 'c' and resid 2 through 35 removed outlier: 3.671A pdb=" N LEU c 7 " --> pdb=" O GLU c 3 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 76 removed outlier: 3.795A pdb=" N LEU c 70 " --> pdb=" O ALA c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 112 Processing helix chain 'c' and resid 114 through 150 Processing helix chain 'c' and resid 154 through 188 Processing helix chain 'c' and resid 190 through 224 Processing helix chain 'k' and resid 2 through 35 removed outlier: 3.703A pdb=" N LEU k 7 " --> pdb=" O GLU k 3 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 76 removed outlier: 3.752A pdb=" N LEU k 70 " --> pdb=" O ALA k 66 " (cutoff:3.500A) Processing helix chain 'k' and resid 77 through 112 Processing helix chain 'k' and resid 114 through 150 Processing helix chain 'k' and resid 154 through 188 Processing helix chain 'k' and resid 190 through 224 Processing helix chain 's' and resid 2 through 35 removed outlier: 3.678A pdb=" N LEU s 7 " --> pdb=" O GLU s 3 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 76 removed outlier: 3.770A pdb=" N LEU s 70 " --> pdb=" O ALA s 66 " (cutoff:3.500A) Processing helix chain 's' and resid 77 through 112 Processing helix chain 's' and resid 114 through 150 Processing helix chain 's' and resid 154 through 188 Processing helix chain 's' and resid 190 through 224 Processing helix chain 'w' and resid 2 through 35 removed outlier: 3.667A pdb=" N LEU w 7 " --> pdb=" O GLU w 3 " (cutoff:3.500A) Processing helix chain 'w' and resid 40 through 76 removed outlier: 3.796A pdb=" N LEU w 70 " --> pdb=" O ALA w 66 " (cutoff:3.500A) Processing helix chain 'w' and resid 77 through 112 Processing helix chain 'w' and resid 114 through 150 Processing helix chain 'w' and resid 154 through 188 Processing helix chain 'w' and resid 190 through 224 Processing helix chain '4' and resid 2 through 35 removed outlier: 3.642A pdb=" N LEU 4 7 " --> pdb=" O GLU 4 3 " (cutoff:3.500A) Processing helix chain '4' and resid 40 through 76 removed outlier: 3.765A pdb=" N LEU 4 70 " --> pdb=" O ALA 4 66 " (cutoff:3.500A) Processing helix chain '4' and resid 77 through 112 Processing helix chain '4' and resid 114 through 150 Processing helix chain '4' and resid 154 through 188 Processing helix chain '4' and resid 190 through 224 Processing helix chain 'Z' and resid 2 through 35 removed outlier: 3.644A pdb=" N LEU Z 7 " --> pdb=" O GLU Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 76 removed outlier: 3.764A pdb=" N LEU Z 70 " --> pdb=" O ALA Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 77 through 112 Processing helix chain 'Z' and resid 114 through 150 Processing helix chain 'Z' and resid 154 through 188 Processing helix chain 'Z' and resid 190 through 224 3760 hydrogen bonds defined for protein. 11280 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: 25.00 Time building geometry restraints manager: 17.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 36780 1.03 - 1.22: 0 1.22 - 1.41: 12527 1.41 - 1.61: 22033 1.61 - 1.80: 80 Bond restraints: 71420 Sorted by residual: bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.34e+00 bond pdb=" N GLY E 1 " pdb=" CA GLY E 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.31e+00 bond pdb=" N GLY U 1 " pdb=" CA GLY U 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.29e+00 bond pdb=" N GLY A 1 " pdb=" CA GLY A 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.28e+00 bond pdb=" N GLY 4 1 " pdb=" CA GLY 4 1 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.27e+00 ... (remaining 71415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 116247 1.00 - 1.99: 13201 1.99 - 2.99: 1025 2.99 - 3.98: 143 3.98 - 4.98: 84 Bond angle restraints: 130700 Sorted by residual: angle pdb=" C ALA D 25 " pdb=" N SER D 26 " pdb=" CA SER D 26 " ideal model delta sigma weight residual 120.31 115.90 4.41 1.52e+00 4.33e-01 8.43e+00 angle pdb=" C ALA H 25 " pdb=" N SER H 26 " pdb=" CA SER H 26 " ideal model delta sigma weight residual 120.31 115.96 4.35 1.52e+00 4.33e-01 8.20e+00 angle pdb=" N LEU J 70 " pdb=" CA LEU J 70 " pdb=" C LEU J 70 " ideal model delta sigma weight residual 112.23 108.75 3.48 1.26e+00 6.30e-01 7.61e+00 angle pdb=" C ALA F 25 " pdb=" N SER F 26 " pdb=" CA SER F 26 " ideal model delta sigma weight residual 120.31 116.12 4.19 1.52e+00 4.33e-01 7.59e+00 angle pdb=" C ALA G 25 " pdb=" N SER G 26 " pdb=" CA SER G 26 " ideal model delta sigma weight residual 120.31 116.13 4.18 1.52e+00 4.33e-01 7.56e+00 ... (remaining 130695 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.07: 30970 14.07 - 28.14: 1130 28.14 - 42.21: 120 42.21 - 56.29: 100 56.29 - 70.36: 40 Dihedral angle restraints: 32360 sinusoidal: 18700 harmonic: 13660 Sorted by residual: dihedral pdb=" CD2 HIS D 204 " pdb=" CG HIS D 204 " pdb=" ND1 HIS D 204 " pdb=" HD1 HIS D 204 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CD2 HIS U 204 " pdb=" CG HIS U 204 " pdb=" ND1 HIS U 204 " pdb=" HD1 HIS U 204 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CD2 HIS M 204 " pdb=" CG HIS M 204 " pdb=" ND1 HIS M 204 " pdb=" HD1 HIS M 204 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 32357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 4386 0.034 - 0.069: 1414 0.069 - 0.103: 296 0.103 - 0.138: 41 0.138 - 0.172: 23 Chirality restraints: 6160 Sorted by residual: chirality pdb=" CA ILE K 30 " pdb=" N ILE K 30 " pdb=" C ILE K 30 " pdb=" CB ILE K 30 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CA ILE F 30 " pdb=" N ILE F 30 " pdb=" C ILE F 30 " pdb=" CB ILE F 30 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CA ILE C 30 " pdb=" N ILE C 30 " pdb=" C ILE C 30 " pdb=" CB ILE C 30 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 6157 not shown) Planarity restraints: 10360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS Z 204 " -0.003 2.00e-02 2.50e+03 4.40e-02 4.35e+01 pdb=" CG HIS Z 204 " -0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS Z 204 " -0.085 2.00e-02 2.50e+03 pdb=" CD2 HIS Z 204 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 HIS Z 204 " -0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS Z 204 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 HIS Z 204 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 HIS Z 204 " 0.037 2.00e-02 2.50e+03 pdb=" HE1 HIS Z 204 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 204 " 0.002 2.00e-02 2.50e+03 4.40e-02 4.35e+01 pdb=" CG HIS E 204 " 0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS E 204 " 0.086 2.00e-02 2.50e+03 pdb=" CD2 HIS E 204 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 204 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 HIS E 204 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS E 204 " -0.087 2.00e-02 2.50e+03 pdb=" HD2 HIS E 204 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 HIS E 204 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 204 " -0.002 2.00e-02 2.50e+03 4.40e-02 4.35e+01 pdb=" CG HIS D 204 " -0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS D 204 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 HIS D 204 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 204 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS D 204 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 HIS D 204 " 0.087 2.00e-02 2.50e+03 pdb=" HD2 HIS D 204 " 0.036 2.00e-02 2.50e+03 pdb=" HE1 HIS D 204 " -0.001 2.00e-02 2.50e+03 ... (remaining 10357 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2471 2.18 - 2.79: 155131 2.79 - 3.39: 208664 3.39 - 4.00: 257751 4.00 - 4.60: 421782 Nonbonded interactions: 1045799 Sorted by model distance: nonbonded pdb=" OE1 GLU k 196 " pdb="HH21 ARG k 199 " model vdw 1.575 2.450 nonbonded pdb=" OE1 GLU U 196 " pdb="HH21 ARG U 199 " model vdw 1.575 2.450 nonbonded pdb=" OE1 GLU 4 196 " pdb="HH21 ARG 4 199 " model vdw 1.584 2.450 nonbonded pdb=" OE1 GLU Q 196 " pdb="HH21 ARG Q 199 " model vdw 1.585 2.450 nonbonded pdb=" OE1 GLU F 196 " pdb="HH21 ARG F 199 " model vdw 1.594 2.450 ... (remaining 1045794 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 '4' 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 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'U' selection = chain 'Z' selection = chain 'c' selection = chain 'k' selection = chain 's' selection = chain 'w' } 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.920 Extract box with map and model: 1.990 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 110.680 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 34640 Z= 0.354 Angle : 0.692 4.662 46920 Z= 0.469 Chirality : 0.036 0.172 6160 Planarity : 0.006 0.027 5960 Dihedral : 9.449 70.358 13240 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.84 (0.11), residues: 4440 helix: 2.50 (0.06), residues: 4120 sheet: None (None), residues: 0 loop : 3.18 (0.52), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.027 0.008 HIS U 204 ARG 0.005 0.001 ARG K 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1088 time to evaluate : 3.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7061 (mmtp) REVERT: A 22 ARG cc_start: 0.6987 (tpp-160) cc_final: 0.6532 (tpp-160) REVERT: A 48 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7195 (mtt90) REVERT: A 83 LYS cc_start: 0.7410 (mmtt) cc_final: 0.7067 (mtpp) REVERT: A 220 GLU cc_start: 0.7145 (tt0) cc_final: 0.6654 (tp30) REVERT: B 14 LYS cc_start: 0.8110 (tttt) cc_final: 0.7670 (ttmt) REVERT: B 15 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7636 (mmtt) REVERT: B 22 ARG cc_start: 0.7396 (tpp-160) cc_final: 0.6847 (tpp-160) REVERT: B 45 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7215 (mm-30) REVERT: B 94 GLU cc_start: 0.7198 (tp30) cc_final: 0.6813 (tt0) REVERT: B 148 ARG cc_start: 0.7304 (ttp-170) cc_final: 0.6631 (ttt90) REVERT: B 159 LYS cc_start: 0.8154 (mtmt) cc_final: 0.7778 (mtpp) REVERT: B 221 LEU cc_start: 0.8450 (mt) cc_final: 0.8246 (mt) REVERT: C 8 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7137 (mmtt) REVERT: C 15 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7078 (mmtt) REVERT: C 28 ARG cc_start: 0.7812 (mpt180) cc_final: 0.7382 (mmt180) REVERT: C 52 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7214 (tt0) REVERT: C 83 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7600 (mtpp) REVERT: C 159 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7840 (mtpp) REVERT: C 177 SER cc_start: 0.8498 (m) cc_final: 0.8152 (t) REVERT: C 181 ILE cc_start: 0.7474 (mt) cc_final: 0.7219 (mt) REVERT: D 7 LEU cc_start: 0.7659 (mt) cc_final: 0.7453 (tt) REVERT: D 15 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7127 (mmtt) REVERT: D 75 VAL cc_start: 0.8189 (t) cc_final: 0.7976 (t) REVERT: D 94 GLU cc_start: 0.7258 (tp30) cc_final: 0.6843 (tt0) REVERT: D 159 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7727 (mttm) REVERT: D 210 GLU cc_start: 0.7733 (tp30) cc_final: 0.7297 (tp30) REVERT: E 7 LEU cc_start: 0.7709 (mt) cc_final: 0.7507 (tt) REVERT: E 15 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7236 (mmtt) REVERT: E 22 ARG cc_start: 0.7412 (tpp-160) cc_final: 0.6581 (tpp-160) REVERT: E 94 GLU cc_start: 0.7257 (tp30) cc_final: 0.6831 (tt0) REVERT: E 159 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7785 (mttm) REVERT: E 210 GLU cc_start: 0.7757 (tp30) cc_final: 0.7314 (tp30) REVERT: F 8 LYS cc_start: 0.7788 (mmtt) cc_final: 0.6951 (mmtt) REVERT: F 15 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7088 (mmtt) REVERT: F 28 ARG cc_start: 0.7825 (mpt180) cc_final: 0.7368 (mmt180) REVERT: F 52 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7212 (tt0) REVERT: F 83 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7541 (mtpp) REVERT: F 159 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7818 (mtpp) REVERT: F 177 SER cc_start: 0.8496 (m) cc_final: 0.8129 (t) REVERT: F 181 ILE cc_start: 0.7455 (mt) cc_final: 0.7190 (mt) REVERT: G 8 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7129 (mmtt) REVERT: G 15 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7076 (mmtt) REVERT: G 28 ARG cc_start: 0.7811 (mpt180) cc_final: 0.7380 (mmt180) REVERT: G 52 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7161 (tt0) REVERT: G 83 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7596 (mtpp) REVERT: G 159 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7836 (mtpp) REVERT: G 177 SER cc_start: 0.8506 (m) cc_final: 0.8156 (t) REVERT: G 181 ILE cc_start: 0.7483 (mt) cc_final: 0.7213 (mt) REVERT: H 7 LEU cc_start: 0.7662 (mt) cc_final: 0.7459 (tt) REVERT: H 15 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7127 (mmtt) REVERT: H 94 GLU cc_start: 0.7255 (tp30) cc_final: 0.6843 (tt0) REVERT: H 159 LYS cc_start: 0.8108 (mtmt) cc_final: 0.7717 (mttm) REVERT: H 210 GLU cc_start: 0.7732 (tp30) cc_final: 0.7294 (tp30) REVERT: J 15 LYS cc_start: 0.7808 (mmtt) cc_final: 0.7245 (mmtt) REVERT: J 22 ARG cc_start: 0.7383 (tpp-160) cc_final: 0.6584 (tpp-160) REVERT: J 94 GLU cc_start: 0.7255 (tp30) cc_final: 0.6829 (tt0) REVERT: J 159 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7791 (mttm) REVERT: J 210 GLU cc_start: 0.7762 (tp30) cc_final: 0.7320 (tp30) REVERT: K 8 LYS cc_start: 0.7784 (mmtt) cc_final: 0.6920 (mmtt) REVERT: K 15 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7081 (mmtt) REVERT: K 28 ARG cc_start: 0.7826 (mpt180) cc_final: 0.7396 (mmt180) REVERT: K 52 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7204 (tt0) REVERT: K 83 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7540 (mtpp) REVERT: K 159 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7843 (mtpp) REVERT: K 177 SER cc_start: 0.8499 (m) cc_final: 0.8133 (t) REVERT: K 181 ILE cc_start: 0.7459 (mt) cc_final: 0.7193 (mt) REVERT: L 14 LYS cc_start: 0.8111 (tttt) cc_final: 0.7671 (ttmt) REVERT: L 15 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7634 (mmtt) REVERT: L 22 ARG cc_start: 0.7393 (tpp-160) cc_final: 0.6838 (tpp-160) REVERT: L 45 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7215 (mm-30) REVERT: L 94 GLU cc_start: 0.7178 (tp30) cc_final: 0.6821 (tt0) REVERT: L 148 ARG cc_start: 0.7297 (ttp-170) cc_final: 0.6629 (ttt90) REVERT: L 159 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7781 (mtpp) REVERT: L 221 LEU cc_start: 0.8448 (mt) cc_final: 0.8243 (mt) REVERT: M 14 LYS cc_start: 0.8126 (tttt) cc_final: 0.7698 (ttmt) REVERT: M 15 LYS cc_start: 0.8195 (mmtt) cc_final: 0.7608 (mmtt) REVERT: M 22 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.6822 (tpp-160) REVERT: M 45 GLU cc_start: 0.7556 (mm-30) cc_final: 0.7253 (mm-30) REVERT: M 94 GLU cc_start: 0.7185 (tp30) cc_final: 0.6815 (tt0) REVERT: M 159 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7714 (mtpp) REVERT: M 221 LEU cc_start: 0.8408 (mt) cc_final: 0.8196 (mt) REVERT: Q 15 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7075 (mmtp) REVERT: Q 48 ARG cc_start: 0.7475 (mtt180) cc_final: 0.7181 (mtt90) REVERT: Q 83 LYS cc_start: 0.7412 (mmtt) cc_final: 0.7044 (mtpp) REVERT: Q 220 GLU cc_start: 0.7095 (tt0) cc_final: 0.6586 (tp30) REVERT: U 8 LYS cc_start: 0.7939 (mmtt) cc_final: 0.7444 (mmtt) REVERT: U 14 LYS cc_start: 0.8106 (tttt) cc_final: 0.7719 (ttmm) REVERT: U 15 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7658 (mmtt) REVERT: U 22 ARG cc_start: 0.7193 (tpp-160) cc_final: 0.6651 (tpp-160) REVERT: U 148 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.6531 (ttm-80) REVERT: U 159 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7486 (mtpp) REVERT: c 15 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7409 (mmtt) REVERT: c 28 ARG cc_start: 0.7643 (mpt180) cc_final: 0.6504 (mmm160) REVERT: c 45 GLU cc_start: 0.7350 (mm-30) cc_final: 0.7008 (mm-30) REVERT: c 83 LYS cc_start: 0.7722 (mmtt) cc_final: 0.7299 (mtpp) REVERT: c 159 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7771 (mtpp) REVERT: c 207 ILE cc_start: 0.8719 (mt) cc_final: 0.8500 (mm) REVERT: c 220 GLU cc_start: 0.7203 (tt0) cc_final: 0.6892 (mm-30) REVERT: k 8 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7452 (mmtt) REVERT: k 14 LYS cc_start: 0.8112 (tttt) cc_final: 0.7724 (ttmm) REVERT: k 15 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7664 (mmtt) REVERT: k 22 ARG cc_start: 0.7194 (tpp-160) cc_final: 0.6654 (tpp-160) REVERT: k 148 ARG cc_start: 0.7869 (ttp-170) cc_final: 0.6541 (ttm-80) REVERT: k 159 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7496 (mtpp) REVERT: s 14 LYS cc_start: 0.8128 (tttt) cc_final: 0.7701 (ttmt) REVERT: s 15 LYS cc_start: 0.8170 (mmtt) cc_final: 0.7583 (mmtt) REVERT: s 22 ARG cc_start: 0.7374 (tpp-160) cc_final: 0.6828 (tpp-160) REVERT: s 45 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7225 (mm-30) REVERT: s 94 GLU cc_start: 0.7182 (tp30) cc_final: 0.6817 (tt0) REVERT: s 159 LYS cc_start: 0.8112 (mtmt) cc_final: 0.7718 (mtpp) REVERT: s 221 LEU cc_start: 0.8406 (mt) cc_final: 0.8191 (mt) REVERT: w 15 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7416 (mmtt) REVERT: w 28 ARG cc_start: 0.7666 (mpt180) cc_final: 0.6470 (mmm160) REVERT: w 45 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7007 (mm-30) REVERT: w 83 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7299 (mtpp) REVERT: w 159 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7773 (mtpp) REVERT: w 207 ILE cc_start: 0.8720 (mt) cc_final: 0.8501 (mm) REVERT: w 220 GLU cc_start: 0.7198 (tt0) cc_final: 0.6892 (mm-30) REVERT: 4 15 LYS cc_start: 0.7854 (mmtt) cc_final: 0.7069 (mmtp) REVERT: 4 48 ARG cc_start: 0.7461 (mtt180) cc_final: 0.7172 (mtt90) REVERT: 4 83 LYS cc_start: 0.7402 (mmtt) cc_final: 0.7038 (mtpp) REVERT: 4 220 GLU cc_start: 0.7091 (tt0) cc_final: 0.6571 (tp30) REVERT: Z 15 LYS cc_start: 0.7861 (mmtt) cc_final: 0.7537 (mmtt) REVERT: Z 48 ARG cc_start: 0.7451 (mtt180) cc_final: 0.7191 (mtt90) REVERT: Z 83 LYS cc_start: 0.7418 (mmtt) cc_final: 0.7073 (mtpp) REVERT: Z 220 GLU cc_start: 0.7144 (tt0) cc_final: 0.6659 (tp30) outliers start: 0 outliers final: 0 residues processed: 1088 average time/residue: 1.1186 time to fit residues: 1854.6038 Evaluate side-chains 869 residues out of total 3760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 869 time to evaluate : 3.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 371 optimal weight: 0.7980 chunk 333 optimal weight: 0.0470 chunk 185 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 344 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 399 optimal weight: 4.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 211 ASN B 47 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 136 ASN ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 211 ASN G 136 ASN ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 136 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 ASN L 47 ASN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 ASN ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 136 ASN ** Q 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 211 ASN ** U 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 ASN ** s 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 ASN 4 136 ASN ** 4 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 211 ASN Z 136 ASN ** Z 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 211 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34640 Z= 0.228 Angle : 0.453 5.329 46920 Z= 0.268 Chirality : 0.031 0.140 6160 Planarity : 0.004 0.061 5960 Dihedral : 2.924 10.447 4720 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.44 % Allowed : 5.29 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.04 (0.11), residues: 4440 helix: 3.98 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : 2.44 (0.46), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS s 53 ARG 0.004 0.000 ARG s 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 885 time to evaluate : 4.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8088 (tttm) cc_final: 0.7756 (ttmm) REVERT: A 15 LYS cc_start: 0.7828 (mmtt) cc_final: 0.7447 (mmmt) REVERT: A 48 ARG cc_start: 0.7510 (mtt180) cc_final: 0.7248 (mtt90) REVERT: A 83 LYS cc_start: 0.7449 (mmtt) cc_final: 0.7106 (mtpp) REVERT: A 94 GLU cc_start: 0.7391 (tt0) cc_final: 0.7103 (tt0) REVERT: A 220 GLU cc_start: 0.7168 (tt0) cc_final: 0.6714 (tp30) REVERT: B 14 LYS cc_start: 0.8082 (tttt) cc_final: 0.7712 (ttmt) REVERT: B 15 LYS cc_start: 0.8246 (mmtt) cc_final: 0.7679 (mmtt) REVERT: B 45 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 69 MET cc_start: 0.8137 (mmm) cc_final: 0.7879 (tpt) REVERT: B 79 GLN cc_start: 0.7596 (mm-40) cc_final: 0.7386 (tp40) REVERT: B 94 GLU cc_start: 0.7166 (tp30) cc_final: 0.6779 (tt0) REVERT: B 116 ASP cc_start: 0.7365 (m-30) cc_final: 0.7061 (m-30) REVERT: B 120 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6689 (mm-30) REVERT: B 148 ARG cc_start: 0.7240 (ttp-170) cc_final: 0.6462 (ttt90) REVERT: B 159 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7718 (mtpp) REVERT: C 8 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7402 (mmtt) REVERT: C 15 LYS cc_start: 0.7814 (mmtt) cc_final: 0.6980 (mmtt) REVERT: C 28 ARG cc_start: 0.7787 (mpt180) cc_final: 0.7358 (mmt180) REVERT: C 52 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7180 (tt0) REVERT: C 83 LYS cc_start: 0.7966 (mmtt) cc_final: 0.7528 (mtpp) REVERT: C 127 GLU cc_start: 0.7447 (tt0) cc_final: 0.7157 (tt0) REVERT: C 159 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7760 (mtpp) REVERT: C 177 SER cc_start: 0.8497 (m) cc_final: 0.8282 (t) REVERT: D 15 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7166 (mmtt) REVERT: D 52 GLU cc_start: 0.7448 (tp30) cc_final: 0.6945 (tt0) REVERT: D 75 VAL cc_start: 0.8223 (t) cc_final: 0.8022 (t) REVERT: D 94 GLU cc_start: 0.7344 (tp30) cc_final: 0.6872 (tt0) REVERT: D 103 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7757 (ttp80) REVERT: D 107 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7248 (mm-30) REVERT: D 159 LYS cc_start: 0.8010 (mtmt) cc_final: 0.7631 (mttm) REVERT: D 210 GLU cc_start: 0.7457 (tp30) cc_final: 0.6944 (tp30) REVERT: E 15 LYS cc_start: 0.7770 (mmtt) cc_final: 0.7270 (mmtt) REVERT: E 22 ARG cc_start: 0.7443 (tpp-160) cc_final: 0.6671 (tpp-160) REVERT: E 45 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6997 (tt0) REVERT: E 52 GLU cc_start: 0.7491 (tp30) cc_final: 0.6938 (tt0) REVERT: E 94 GLU cc_start: 0.7295 (tp30) cc_final: 0.6837 (tt0) REVERT: E 103 ARG cc_start: 0.8045 (ttp80) cc_final: 0.7801 (ttp80) REVERT: E 107 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7256 (mm-30) REVERT: E 159 LYS cc_start: 0.8038 (mtmt) cc_final: 0.7683 (mttm) REVERT: E 210 GLU cc_start: 0.7471 (tp30) cc_final: 0.6949 (tp30) REVERT: F 8 LYS cc_start: 0.7858 (mmtt) cc_final: 0.6966 (mmtt) REVERT: F 15 LYS cc_start: 0.7863 (mmtt) cc_final: 0.6964 (mmtt) REVERT: F 28 ARG cc_start: 0.7789 (mpt180) cc_final: 0.7387 (mmt180) REVERT: F 52 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7176 (tt0) REVERT: F 83 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7470 (mtpp) REVERT: F 127 GLU cc_start: 0.7425 (tt0) cc_final: 0.7125 (tt0) REVERT: F 159 LYS cc_start: 0.8086 (mtmt) cc_final: 0.7761 (mtpp) REVERT: F 177 SER cc_start: 0.8483 (m) cc_final: 0.8255 (t) REVERT: F 181 ILE cc_start: 0.7374 (mt) cc_final: 0.7156 (mt) REVERT: G 8 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7360 (mmtt) REVERT: G 15 LYS cc_start: 0.7788 (mmtt) cc_final: 0.6977 (mmtt) REVERT: G 28 ARG cc_start: 0.7787 (mpt180) cc_final: 0.7356 (mmt180) REVERT: G 52 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7181 (tt0) REVERT: G 83 LYS cc_start: 0.7962 (mmtt) cc_final: 0.7523 (mtpp) REVERT: G 127 GLU cc_start: 0.7453 (tt0) cc_final: 0.7148 (tt0) REVERT: G 159 LYS cc_start: 0.8117 (mtmt) cc_final: 0.7761 (mtpp) REVERT: G 177 SER cc_start: 0.8503 (m) cc_final: 0.8290 (t) REVERT: G 181 ILE cc_start: 0.7437 (mt) cc_final: 0.7237 (mt) REVERT: H 15 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7168 (mmtt) REVERT: H 52 GLU cc_start: 0.7412 (tp30) cc_final: 0.6826 (tt0) REVERT: H 94 GLU cc_start: 0.7346 (tp30) cc_final: 0.6873 (tt0) REVERT: H 103 ARG cc_start: 0.8031 (ttp80) cc_final: 0.7778 (ttp80) REVERT: H 107 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7257 (mm-30) REVERT: H 159 LYS cc_start: 0.8009 (mtmt) cc_final: 0.7634 (mttm) REVERT: H 210 GLU cc_start: 0.7456 (tp30) cc_final: 0.6932 (tp30) REVERT: J 15 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7280 (mmtt) REVERT: J 22 ARG cc_start: 0.7419 (tpp-160) cc_final: 0.6658 (tpp-160) REVERT: J 45 GLU cc_start: 0.7236 (mm-30) cc_final: 0.6997 (tt0) REVERT: J 52 GLU cc_start: 0.7486 (tp30) cc_final: 0.6939 (tt0) REVERT: J 94 GLU cc_start: 0.7333 (tp30) cc_final: 0.6866 (tt0) REVERT: J 103 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7804 (ttp80) REVERT: J 107 GLU cc_start: 0.7482 (mm-30) cc_final: 0.7255 (mm-30) REVERT: J 159 LYS cc_start: 0.8039 (mtmt) cc_final: 0.7687 (mttm) REVERT: J 210 GLU cc_start: 0.7475 (tp30) cc_final: 0.6954 (tp30) REVERT: K 8 LYS cc_start: 0.7858 (mmtt) cc_final: 0.6967 (mmtt) REVERT: K 15 LYS cc_start: 0.7819 (mmtt) cc_final: 0.6945 (mmtt) REVERT: K 28 ARG cc_start: 0.7812 (mpt180) cc_final: 0.7398 (mmt180) REVERT: K 52 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7173 (tt0) REVERT: K 83 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7470 (mtpp) REVERT: K 127 GLU cc_start: 0.7438 (tt0) cc_final: 0.7136 (tt0) REVERT: K 159 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7759 (mtpp) REVERT: K 177 SER cc_start: 0.8488 (m) cc_final: 0.8260 (t) REVERT: K 181 ILE cc_start: 0.7378 (mt) cc_final: 0.7159 (mt) REVERT: L 14 LYS cc_start: 0.8084 (tttt) cc_final: 0.7712 (ttmt) REVERT: L 15 LYS cc_start: 0.8244 (mmtt) cc_final: 0.7675 (mmtt) REVERT: L 45 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7161 (mm-30) REVERT: L 69 MET cc_start: 0.8135 (mmm) cc_final: 0.7877 (tpt) REVERT: L 94 GLU cc_start: 0.7175 (tp30) cc_final: 0.6780 (tt0) REVERT: L 120 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6685 (mm-30) REVERT: L 148 ARG cc_start: 0.7234 (ttp-170) cc_final: 0.6465 (ttt90) REVERT: L 159 LYS cc_start: 0.8213 (mtmt) cc_final: 0.7719 (mtpp) REVERT: M 14 LYS cc_start: 0.8080 (tttt) cc_final: 0.7718 (ttmt) REVERT: M 15 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7625 (mmtt) REVERT: M 22 ARG cc_start: 0.7418 (tpp-160) cc_final: 0.6871 (tpp-160) REVERT: M 45 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7188 (mm-30) REVERT: M 69 MET cc_start: 0.8162 (tpp) cc_final: 0.7366 (tpt) REVERT: M 94 GLU cc_start: 0.7154 (tp30) cc_final: 0.6770 (tt0) REVERT: M 116 ASP cc_start: 0.7421 (m-30) cc_final: 0.7124 (m-30) REVERT: M 120 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6697 (mm-30) REVERT: M 159 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7718 (mtpp) REVERT: Q 14 LYS cc_start: 0.8084 (tttm) cc_final: 0.7741 (ttmm) REVERT: Q 15 LYS cc_start: 0.7836 (mmtt) cc_final: 0.7441 (mmmt) REVERT: Q 48 ARG cc_start: 0.7531 (mtt180) cc_final: 0.7271 (mtt90) REVERT: Q 83 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7048 (mtpp) REVERT: Q 94 GLU cc_start: 0.7406 (tt0) cc_final: 0.7115 (tt0) REVERT: Q 220 GLU cc_start: 0.7128 (tt0) cc_final: 0.6633 (tp30) REVERT: U 14 LYS cc_start: 0.8132 (tttt) cc_final: 0.7763 (ttmm) REVERT: U 15 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7596 (mmtt) REVERT: U 22 ARG cc_start: 0.7217 (tpp-160) cc_final: 0.6808 (tpp-160) REVERT: U 148 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.6539 (ttm-80) REVERT: U 159 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7564 (mtpp) REVERT: c 13 LEU cc_start: 0.7574 (mt) cc_final: 0.7337 (tt) REVERT: c 15 LYS cc_start: 0.7904 (mmtt) cc_final: 0.7348 (mmtt) REVERT: c 28 ARG cc_start: 0.7526 (mpt180) cc_final: 0.5937 (mpt180) REVERT: c 45 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6908 (mm-30) REVERT: c 83 LYS cc_start: 0.7567 (mmtt) cc_final: 0.7114 (mtpp) REVERT: c 159 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7662 (mtpp) REVERT: c 210 GLU cc_start: 0.6981 (tp30) cc_final: 0.6462 (tp30) REVERT: c 220 GLU cc_start: 0.7174 (tt0) cc_final: 0.6901 (mm-30) REVERT: k 14 LYS cc_start: 0.8140 (tttt) cc_final: 0.7766 (ttmm) REVERT: k 15 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7600 (mmtt) REVERT: k 148 ARG cc_start: 0.7771 (ttp-170) cc_final: 0.6517 (ttm-80) REVERT: k 159 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7563 (mtpp) REVERT: s 14 LYS cc_start: 0.8117 (tttt) cc_final: 0.7724 (ttmt) REVERT: s 15 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7642 (mmtt) REVERT: s 45 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7187 (mm-30) REVERT: s 69 MET cc_start: 0.8157 (tpp) cc_final: 0.7360 (tpt) REVERT: s 94 GLU cc_start: 0.7151 (tp30) cc_final: 0.6765 (tt0) REVERT: s 120 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6696 (mm-30) REVERT: s 159 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7720 (mtpp) REVERT: w 13 LEU cc_start: 0.7586 (mt) cc_final: 0.7349 (tt) REVERT: w 15 LYS cc_start: 0.7907 (mmtt) cc_final: 0.7351 (mmtt) REVERT: w 28 ARG cc_start: 0.7520 (mpt180) cc_final: 0.5933 (mpt180) REVERT: w 45 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6907 (mm-30) REVERT: w 83 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7109 (mtpp) REVERT: w 159 LYS cc_start: 0.8137 (mtmt) cc_final: 0.7687 (mtpp) REVERT: w 210 GLU cc_start: 0.6979 (tp30) cc_final: 0.6464 (tp30) REVERT: w 220 GLU cc_start: 0.7169 (tt0) cc_final: 0.6900 (mm-30) REVERT: 4 14 LYS cc_start: 0.8079 (tttm) cc_final: 0.7738 (ttmm) REVERT: 4 15 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7436 (mmmt) REVERT: 4 48 ARG cc_start: 0.7533 (mtt180) cc_final: 0.7284 (mtt90) REVERT: 4 83 LYS cc_start: 0.7419 (mmtt) cc_final: 0.7049 (mtpp) REVERT: 4 94 GLU cc_start: 0.7408 (tt0) cc_final: 0.7117 (tt0) REVERT: 4 220 GLU cc_start: 0.7124 (tt0) cc_final: 0.6634 (tp30) REVERT: Z 14 LYS cc_start: 0.8097 (tttm) cc_final: 0.7758 (ttmm) REVERT: Z 15 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7440 (mmmt) REVERT: Z 48 ARG cc_start: 0.7509 (mtt180) cc_final: 0.7252 (mtt90) REVERT: Z 83 LYS cc_start: 0.7434 (mmtt) cc_final: 0.7088 (mtpp) REVERT: Z 94 GLU cc_start: 0.7390 (tt0) cc_final: 0.7097 (tt0) REVERT: Z 220 GLU cc_start: 0.7169 (tt0) cc_final: 0.6705 (tp30) outliers start: 54 outliers final: 41 residues processed: 913 average time/residue: 1.0703 time to fit residues: 1502.3951 Evaluate side-chains 831 residues out of total 3760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 790 time to evaluate : 4.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 13 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain J residue 13 LEU Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 102 LEU Chi-restraints excluded: chain s residue 126 VAL Chi-restraints excluded: chain s residue 132 ILE Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 91 SER Chi-restraints excluded: chain 4 residue 13 LEU Chi-restraints excluded: chain Z residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 222 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 332 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 400 optimal weight: 0.8980 chunk 432 optimal weight: 1.9990 chunk 356 optimal weight: 0.9990 chunk 396 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 321 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 ASN E 136 ASN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN J 136 ASN ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN ** K 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 ASN M 136 ASN ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 ASN ** Q 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 136 ASN ** U 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 211 ASN c 136 ASN c 211 ASN k 136 ASN ** k 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 211 ASN s 136 ASN ** s 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 211 ASN w 136 ASN w 211 ASN ** 4 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34640 Z= 0.217 Angle : 0.408 5.092 46920 Z= 0.243 Chirality : 0.030 0.110 6160 Planarity : 0.003 0.049 5960 Dihedral : 2.898 12.283 4720 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Rotamer: Outliers : 1.20 % Allowed : 7.05 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.11 (0.11), residues: 4440 helix: 4.04 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : 2.18 (0.47), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS L 53 ARG 0.005 0.000 ARG L 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 3760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 819 time to evaluate : 3.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8124 (tttm) cc_final: 0.7775 (ttmm) REVERT: A 15 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7474 (mmtp) REVERT: A 48 ARG cc_start: 0.7497 (mtt180) cc_final: 0.7232 (mtt90) REVERT: A 83 LYS cc_start: 0.7434 (mmtt) cc_final: 0.7026 (mtpp) REVERT: A 105 ILE cc_start: 0.7881 (mm) cc_final: 0.7585 (mm) REVERT: A 220 GLU cc_start: 0.7164 (tt0) cc_final: 0.6690 (tp30) REVERT: B 14 LYS cc_start: 0.8110 (tttt) cc_final: 0.7551 (ttmt) REVERT: B 15 LYS cc_start: 0.8200 (mmtt) cc_final: 0.7636 (mmtt) REVERT: B 45 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7125 (mm-30) REVERT: B 48 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7213 (mtt-85) REVERT: B 69 MET cc_start: 0.8163 (mmm) cc_final: 0.7949 (tpt) REVERT: B 94 GLU cc_start: 0.7164 (tp30) cc_final: 0.6783 (tt0) REVERT: B 116 ASP cc_start: 0.7331 (m-30) cc_final: 0.7014 (m-30) REVERT: B 120 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6692 (mm-30) REVERT: B 148 ARG cc_start: 0.7268 (ttp-170) cc_final: 0.6620 (ttt90) REVERT: B 159 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7681 (mtpp) REVERT: C 8 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7576 (mmtt) REVERT: C 15 LYS cc_start: 0.7792 (mmtt) cc_final: 0.6990 (mmtt) REVERT: C 28 ARG cc_start: 0.7731 (mpt180) cc_final: 0.7390 (mmt180) REVERT: C 32 GLU cc_start: 0.5887 (mm-30) cc_final: 0.5678 (tt0) REVERT: C 52 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7170 (tt0) REVERT: C 83 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7520 (mtpp) REVERT: C 159 LYS cc_start: 0.8128 (mtmt) cc_final: 0.7824 (mtpp) REVERT: D 15 LYS cc_start: 0.7651 (mmtt) cc_final: 0.7178 (mmtt) REVERT: D 75 VAL cc_start: 0.8218 (t) cc_final: 0.7968 (t) REVERT: D 94 GLU cc_start: 0.7301 (tp30) cc_final: 0.6827 (tt0) REVERT: D 103 ARG cc_start: 0.8072 (ttp80) cc_final: 0.7785 (ttp80) REVERT: D 159 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7605 (mttm) REVERT: D 210 GLU cc_start: 0.7427 (tp30) cc_final: 0.7037 (tp30) REVERT: D 220 GLU cc_start: 0.7135 (tp30) cc_final: 0.6830 (tp30) REVERT: E 15 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7277 (mmtt) REVERT: E 22 ARG cc_start: 0.7481 (tpp-160) cc_final: 0.6650 (tpp-160) REVERT: E 94 GLU cc_start: 0.7336 (tp30) cc_final: 0.6857 (tt0) REVERT: E 103 ARG cc_start: 0.8093 (ttp80) cc_final: 0.7821 (ttp80) REVERT: E 159 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7650 (mttm) REVERT: E 210 GLU cc_start: 0.7446 (tp30) cc_final: 0.7061 (tp30) REVERT: E 220 GLU cc_start: 0.7169 (tp30) cc_final: 0.6866 (tp30) REVERT: F 8 LYS cc_start: 0.7867 (mmtt) cc_final: 0.6978 (mmtt) REVERT: F 15 LYS cc_start: 0.7875 (mmtt) cc_final: 0.7024 (mmtt) REVERT: F 28 ARG cc_start: 0.7738 (mpt180) cc_final: 0.7372 (mmt180) REVERT: F 52 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7156 (tt0) REVERT: F 83 LYS cc_start: 0.7900 (mmtt) cc_final: 0.7463 (mtpp) REVERT: F 127 GLU cc_start: 0.7535 (tt0) cc_final: 0.7242 (tt0) REVERT: F 159 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7791 (mtpp) REVERT: F 177 SER cc_start: 0.8508 (m) cc_final: 0.8252 (t) REVERT: F 181 ILE cc_start: 0.7388 (mt) cc_final: 0.7178 (mt) REVERT: G 8 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7574 (mmtt) REVERT: G 15 LYS cc_start: 0.7791 (mmtt) cc_final: 0.6980 (mmtt) REVERT: G 28 ARG cc_start: 0.7731 (mpt180) cc_final: 0.7379 (mmt180) REVERT: G 83 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7516 (mtpp) REVERT: G 159 LYS cc_start: 0.8104 (mtmt) cc_final: 0.7797 (mtpp) REVERT: G 177 SER cc_start: 0.8524 (m) cc_final: 0.8276 (t) REVERT: G 181 ILE cc_start: 0.7447 (mt) cc_final: 0.7242 (mt) REVERT: H 15 LYS cc_start: 0.7656 (mmtt) cc_final: 0.7180 (mmtt) REVERT: H 94 GLU cc_start: 0.7342 (tp30) cc_final: 0.6858 (tt0) REVERT: H 103 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7781 (ttp80) REVERT: H 159 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7610 (mttm) REVERT: H 210 GLU cc_start: 0.7428 (tp30) cc_final: 0.7036 (tp30) REVERT: H 220 GLU cc_start: 0.7136 (tp30) cc_final: 0.6833 (tp30) REVERT: J 15 LYS cc_start: 0.7788 (mmtt) cc_final: 0.7284 (mmtt) REVERT: J 22 ARG cc_start: 0.7484 (tpp-160) cc_final: 0.6656 (tpp-160) REVERT: J 45 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6926 (tt0) REVERT: J 94 GLU cc_start: 0.7332 (tp30) cc_final: 0.6858 (tt0) REVERT: J 103 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7823 (ttp80) REVERT: J 159 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7654 (mttm) REVERT: J 210 GLU cc_start: 0.7452 (tp30) cc_final: 0.7061 (tp30) REVERT: J 220 GLU cc_start: 0.7173 (tp30) cc_final: 0.6872 (tp30) REVERT: K 8 LYS cc_start: 0.7870 (mmtt) cc_final: 0.6976 (mmtt) REVERT: K 15 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7016 (mmtt) REVERT: K 28 ARG cc_start: 0.7736 (mpt180) cc_final: 0.7395 (mmt180) REVERT: K 32 GLU cc_start: 0.5902 (mm-30) cc_final: 0.5669 (tt0) REVERT: K 83 LYS cc_start: 0.7901 (mmtt) cc_final: 0.7465 (mtpp) REVERT: K 159 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7823 (mtpp) REVERT: K 177 SER cc_start: 0.8512 (m) cc_final: 0.8257 (t) REVERT: K 181 ILE cc_start: 0.7390 (mt) cc_final: 0.7182 (mt) REVERT: L 14 LYS cc_start: 0.8113 (tttt) cc_final: 0.7552 (ttmt) REVERT: L 15 LYS cc_start: 0.8178 (mmtt) cc_final: 0.7608 (mmtt) REVERT: L 45 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7127 (mm-30) REVERT: L 48 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.7210 (mtt-85) REVERT: L 69 MET cc_start: 0.8193 (mmm) cc_final: 0.7979 (tpt) REVERT: L 94 GLU cc_start: 0.7224 (tp30) cc_final: 0.6809 (tt0) REVERT: L 116 ASP cc_start: 0.7442 (m-30) cc_final: 0.7136 (m-30) REVERT: L 120 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6694 (mm-30) REVERT: L 148 ARG cc_start: 0.7259 (ttp-170) cc_final: 0.6615 (ttt90) REVERT: L 159 LYS cc_start: 0.8185 (mtmt) cc_final: 0.7672 (mtpp) REVERT: M 14 LYS cc_start: 0.8088 (tttt) cc_final: 0.7549 (ttmt) REVERT: M 15 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7563 (mmtt) REVERT: M 45 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7152 (mm-30) REVERT: M 48 ARG cc_start: 0.7424 (mtt-85) cc_final: 0.7134 (mtt-85) REVERT: M 69 MET cc_start: 0.8089 (tpp) cc_final: 0.7352 (tpt) REVERT: M 94 GLU cc_start: 0.7201 (tp30) cc_final: 0.6802 (tt0) REVERT: M 116 ASP cc_start: 0.7367 (m-30) cc_final: 0.7057 (m-30) REVERT: M 120 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6739 (mm-30) REVERT: M 159 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7714 (mtpp) REVERT: Q 14 LYS cc_start: 0.8115 (tttm) cc_final: 0.7765 (ttmm) REVERT: Q 15 LYS cc_start: 0.7837 (mmtt) cc_final: 0.7473 (mmtp) REVERT: Q 48 ARG cc_start: 0.7544 (mtt180) cc_final: 0.7257 (mtt90) REVERT: Q 83 LYS cc_start: 0.7414 (mmtt) cc_final: 0.6996 (mtpp) REVERT: Q 105 ILE cc_start: 0.7813 (mm) cc_final: 0.7490 (mm) REVERT: Q 220 GLU cc_start: 0.7130 (tt0) cc_final: 0.6610 (tp30) REVERT: U 14 LYS cc_start: 0.8158 (tttt) cc_final: 0.7684 (ttmm) REVERT: U 15 LYS cc_start: 0.8041 (mmtt) cc_final: 0.7604 (mmtt) REVERT: U 148 ARG cc_start: 0.7800 (ttp-170) cc_final: 0.6532 (tpt90) REVERT: U 159 LYS cc_start: 0.7890 (mtmt) cc_final: 0.7521 (mtpp) REVERT: c 13 LEU cc_start: 0.7537 (mt) cc_final: 0.7315 (tt) REVERT: c 14 LYS cc_start: 0.8133 (tttt) cc_final: 0.7381 (ttpp) REVERT: c 28 ARG cc_start: 0.7575 (mpt180) cc_final: 0.6406 (mmm160) REVERT: c 45 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6940 (mm-30) REVERT: c 83 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7140 (mtpp) REVERT: c 159 LYS cc_start: 0.8138 (mtmt) cc_final: 0.7651 (mtpp) REVERT: c 210 GLU cc_start: 0.6974 (tp30) cc_final: 0.6463 (tp30) REVERT: c 220 GLU cc_start: 0.7149 (tt0) cc_final: 0.6880 (mm-30) REVERT: k 14 LYS cc_start: 0.8168 (tttt) cc_final: 0.7798 (ttmm) REVERT: k 15 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7614 (mmtt) REVERT: k 45 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6998 (mt-10) REVERT: k 148 ARG cc_start: 0.7797 (ttp-170) cc_final: 0.6540 (tpt90) REVERT: k 159 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7521 (mtpp) REVERT: s 14 LYS cc_start: 0.8096 (tttt) cc_final: 0.7518 (ttmt) REVERT: s 15 LYS cc_start: 0.8149 (mmtt) cc_final: 0.7568 (mmtt) REVERT: s 45 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7153 (mm-30) REVERT: s 48 ARG cc_start: 0.7394 (mtt-85) cc_final: 0.7083 (mtt-85) REVERT: s 69 MET cc_start: 0.8083 (tpp) cc_final: 0.7346 (tpt) REVERT: s 94 GLU cc_start: 0.7149 (tp30) cc_final: 0.6765 (tt0) REVERT: s 120 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6730 (mm-30) REVERT: s 159 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7716 (mtpp) REVERT: w 13 LEU cc_start: 0.7550 (mt) cc_final: 0.7326 (tt) REVERT: w 14 LYS cc_start: 0.8164 (tttt) cc_final: 0.7389 (ttpp) REVERT: w 28 ARG cc_start: 0.7567 (mpt180) cc_final: 0.6399 (mmm160) REVERT: w 45 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6937 (mm-30) REVERT: w 83 LYS cc_start: 0.7606 (mmtt) cc_final: 0.7133 (mtpp) REVERT: w 159 LYS cc_start: 0.8144 (mtmt) cc_final: 0.7660 (mtpp) REVERT: w 210 GLU cc_start: 0.6970 (tp30) cc_final: 0.6484 (tp30) REVERT: w 220 GLU cc_start: 0.7146 (tt0) cc_final: 0.6907 (mm-30) REVERT: 4 14 LYS cc_start: 0.8110 (tttm) cc_final: 0.7759 (ttmm) REVERT: 4 15 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7509 (mmtp) REVERT: 4 48 ARG cc_start: 0.7538 (mtt180) cc_final: 0.7259 (mtt90) REVERT: 4 83 LYS cc_start: 0.7413 (mmtt) cc_final: 0.6990 (mtpp) REVERT: 4 105 ILE cc_start: 0.7793 (mm) cc_final: 0.7494 (mm) REVERT: 4 220 GLU cc_start: 0.7124 (tt0) cc_final: 0.6610 (tp30) REVERT: Z 14 LYS cc_start: 0.8129 (tttm) cc_final: 0.7785 (ttmm) REVERT: Z 15 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7483 (mmtp) REVERT: Z 48 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7243 (mtt90) REVERT: Z 83 LYS cc_start: 0.7444 (mmtt) cc_final: 0.7032 (mtpp) REVERT: Z 105 ILE cc_start: 0.7865 (mm) cc_final: 0.7570 (mm) REVERT: Z 220 GLU cc_start: 0.7164 (tt0) cc_final: 0.6684 (tp30) outliers start: 45 outliers final: 37 residues processed: 839 average time/residue: 1.1054 time to fit residues: 1411.0209 Evaluate side-chains 816 residues out of total 3760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 779 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 148 ARG Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 148 ARG Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain U residue 97 ARG Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain s residue 102 LEU Chi-restraints excluded: chain s residue 126 VAL Chi-restraints excluded: chain s residue 132 ILE Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 91 SER Chi-restraints excluded: chain 4 residue 13 LEU Chi-restraints excluded: chain Z residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 395 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 191 optimal weight: 0.5980 chunk 268 optimal weight: 2.9990 chunk 401 optimal weight: 1.9990 chunk 425 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 380 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS B 136 ASN B 211 ASN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 211 ASN E 136 ASN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN ** F 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 ASN ** H 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 211 ASN J 136 ASN ** J 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 211 ASN L 53 HIS L 136 ASN L 211 ASN M 53 HIS M 136 ASN M 211 ASN ** Q 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 79 GLN ** k 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 136 ASN s 211 ASN w 79 GLN ** 4 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 34640 Z= 0.325 Angle : 0.460 4.986 46920 Z= 0.274 Chirality : 0.031 0.110 6160 Planarity : 0.003 0.043 5960 Dihedral : 3.003 12.560 4720 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Rotamer: Outliers : 2.58 % Allowed : 5.74 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.52 (0.11), residues: 4440 helix: 3.66 (0.07), residues: 4180 sheet: None (None), residues: 0 loop : 2.19 (0.49), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS L 53 ARG 0.006 0.001 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8880 Ramachandran restraints generated. 4440 Oldfield, 0 Emsley, 4440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 3760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 788 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 LYS cc_start: 0.8140 (tttm) cc_final: 0.7782 (ttmm) REVERT: A 15 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7585 (mmtt) REVERT: A 48 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7220 (mtt90) REVERT: A 83 LYS cc_start: 0.7472 (mmtt) cc_final: 0.7079 (mtpp) REVERT: A 105 ILE cc_start: 0.7876 (mm) cc_final: 0.7585 (mm) REVERT: A 220 GLU cc_start: 0.7178 (tt0) cc_final: 0.6672 (tp30) REVERT: B 14 LYS cc_start: 0.8105 (tttt) cc_final: 0.7696 (ttmt) REVERT: B 15 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7629 (mmtt) REVERT: B 19 GLU cc_start: 0.8616 (tt0) cc_final: 0.8377 (tt0) REVERT: B 45 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7086 (mm-30) REVERT: B 94 GLU cc_start: 0.7264 (tp30) cc_final: 0.6818 (tt0) REVERT: B 116 ASP cc_start: 0.7371 (m-30) cc_final: 0.7034 (m-30) REVERT: B 120 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6704 (mm-30) REVERT: B 148 ARG cc_start: 0.7292 (ttp-170) cc_final: 0.6681 (ttt90) REVERT: B 159 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7696 (mtpp) REVERT: C 8 LYS cc_start: 0.8045 (mmtt) cc_final: 0.7738 (mmtt) REVERT: C 15 LYS cc_start: 0.7895 (mmtt) cc_final: 0.7111 (mmtt) REVERT: C 28 ARG cc_start: 0.7763 (mpt180) cc_final: 0.7399 (mmt180) REVERT: C 32 GLU cc_start: 0.6177 (mm-30) cc_final: 0.5882 (tt0) REVERT: C 83 LYS cc_start: 0.7911 (mmtt) cc_final: 0.7531 (mtpp) REVERT: C 148 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7621 (ttp80) REVERT: C 159 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7849 (mtpp) REVERT: C 203 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6961 (mt-10) REVERT: D 15 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7230 (mmtt) REVERT: D 75 VAL cc_start: 0.8213 (t) cc_final: 0.7980 (t) REVERT: D 94 GLU cc_start: 0.7386 (tp30) cc_final: 0.6893 (tt0) REVERT: D 103 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7856 (ttp80) REVERT: D 118 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6754 (tp) REVERT: D 148 ARG cc_start: 0.8019 (ttm170) cc_final: 0.7775 (ttm170) REVERT: D 159 LYS cc_start: 0.8059 (mtmt) cc_final: 0.7631 (mttm) REVERT: D 210 GLU cc_start: 0.7541 (tp30) cc_final: 0.7093 (tp30) REVERT: E 15 LYS cc_start: 0.7808 (mmtt) cc_final: 0.7236 (mmtt) REVERT: E 22 ARG cc_start: 0.7530 (tpp-160) cc_final: 0.6714 (tpp-160) REVERT: E 94 GLU cc_start: 0.7380 (tp30) cc_final: 0.6876 (tt0) REVERT: E 103 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7860 (ttp80) REVERT: E 107 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7280 (mm-30) REVERT: E 118 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6724 (tp) REVERT: E 159 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7682 (mttm) REVERT: E 210 GLU cc_start: 0.7582 (tp30) cc_final: 0.7141 (tp30) REVERT: F 8 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7062 (mmtt) REVERT: F 15 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7123 (mmtt) REVERT: F 28 ARG cc_start: 0.7785 (mpt180) cc_final: 0.7411 (mmt180) REVERT: F 83 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7480 (mtpp) REVERT: F 159 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7851 (mtpp) REVERT: F 177 SER cc_start: 0.8559 (m) cc_final: 0.8279 (t) REVERT: F 181 ILE cc_start: 0.7460 (mt) cc_final: 0.7243 (mt) REVERT: G 8 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7718 (mmtt) REVERT: G 15 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7109 (mmtt) REVERT: G 28 ARG cc_start: 0.7759 (mpt180) cc_final: 0.7400 (mmt180) REVERT: G 32 GLU cc_start: 0.6184 (mm-30) cc_final: 0.5948 (tt0) REVERT: G 83 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7524 (mtpp) REVERT: G 148 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7605 (ttp80) REVERT: G 159 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7846 (mtpp) REVERT: H 15 LYS cc_start: 0.7718 (mmtt) cc_final: 0.7232 (mmtt) REVERT: H 94 GLU cc_start: 0.7390 (tp30) cc_final: 0.6894 (tt0) REVERT: H 103 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7866 (ttp80) REVERT: H 118 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6740 (tp) REVERT: H 148 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7782 (ttm170) REVERT: H 159 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7631 (mttm) REVERT: H 210 GLU cc_start: 0.7556 (tp30) cc_final: 0.7118 (tp30) REVERT: H 220 GLU cc_start: 0.7145 (tp30) cc_final: 0.6595 (mm-30) REVERT: J 15 LYS cc_start: 0.7814 (mmtt) cc_final: 0.7310 (mmtt) REVERT: J 22 ARG cc_start: 0.7531 (tpp-160) cc_final: 0.6717 (tpp-160) REVERT: J 45 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6956 (tt0) REVERT: J 94 GLU cc_start: 0.7386 (tp30) cc_final: 0.6877 (tt0) REVERT: J 103 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7865 (ttp80) REVERT: J 107 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7289 (mm-30) REVERT: J 118 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6734 (tp) REVERT: J 159 LYS cc_start: 0.8078 (mtmt) cc_final: 0.7686 (mttm) REVERT: J 210 GLU cc_start: 0.7581 (tp30) cc_final: 0.7142 (tp30) REVERT: K 8 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7058 (mmtt) REVERT: K 15 LYS cc_start: 0.7910 (mmtt) cc_final: 0.7122 (mmtt) REVERT: K 28 ARG cc_start: 0.7762 (mpt180) cc_final: 0.7412 (mmt180) REVERT: K 32 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5890 (tt0) REVERT: K 83 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7479 (mtpp) REVERT: K 159 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7848 (mtpp) REVERT: K 177 SER cc_start: 0.8562 (m) cc_final: 0.8280 (t) REVERT: K 181 ILE cc_start: 0.7459 (mt) cc_final: 0.7245 (mt) REVERT: L 14 LYS cc_start: 0.8104 (tttt) cc_final: 0.7694 (ttmt) REVERT: L 15 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7622 (mmtt) REVERT: L 19 GLU cc_start: 0.8621 (tt0) cc_final: 0.8377 (tt0) REVERT: L 45 GLU cc_start: 0.7406 (mm-30) cc_final: 0.7086 (mm-30) REVERT: L 94 GLU cc_start: 0.7270 (tp30) cc_final: 0.6815 (tt0) REVERT: L 120 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6689 (mm-30) REVERT: L 148 ARG cc_start: 0.7261 (ttp-170) cc_final: 0.6640 (ttt90) REVERT: L 159 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7700 (mtpp) REVERT: M 14 LYS cc_start: 0.8094 (tttt) cc_final: 0.7663 (ttmt) REVERT: M 15 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7575 (mmtt) REVERT: M 19 GLU cc_start: 0.8601 (tt0) cc_final: 0.8376 (tt0) REVERT: M 45 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7083 (mm-30) REVERT: M 94 GLU cc_start: 0.7245 (tp30) cc_final: 0.6800 (tt0) REVERT: M 116 ASP cc_start: 0.7403 (m-30) cc_final: 0.7117 (m-30) REVERT: M 120 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6730 (mm-30) REVERT: M 159 LYS cc_start: 0.8229 (mtmt) cc_final: 0.7743 (mtpp) REVERT: Q 14 LYS cc_start: 0.8131 (tttm) cc_final: 0.7773 (ttmm) REVERT: Q 15 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7593 (mmtt) REVERT: Q 48 ARG cc_start: 0.7514 (mtt180) cc_final: 0.7235 (mtt90) REVERT: Q 83 LYS cc_start: 0.7446 (mmtt) cc_final: 0.7053 (mtpp) REVERT: Q 105 ILE cc_start: 0.7838 (mm) cc_final: 0.7558 (mm) REVERT: Q 220 GLU cc_start: 0.7147 (tt0) cc_final: 0.6595 (tp30) REVERT: U 14 LYS cc_start: 0.8208 (tttt) cc_final: 0.7735 (ttmm) REVERT: U 15 LYS cc_start: 0.8051 (mmtt) cc_final: 0.7601 (mmtt) REVERT: U 148 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.6582 (tpt90) REVERT: U 159 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7612 (mtpp) REVERT: c 13 LEU cc_start: 0.7631 (mt) cc_final: 0.7393 (tt) REVERT: c 14 LYS cc_start: 0.8157 (tttt) cc_final: 0.7416 (ttpp) REVERT: c 15 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7420 (mmtt) REVERT: c 28 ARG cc_start: 0.7531 (mpt180) cc_final: 0.6350 (mmm160) REVERT: c 45 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6908 (mm-30) REVERT: c 83 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7196 (mtpp) REVERT: c 159 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7635 (mtpp) REVERT: c 210 GLU cc_start: 0.6985 (tp30) cc_final: 0.6488 (tp30) REVERT: c 220 GLU cc_start: 0.7153 (tt0) cc_final: 0.6879 (mm-30) REVERT: k 14 LYS cc_start: 0.8217 (tttt) cc_final: 0.7744 (ttmm) REVERT: k 15 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7607 (mmtt) REVERT: k 45 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7046 (mt-10) REVERT: k 148 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.6594 (tpt90) REVERT: k 159 LYS cc_start: 0.7975 (mtmt) cc_final: 0.7611 (mtpp) REVERT: s 14 LYS cc_start: 0.8054 (tttt) cc_final: 0.7642 (ttmt) REVERT: s 15 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7584 (mmtt) REVERT: s 19 GLU cc_start: 0.8611 (tt0) cc_final: 0.8391 (tt0) REVERT: s 45 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7120 (mm-30) REVERT: s 94 GLU cc_start: 0.7225 (tp30) cc_final: 0.6786 (tt0) REVERT: s 120 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6733 (mm-30) REVERT: s 159 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7741 (mtpp) REVERT: w 13 LEU cc_start: 0.7638 (mt) cc_final: 0.7400 (tt) REVERT: w 14 LYS cc_start: 0.8174 (tttt) cc_final: 0.7423 (ttpp) REVERT: w 15 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7427 (mmtt) REVERT: w 28 ARG cc_start: 0.7522 (mpt180) cc_final: 0.6341 (mmm160) REVERT: w 45 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6907 (mm-30) REVERT: w 83 LYS cc_start: 0.7735 (mmtt) cc_final: 0.7211 (mtpp) REVERT: w 159 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7622 (mtpp) REVERT: w 210 GLU cc_start: 0.6989 (tp30) cc_final: 0.6504 (tp30) REVERT: w 220 GLU cc_start: 0.7138 (tt0) cc_final: 0.6868 (mm-30) REVERT: 4 14 LYS cc_start: 0.8126 (tttm) cc_final: 0.7770 (ttmm) REVERT: 4 15 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7587 (mmtt) REVERT: 4 48 ARG cc_start: 0.7515 (mtt180) cc_final: 0.7234 (mtt90) REVERT: 4 83 LYS cc_start: 0.7441 (mmtt) cc_final: 0.7046 (mtpp) REVERT: 4 105 ILE cc_start: 0.7843 (mm) cc_final: 0.7559 (mm) REVERT: 4 220 GLU cc_start: 0.7143 (tt0) cc_final: 0.6598 (tp30) REVERT: Z 14 LYS cc_start: 0.8145 (tttm) cc_final: 0.7793 (ttmm) REVERT: Z 15 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7605 (mmtt) REVERT: Z 48 ARG cc_start: 0.7481 (mtt180) cc_final: 0.7211 (mtt90) REVERT: Z 83 LYS cc_start: 0.7479 (mmtt) cc_final: 0.7094 (mtpp) REVERT: Z 105 ILE cc_start: 0.7861 (mm) cc_final: 0.7570 (mm) REVERT: Z 220 GLU cc_start: 0.7177 (tt0) cc_final: 0.6663 (tp30) outliers start: 97 outliers final: 67 residues processed: 848 average time/residue: 1.0550 time to fit residues: 1350.4366 Evaluate side-chains 842 residues out of total 3760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 768 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain B residue 101 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 24 THR Chi-restraints excluded: chain C residue 45 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 148 ARG Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 72 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 45 GLU Chi-restraints excluded: chain F residue 101 SER Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain G residue 148 ARG Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain J residue 72 VAL Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 126 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain L residue 101 SER Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 126 VAL Chi-restraints excluded: chain L residue 132 ILE Chi-restraints excluded: chain M residue 101 SER Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 126 VAL Chi-restraints excluded: chain M residue 132 ILE Chi-restraints excluded: chain Q residue 5 GLU Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 126 VAL Chi-restraints excluded: chain U residue 97 ARG Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 72 VAL Chi-restraints excluded: chain c residue 91 SER Chi-restraints excluded: chain k residue 45 GLU Chi-restraints excluded: chain k residue 97 ARG Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 102 LEU Chi-restraints excluded: chain s residue 126 VAL Chi-restraints excluded: chain s residue 132 ILE Chi-restraints excluded: chain w residue 24 THR Chi-restraints excluded: chain w residue 72 VAL Chi-restraints excluded: chain w residue 91 SER Chi-restraints excluded: chain 4 residue 5 GLU Chi-restraints excluded: chain 4 residue 13 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 126 VAL Chi-restraints excluded: chain Z residue 5 GLU Chi-restraints excluded: chain Z residue 13 LEU Chi-restraints excluded: chain Z residue 24 THR Chi-restraints excluded: chain Z residue 126 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 354 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 316 optimal weight: 1.9990 chunk 175 optimal weight: 0.9990 chunk 362 optimal weight: 2.9990 chunk 293 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 381 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: