Starting phenix.real_space_refine on Wed Mar 20 16:01:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c99_16506/03_2024/8c99_16506.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c99_16506/03_2024/8c99_16506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c99_16506/03_2024/8c99_16506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c99_16506/03_2024/8c99_16506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c99_16506/03_2024/8c99_16506.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c99_16506/03_2024/8c99_16506.pdb" } resolution = 3.29 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= 0.005 sd= 0.091 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 P 945 5.49 5 S 18 5.16 5 C 13888 2.51 5 N 5234 2.21 5 O 7903 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27988 Number of models: 1 Model: "" Number of chains: 11 Chain: "2" Number of atoms: 286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 286 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1454 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain breaks: 1 Chain: "J" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1055 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain breaks: 1 Chain: "L" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 676 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain breaks: 1 Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 734 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 93} Chain breaks: 1 Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "A" Number of atoms: 20293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 945, 20293 Classifications: {'DNA': 1, 'RNA': 944} Modifications used: {'rna2p_pur': 92, 'rna2p_pyr': 44, 'rna3p_pur': 465, 'rna3p_pyr': 343} Incomplete info: {'p_only': 1} Link IDs: {'rna2p': 136, 'rna3p': 808} Unresolved chain links: 1 Chain breaks: 4 Unresolved chain link angles: 7 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' G:plan2': 1, ' G:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 13.86, per 1000 atoms: 0.50 Number of scatterers: 27988 At special positions: 0 Unit cell: (132.5, 176.25, 168.75, 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 18 16.00 P 945 15.00 O 7903 8.00 N 5234 7.00 C 13888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.17 Conformation dependent library (CDL) restraints added in 1.4 seconds 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1828 Finding SS restraints... Warning! O4 atom is missing from residue U A 358 Was trying to link: A A 282 N6 with U A 358 O4, Saenger class: 20 Warning! O4 atom is missing from residue U A 358 Was trying to link: A A 282 N6 with U A 358 O4, Saenger class: 23 Secondary structure from input PDB file: 34 helices and 11 sheets defined 41.6% alpha, 12.4% beta 310 base pairs and 465 stacking pairs defined. Time for finding SS restraints: 13.25 Creating SS restraints... Processing helix chain '2' and resid 10 through 17 removed outlier: 3.535A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 24 removed outlier: 3.976A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 removed outlier: 3.516A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.513A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 164 removed outlier: 4.416A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.548A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'J' and resid 7 through 11 removed outlier: 3.681A pdb=" N VAL J 11 " --> pdb=" O PRO J 8 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 37 Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 96 through 108 removed outlier: 4.151A pdb=" N VAL J 100 " --> pdb=" O ARG J 96 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.786A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 136 removed outlier: 4.028A pdb=" N ALA J 134 " --> pdb=" O ASN J 131 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 135 removed outlier: 4.419A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.919A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.351A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.890A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.512A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.106A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 4.193A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 8 removed outlier: 4.108A pdb=" N ARG Y 7 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 34 removed outlier: 4.351A pdb=" N PHE Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 56 removed outlier: 3.590A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing sheet with id=AA1, first strand: chain 'E' and resid 2 through 3 removed outlier: 3.648A pdb=" N LEU E 3 " --> pdb=" O LEU E 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 118 through 121 removed outlier: 3.924A pdb=" N VAL E 121 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N THR E 189 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ILE E 149 " --> pdb=" O THR E 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 123 through 124 Processing sheet with id=AA4, first strand: chain 'R' and resid 2 through 6 Processing sheet with id=AA5, first strand: chain 'R' and resid 20 through 22 removed outlier: 6.556A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 72 through 74 Processing sheet with id=AA7, first strand: chain 'S' and resid 3 through 10 removed outlier: 3.624A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.887A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AB1, first strand: chain 'U' and resid 82 through 86 Processing sheet with id=AB2, first strand: chain 'Z' and resid 34 through 37 317 hydrogen bonds defined for protein. 897 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 790 hydrogen bonds 1254 hydrogen bond angles 0 basepair planarities 310 basepair parallelities 465 stacking parallelities Total time for adding SS restraints: 17.15 Time building geometry restraints manager: 15.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4015 1.33 - 1.45: 12679 1.45 - 1.57: 11893 1.57 - 1.69: 1884 1.69 - 1.81: 36 Bond restraints: 30507 Sorted by residual: bond pdb=" C1' U A 827 " pdb=" N1 U A 827 " ideal model delta sigma weight residual 1.480 1.573 -0.093 1.50e-02 4.44e+03 3.87e+01 bond pdb=" C1' A A 526 " pdb=" N9 A A 526 " ideal model delta sigma weight residual 1.475 1.391 0.084 1.50e-02 4.44e+03 3.14e+01 bond pdb=" N MET Y 1 " pdb=" CA MET Y 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.94e+00 bond pdb=" N MET S 1 " pdb=" CA MET S 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.90e+00 ... (remaining 30502 not shown) Histogram of bond angle deviations from ideal: 99.73 - 106.58: 5696 106.58 - 113.43: 18107 113.43 - 120.28: 11157 120.28 - 127.13: 8680 127.13 - 133.97: 2226 Bond angle restraints: 45866 Sorted by residual: angle pdb=" N VAL Q 33 " pdb=" CA VAL Q 33 " pdb=" C VAL Q 33 " ideal model delta sigma weight residual 112.96 109.37 3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" N ILE L 103 " pdb=" CA ILE L 103 " pdb=" C ILE L 103 " ideal model delta sigma weight residual 111.62 108.83 2.79 7.90e-01 1.60e+00 1.25e+01 angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 121.54 128.08 -6.54 1.91e+00 2.74e-01 1.17e+01 angle pdb=" N ILE U 38 " pdb=" CA ILE U 38 " pdb=" C ILE U 38 " ideal model delta sigma weight residual 112.12 109.29 2.83 8.40e-01 1.42e+00 1.14e+01 angle pdb=" C4' A A 404 " pdb=" C3' A A 404 " pdb=" O3' A A 404 " ideal model delta sigma weight residual 109.40 112.84 -3.44 1.50e+00 4.44e-01 5.25e+00 ... (remaining 45861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.09: 17159 35.09 - 70.19: 2066 70.19 - 105.28: 248 105.28 - 140.38: 6 140.38 - 175.47: 3 Dihedral angle restraints: 19482 sinusoidal: 16664 harmonic: 2818 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual -160.00 15.06 -175.06 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 36.76 -164.76 1 1.70e+01 3.46e-03 6.53e+01 dihedral pdb=" C4' G A 271 " pdb=" C3' G A 271 " pdb=" O3' G A 271 " pdb=" P A A 272 " ideal model delta sinusoidal sigma weight residual -110.00 65.47 -175.47 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 19479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4776 0.033 - 0.065: 962 0.065 - 0.098: 120 0.098 - 0.131: 63 0.131 - 0.163: 4 Chirality restraints: 5925 Sorted by residual: chirality pdb=" C1' U A 827 " pdb=" O4' U A 827 " pdb=" C2' U A 827 " pdb=" N1 U A 827 " both_signs ideal model delta sigma weight residual False 2.47 2.63 -0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" C1' A A 526 " pdb=" O4' A A 526 " pdb=" C2' A A 526 " pdb=" N9 A A 526 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.60 -0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 5922 not shown) Planarity restraints: 2271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A1138 " -0.028 2.00e-02 2.50e+03 1.20e-02 4.35e+00 pdb=" N9 G A1138 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G A1138 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G A1138 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A1138 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G A1138 " -0.008 2.00e-02 2.50e+03 pdb=" O6 G A1138 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G A1138 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A1138 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G A1138 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G A1138 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G A1138 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 481 " 0.024 2.00e-02 2.50e+03 1.09e-02 3.54e+00 pdb=" N9 G A 481 " -0.028 2.00e-02 2.50e+03 pdb=" C8 G A 481 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G A 481 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G A 481 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G A 481 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G A 481 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G A 481 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G A 481 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G A 481 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G A 481 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G A 481 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A 308 " -0.023 2.00e-02 2.50e+03 1.03e-02 3.21e+00 pdb=" N9 G A 308 " 0.026 2.00e-02 2.50e+03 pdb=" C8 G A 308 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G A 308 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G A 308 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G A 308 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G A 308 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G A 308 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G A 308 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A 308 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G A 308 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G A 308 " 0.002 2.00e-02 2.50e+03 ... (remaining 2268 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 229 2.55 - 3.13: 21171 3.13 - 3.72: 53007 3.72 - 4.31: 72752 4.31 - 4.90: 101233 Nonbonded interactions: 248392 Sorted by model distance: nonbonded pdb=" OD2 ASP Q 48 " pdb=" O2' U A 534 " model vdw 1.957 2.440 nonbonded pdb=" OP2 G A 117 " pdb=" O2' A A 119 " model vdw 1.962 2.440 nonbonded pdb=" O2' A A 126 " pdb=" O4' A A 127 " model vdw 1.968 2.440 nonbonded pdb=" O2' U A 369 " pdb=" OP2 A A 422 " model vdw 2.002 2.440 nonbonded pdb=" O2' C A 957 " pdb=" OP1 A A 959 " model vdw 2.011 2.440 ... (remaining 248387 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.280 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: 0.020 Extract box with map and model: 7.160 Check model and map are aligned: 0.380 Set scattering table: 0.230 Process input model: 85.960 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.002 0.093 30507 Z= 0.116 Angle : 0.392 6.995 45866 Z= 0.210 Chirality : 0.027 0.163 5925 Planarity : 0.003 0.039 2271 Dihedral : 22.330 175.471 17654 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.28), residues: 959 helix: 2.46 (0.29), residues: 337 sheet: 0.07 (0.50), residues: 120 loop : -0.48 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP R 92 HIS 0.002 0.001 HIS E 29 PHE 0.016 0.001 PHE R 53 TYR 0.023 0.001 TYR Q 24 ARG 0.004 0.000 ARG Q 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: J 16 TYR cc_start: 0.8401 (m-80) cc_final: 0.8156 (m-10) REVERT: J 138 GLN cc_start: 0.7310 (tt0) cc_final: 0.7022 (tt0) REVERT: L 126 ARG cc_start: 0.4765 (mtm180) cc_final: 0.3627 (tpt-90) REVERT: Q 96 ASP cc_start: 0.7714 (t70) cc_final: 0.7457 (t70) REVERT: Z 44 ARG cc_start: 0.8049 (mmp80) cc_final: 0.7705 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.3946 time to fit residues: 68.8032 Evaluate side-chains 74 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 0.0570 chunk 147 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 chunk 170 optimal weight: 10.0000 overall best weight: 2.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 ASN R 18 GLN S 57 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30507 Z= 0.206 Angle : 0.499 8.308 45866 Z= 0.255 Chirality : 0.029 0.180 5925 Planarity : 0.004 0.042 2271 Dihedral : 22.808 176.526 15736 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.13 % Allowed : 6.01 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 959 helix: 1.62 (0.28), residues: 356 sheet: -0.23 (0.46), residues: 147 loop : -0.59 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 92 HIS 0.004 0.001 HIS E 29 PHE 0.013 0.002 PHE R 77 TYR 0.012 0.001 TYR J 74 ARG 0.003 0.000 ARG U 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 1.539 Fit side-chains revert: symmetry clash REVERT: J 16 TYR cc_start: 0.8444 (m-80) cc_final: 0.7984 (m-80) REVERT: J 138 GLN cc_start: 0.7548 (tt0) cc_final: 0.7330 (tt0) REVERT: J 142 ILE cc_start: 0.5234 (mt) cc_final: 0.4940 (mm) REVERT: L 126 ARG cc_start: 0.4785 (mtm180) cc_final: 0.3583 (tpt-90) REVERT: Y 2 LYS cc_start: 0.7702 (mttm) cc_final: 0.6813 (mttp) REVERT: Z 44 ARG cc_start: 0.8034 (mmp80) cc_final: 0.7659 (mmp80) outliers start: 9 outliers final: 4 residues processed: 86 average time/residue: 0.3934 time to fit residues: 54.7476 Evaluate side-chains 77 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 169 optimal weight: 40.0000 chunk 58 optimal weight: 0.0980 chunk 137 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 132 HIS Q 80 ASN R 18 GLN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 30507 Z= 0.328 Angle : 0.592 9.450 45866 Z= 0.301 Chirality : 0.034 0.205 5925 Planarity : 0.004 0.044 2271 Dihedral : 22.980 179.293 15736 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.13 % Allowed : 10.26 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.27), residues: 959 helix: 1.18 (0.27), residues: 350 sheet: -0.57 (0.45), residues: 143 loop : -0.85 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 92 HIS 0.004 0.001 HIS E 29 PHE 0.015 0.002 PHE E 23 TYR 0.018 0.002 TYR J 74 ARG 0.007 0.001 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: J 142 ILE cc_start: 0.5803 (mt) cc_final: 0.5551 (mm) REVERT: L 126 ARG cc_start: 0.4592 (mtm180) cc_final: 0.3466 (ttt-90) REVERT: Q 80 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7314 (m110) REVERT: Y 2 LYS cc_start: 0.7582 (mttm) cc_final: 0.6691 (mttp) REVERT: Z 44 ARG cc_start: 0.8127 (mmp80) cc_final: 0.7721 (mmp80) outliers start: 17 outliers final: 8 residues processed: 91 average time/residue: 0.3901 time to fit residues: 57.6009 Evaluate side-chains 81 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 30.0000 chunk 128 optimal weight: 20.0000 chunk 88 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30507 Z= 0.284 Angle : 0.553 9.840 45866 Z= 0.282 Chirality : 0.033 0.223 5925 Planarity : 0.004 0.041 2271 Dihedral : 23.029 179.792 15736 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.75 % Allowed : 12.27 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 959 helix: 1.07 (0.27), residues: 354 sheet: -0.80 (0.44), residues: 148 loop : -0.99 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 92 HIS 0.004 0.001 HIS E 29 PHE 0.012 0.002 PHE E 23 TYR 0.015 0.002 TYR J 74 ARG 0.005 0.000 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 82 time to evaluate : 1.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8048 (ptp) cc_final: 0.7224 (ptp) REVERT: E 105 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7608 (mp) REVERT: E 188 MET cc_start: 0.8478 (ttm) cc_final: 0.8249 (ttp) REVERT: J 138 GLN cc_start: 0.7341 (tt0) cc_final: 0.6969 (tt0) REVERT: J 142 ILE cc_start: 0.5921 (mt) cc_final: 0.5679 (mm) REVERT: Y 2 LYS cc_start: 0.7564 (mttm) cc_final: 0.6647 (mttp) REVERT: Z 44 ARG cc_start: 0.8129 (mmp80) cc_final: 0.7711 (mmp80) outliers start: 14 outliers final: 10 residues processed: 91 average time/residue: 0.4000 time to fit residues: 58.5509 Evaluate side-chains 86 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 155 optimal weight: 50.0000 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 ASN Q 80 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 30507 Z= 0.426 Angle : 0.677 9.745 45866 Z= 0.342 Chirality : 0.038 0.237 5925 Planarity : 0.005 0.043 2271 Dihedral : 23.202 176.506 15736 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 2.50 % Allowed : 13.27 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 959 helix: 0.79 (0.27), residues: 349 sheet: -1.08 (0.43), residues: 148 loop : -1.25 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 92 HIS 0.005 0.001 HIS E 29 PHE 0.017 0.002 PHE R 53 TYR 0.017 0.002 TYR J 74 ARG 0.005 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.8109 (ptp) cc_final: 0.7810 (ptp) REVERT: E 105 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7634 (mp) REVERT: J 138 GLN cc_start: 0.7054 (tt0) cc_final: 0.6683 (tt0) REVERT: J 142 ILE cc_start: 0.6211 (mt) cc_final: 0.5990 (mm) REVERT: Y 2 LYS cc_start: 0.7603 (mttm) cc_final: 0.6678 (mttp) outliers start: 20 outliers final: 11 residues processed: 96 average time/residue: 0.4184 time to fit residues: 64.3584 Evaluate side-chains 88 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 106 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 181 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 0.2980 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30507 Z= 0.232 Angle : 0.530 10.128 45866 Z= 0.273 Chirality : 0.032 0.235 5925 Planarity : 0.004 0.039 2271 Dihedral : 23.130 178.640 15736 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 2.13 % Allowed : 13.89 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.27), residues: 959 helix: 1.16 (0.28), residues: 353 sheet: -1.04 (0.44), residues: 137 loop : -1.25 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 92 HIS 0.003 0.001 HIS E 29 PHE 0.016 0.002 PHE R 77 TYR 0.008 0.001 TYR E 101 ARG 0.003 0.000 ARG Q 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 77 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.7986 (ptp) cc_final: 0.7539 (ptp) REVERT: J 138 GLN cc_start: 0.7311 (tt0) cc_final: 0.6997 (tt0) REVERT: J 142 ILE cc_start: 0.5893 (mt) cc_final: 0.5681 (mm) REVERT: Q 80 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8148 (m-40) REVERT: Y 2 LYS cc_start: 0.7533 (mttm) cc_final: 0.6652 (mttp) REVERT: Z 44 ARG cc_start: 0.8060 (mmt-90) cc_final: 0.7846 (mmt-90) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.3956 time to fit residues: 57.7744 Evaluate side-chains 88 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 132 optimal weight: 40.0000 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 overall best weight: 6.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 30507 Z= 0.504 Angle : 0.737 10.463 45866 Z= 0.369 Chirality : 0.040 0.246 5925 Planarity : 0.005 0.045 2271 Dihedral : 23.313 177.357 15736 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.13 % Allowed : 15.02 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.26), residues: 959 helix: 0.70 (0.27), residues: 349 sheet: -1.18 (0.45), residues: 131 loop : -1.51 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP R 92 HIS 0.004 0.001 HIS E 29 PHE 0.025 0.002 PHE Q 56 TYR 0.017 0.003 TYR J 74 ARG 0.006 0.001 ARG 2 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 1 MET cc_start: 0.7228 (tmm) cc_final: 0.7005 (tmm) REVERT: J 138 GLN cc_start: 0.7343 (tt0) cc_final: 0.6904 (tt0) REVERT: J 142 ILE cc_start: 0.6464 (mt) cc_final: 0.6209 (mm) REVERT: R 32 THR cc_start: 0.8917 (m) cc_final: 0.8554 (t) REVERT: Y 2 LYS cc_start: 0.7647 (mttm) cc_final: 0.6736 (mttp) REVERT: Z 44 ARG cc_start: 0.8095 (mmt-90) cc_final: 0.7842 (mmt-90) outliers start: 17 outliers final: 11 residues processed: 95 average time/residue: 0.4039 time to fit residues: 61.9131 Evaluate side-chains 91 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 108 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 115 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30507 Z= 0.207 Angle : 0.534 10.377 45866 Z= 0.274 Chirality : 0.032 0.241 5925 Planarity : 0.004 0.036 2271 Dihedral : 23.204 177.725 15736 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.50 % Allowed : 16.15 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.27), residues: 959 helix: 1.15 (0.28), residues: 352 sheet: -1.16 (0.43), residues: 135 loop : -1.38 (0.27), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 92 HIS 0.003 0.001 HIS S 60 PHE 0.014 0.002 PHE R 53 TYR 0.008 0.001 TYR J 74 ARG 0.003 0.000 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 138 GLN cc_start: 0.7411 (tt0) cc_final: 0.7066 (tt0) REVERT: J 142 ILE cc_start: 0.5989 (mt) cc_final: 0.5748 (mm) REVERT: Q 80 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7586 (m110) REVERT: Y 2 LYS cc_start: 0.7519 (mttm) cc_final: 0.6647 (mttp) outliers start: 12 outliers final: 10 residues processed: 88 average time/residue: 0.4145 time to fit residues: 58.3589 Evaluate side-chains 86 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 132 optimal weight: 40.0000 chunk 51 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 159 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 30507 Z= 0.566 Angle : 0.782 9.689 45866 Z= 0.390 Chirality : 0.043 0.253 5925 Planarity : 0.006 0.051 2271 Dihedral : 23.396 177.576 15736 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 2.25 % Allowed : 15.89 % Favored : 81.85 % 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: -1.19 (0.26), residues: 959 helix: 0.39 (0.26), residues: 355 sheet: -1.18 (0.46), residues: 125 loop : -1.60 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP R 92 HIS 0.005 0.001 HIS E 29 PHE 0.032 0.003 PHE R 53 TYR 0.031 0.003 TYR R 83 ARG 0.007 0.001 ARG 2 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.584 Fit side-chains revert: symmetry clash REVERT: J 138 GLN cc_start: 0.7430 (tt0) cc_final: 0.6941 (tt0) REVERT: J 142 ILE cc_start: 0.6527 (mt) cc_final: 0.6137 (mm) REVERT: L 126 ARG cc_start: 0.4105 (mtm180) cc_final: 0.3133 (tpt-90) REVERT: R 32 THR cc_start: 0.8938 (m) cc_final: 0.8569 (t) REVERT: R 79 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.5013 (ptt-90) REVERT: Y 2 LYS cc_start: 0.7602 (mttm) cc_final: 0.6722 (mttp) outliers start: 18 outliers final: 16 residues processed: 89 average time/residue: 0.4219 time to fit residues: 60.0296 Evaluate side-chains 93 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 69 LEU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30507 Z= 0.240 Angle : 0.562 10.384 45866 Z= 0.288 Chirality : 0.033 0.244 5925 Planarity : 0.004 0.035 2271 Dihedral : 23.288 179.265 15736 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.63 % Allowed : 17.15 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.27), residues: 959 helix: 0.88 (0.27), residues: 358 sheet: -1.09 (0.45), residues: 135 loop : -1.53 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP R 92 HIS 0.004 0.001 HIS E 29 PHE 0.019 0.002 PHE R 53 TYR 0.011 0.001 TYR J 74 ARG 0.004 0.000 ARG R 79 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1918 Ramachandran restraints generated. 959 Oldfield, 0 Emsley, 959 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 1 MET cc_start: 0.7909 (pmm) cc_final: 0.7505 (ptp) REVERT: J 138 GLN cc_start: 0.7363 (tt0) cc_final: 0.7012 (tt0) REVERT: J 142 ILE cc_start: 0.6090 (mt) cc_final: 0.5820 (mm) REVERT: Y 2 LYS cc_start: 0.7589 (mttm) cc_final: 0.6672 (mttp) outliers start: 13 outliers final: 12 residues processed: 90 average time/residue: 0.4052 time to fit residues: 58.5353 Evaluate side-chains 92 residues out of total 799 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 33 VAL Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 80 ASN Chi-restraints excluded: chain R residue 26 ASP Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain Z residue 34 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 153 optimal weight: 10.0000 chunk 18 optimal weight: 0.0060 chunk 27 optimal weight: 9.9990 chunk 131 optimal weight: 40.0000 chunk 8 optimal weight: 10.0000 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 80 ASN ** U 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.075398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.051578 restraints weight = 123084.154| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.79 r_work: 0.3015 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30507 Z= 0.395 Angle : 0.647 10.037 45866 Z= 0.327 Chirality : 0.037 0.241 5925 Planarity : 0.005 0.037 2271 Dihedral : 23.325 177.613 15736 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.55 % Favored : 91.45 % Rotamer: Outliers : 2.00 % Allowed : 16.77 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 959 helix: 0.74 (0.27), residues: 354 sheet: -1.19 (0.45), residues: 136 loop : -1.60 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 92 HIS 0.004 0.001 HIS E 29 PHE 0.025 0.002 PHE R 53 TYR 0.017 0.002 TYR R 83 ARG 0.004 0.001 ARG 2 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3724.87 seconds wall clock time: 69 minutes 58.50 seconds (4198.50 seconds total)