Starting phenix.real_space_refine on Thu Oct 29 11:16:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bof_12241/10_2026/7bof_12241.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bof_12241/10_2026/7bof_12241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bof_12241/10_2026/7bof_12241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bof_12241/10_2026/7bof_12241.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bof_12241/10_2026/7bof_12241.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bof_12241/10_2026/7bof_12241.cif" model { file = "/net/cci-nas-00/data/ceres_data/7bof_12241/10_2026/7bof_12241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bof_12241/10_2026/7bof_12241.cif" } resolution = 2.92 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians P 1070 5.49 5 Mg 129 5.21 5 S 40 5.16 5 C 16302 2.51 5 N 6099 2.21 5 O 9174 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.22s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32814 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 22995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 22995 Classifications: {'RNA': 4, 'RNAv2': 1066} Modifications used: {'rna2p_pur': 82, 'rna2p_pyr': 56, 'rna3p': 5, 'rna3p_pur': 534, 'rna3p_pyr': 393} Link IDs: {'rna2p': 137, 'rna3p': 932} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1156 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 5, 'TRANS': 151} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 129 Unusual residues: {' MG': 129} Classifications: {'undetermined': 129} Link IDs: {None: 128} Time building chain proxies: 6.29, per 1000 atoms: 0.19 Number of scatterers: 32814 At special positions: 0 Unit cell: (183.75, 150.15, 177.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 1070 15.00 Mg 129 11.99 O 9174 8.00 N 6099 7.00 C 16302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 674.5 milliseconds 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 41.5% alpha, 22.9% beta 363 base pairs and 611 stacking pairs defined. Time for finding SS restraints: 5.35 Creating SS restraints... Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.574A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 31 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 82 Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 152 through 165 removed outlier: 4.016A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU D 159 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU D 161 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.803A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 69 removed outlier: 3.783A pdb=" N ARG E 69 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 119 removed outlier: 3.575A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 146 Processing helix chain 'E' and resid 149 through 157 Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'F' and resid 12 through 15 Processing helix chain 'F' and resid 17 through 32 removed outlier: 4.180A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 81 removed outlier: 3.530A pdb=" N ILE F 71 " --> pdb=" O PRO F 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 30 through 43 Processing helix chain 'H' and resid 113 through 120 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 53 through 58 Processing helix chain 'K' and resid 59 through 75 removed outlier: 3.589A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 103 removed outlier: 4.421A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 Processing helix chain 'L' and resid 21 through 25 removed outlier: 3.746A pdb=" N LEU L 24 " --> pdb=" O VAL L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.742A pdb=" N GLY L 118 " --> pdb=" O SER L 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 46 removed outlier: 4.117A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 4.082A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 86 Processing helix chain 'P' and resid 53 through 63 Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'Q' and resid 49 through 52 removed outlier: 3.600A pdb=" N GLU Q 52 " --> pdb=" O GLU Q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 49 through 52' Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.564A pdb=" N ALA R 15 " --> pdb=" O CYS R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 33 removed outlier: 4.045A pdb=" N LYS R 30 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN R 31 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE R 33 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 65 Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 43 through 64 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 85 Processing sheet with id=AA1, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AA2, first strand: chain 'E' and resid 12 through 22 removed outlier: 5.295A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 85 through 89 removed outlier: 5.623A pdb=" N GLY E 104 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ALA E 125 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE E 106 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ALA E 127 " --> pdb=" O ILE E 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 38 through 44 removed outlier: 5.367A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 38 through 44 removed outlier: 5.367A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 24 through 28 Processing sheet with id=AA7, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AA8, first strand: chain 'H' and resid 74 through 77 removed outlier: 5.604A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 43 through 46 removed outlier: 3.929A pdb=" N GLY K 43 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL K 32 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU K 82 " --> pdb=" O THR K 108 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE K 110 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL K 84 " --> pdb=" O ILE K 110 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ASP K 112 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL K 86 " --> pdb=" O ASP K 112 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 62 through 66 removed outlier: 6.224A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 50 through 52 removed outlier: 6.548A pdb=" N VAL P 19 " --> pdb=" O VAL P 36 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE P 38 " --> pdb=" O TYR P 17 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR P 17 " --> pdb=" O PHE P 38 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL P 2 " --> pdb=" O THR P 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 8 through 17 removed outlier: 8.172A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP Q 15 " --> pdb=" O SER Q 20 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER Q 20 " --> pdb=" O ASP Q 15 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TRP Q 73 " --> pdb=" O HIS Q 45 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N VAL Q 78 " --> pdb=" O VAL Q 58 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL Q 58 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) 498 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 900 hydrogen bonds 1388 hydrogen bond angles 0 basepair planarities 363 basepair parallelities 611 stacking parallelities Total time for adding SS restraints: 14.67 Time building geometry restraints manager: 3.46 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: 5701 1.33 - 1.45: 14616 1.45 - 1.57: 13055 1.57 - 1.70: 2136 1.70 - 1.82: 69 Bond restraints: 35577 Sorted by residual: bond pdb=" C5 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.382 1.466 -0.084 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C4 PSU A 516 " pdb=" C5 PSU A 516 " ideal model delta sigma weight residual 1.390 1.471 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C5 MA6 A1519 " pdb=" C4 MA6 A1519 " ideal model delta sigma weight residual 1.394 1.469 -0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C5 MA6 A1518 " pdb=" C4 MA6 A1518 " ideal model delta sigma weight residual 1.394 1.460 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" N LYS L 44 " pdb=" CA LYS L 44 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.04e-02 9.25e+03 9.84e+00 ... (remaining 35572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 52859 3.81 - 7.61: 464 7.61 - 11.42: 18 11.42 - 15.23: 2 15.23 - 19.03: 1 Bond angle restraints: 53344 Sorted by residual: angle pdb=" CA D2T L 89 " pdb=" CB D2T L 89 " pdb=" SB D2T L 89 " ideal model delta sigma weight residual 114.38 95.35 19.03 3.00e+00 1.11e-01 4.03e+01 angle pdb=" N VAL L 87 " pdb=" CA VAL L 87 " pdb=" C VAL L 87 " ideal model delta sigma weight residual 108.17 101.55 6.62 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C6 MA6 A1519 " pdb=" N6 MA6 A1519 " pdb=" C9 MA6 A1519 " ideal model delta sigma weight residual 122.78 109.19 13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C3' A A 78 " pdb=" O3' A A 78 " pdb=" P G A 79 " ideal model delta sigma weight residual 119.70 125.11 -5.41 1.20e+00 6.94e-01 2.03e+01 angle pdb=" C3' A A1531 " pdb=" O3' A A1531 " pdb=" P U A1532 " ideal model delta sigma weight residual 119.70 124.94 -5.24 1.20e+00 6.94e-01 1.90e+01 ... (remaining 53339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 16939 34.37 - 68.74: 1856 68.74 - 103.11: 155 103.11 - 137.48: 0 137.48 - 171.84: 1 Dihedral angle restraints: 18951 sinusoidal: 15404 harmonic: 3547 Sorted by residual: dihedral pdb=" C4' C A 90 " pdb=" C3' C A 90 " pdb=" C2' C A 90 " pdb=" C1' C A 90 " ideal model delta sinusoidal sigma weight residual 36.34 -39.71 76.06 1 3.10e+00 1.04e-01 7.58e+02 dihedral pdb=" C4' A A 246 " pdb=" C3' A A 246 " pdb=" C2' A A 246 " pdb=" C1' A A 246 " ideal model delta sinusoidal sigma weight residual 36.34 -39.56 75.90 1 3.10e+00 1.04e-01 7.56e+02 dihedral pdb=" C4' G A1486 " pdb=" C3' G A1486 " pdb=" C2' G A1486 " pdb=" C1' G A1486 " ideal model delta sinusoidal sigma weight residual 36.34 -39.32 75.66 1 3.10e+00 1.04e-01 7.52e+02 ... (remaining 18948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5318 0.095 - 0.189: 370 0.189 - 0.284: 1085 0.284 - 0.379: 48 0.379 - 0.473: 1 Chirality restraints: 6822 Sorted by residual: chirality pdb=" CB D2T L 89 " pdb=" CA D2T L 89 " pdb=" SB D2T L 89 " pdb=" CG D2T L 89 " both_signs ideal model delta sigma weight residual False -3.02 -3.49 0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" C3' G A1486 " pdb=" C4' G A1486 " pdb=" O3' G A1486 " pdb=" C2' G A1486 " both_signs ideal model delta sigma weight residual False -2.50 -2.87 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C2' A A 792 " pdb=" C3' A A 792 " pdb=" O2' A A 792 " pdb=" C1' A A 792 " both_signs ideal model delta sigma weight residual False -2.79 -2.46 -0.33 2.00e-01 2.50e+01 2.77e+00 ... (remaining 6819 not shown) Planarity restraints: 2783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " 0.077 2.00e-02 2.50e+03 1.43e-01 6.61e+02 pdb=" N9 2MG A1516 " 0.012 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " -0.071 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " -0.096 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " -0.028 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " -0.011 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " -0.070 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " 0.069 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " 0.140 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " 0.205 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " 0.121 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " 0.045 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " -0.393 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " -0.127 2.00e-02 2.50e+03 2.08e-01 4.33e+02 pdb=" N6 MA6 A1519 " 0.360 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " -0.118 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1518 " 0.124 2.00e-02 2.50e+03 2.07e-01 4.27e+02 pdb=" N6 MA6 A1518 " -0.358 2.00e-02 2.50e+03 pdb=" C10 MA6 A1518 " 0.117 2.00e-02 2.50e+03 pdb=" C9 MA6 A1518 " 0.118 2.00e-02 2.50e+03 ... (remaining 2780 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 297 2.50 - 3.10: 22953 3.10 - 3.70: 65597 3.70 - 4.30: 94325 4.30 - 4.90: 125086 Nonbonded interactions: 308258 Sorted by model distance: nonbonded pdb=" OP1 G A 450 " pdb="MG MG A1663 " model vdw 1.894 2.170 nonbonded pdb=" OP2 G A 100 " pdb="MG MG A1642 " model vdw 1.915 2.170 nonbonded pdb=" OP2 G A 117 " pdb="MG MG A1701 " model vdw 1.922 2.170 nonbonded pdb=" OP2 A A 608 " pdb="MG MG A1622 " model vdw 1.930 2.170 nonbonded pdb=" OP2 G A 597 " pdb="MG MG A1672 " model vdw 1.931 2.170 ... (remaining 308253 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 ========== 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 39.590 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 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 : 0.008 0.084 35577 Z= 0.422 Angle : 0.966 19.034 53344 Z= 0.413 Chirality : 0.104 0.473 6822 Planarity : 0.007 0.208 2783 Dihedral : 20.435 171.844 16663 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.22), residues: 1213 helix: -0.79 (0.21), residues: 460 sheet: -2.31 (0.31), residues: 231 loop : -2.02 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 56 TYR 0.012 0.001 TYR R 51 PHE 0.018 0.002 PHE H 66 TRP 0.005 0.001 TRP P 60 HIS 0.004 0.001 HIS O 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.42 (35577) covalent geometry : angle 0.96613 / 0.41 (53344) hydrogen bonds : bond 0.20605 / 10.77 ( 1379) hydrogen bonds : angle 6.45525 / 2.61 ( 2783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.7834 (tmm160) cc_final: 0.7319 (ttp80) REVERT: D 141 ASP cc_start: 0.8203 (m-30) cc_final: 0.7797 (m-30) REVERT: E 12 GLN cc_start: 0.9103 (pt0) cc_final: 0.8879 (pt0) REVERT: E 23 LYS cc_start: 0.7636 (ttpt) cc_final: 0.6572 (mptt) REVERT: E 45 ARG cc_start: 0.8195 (ttt-90) cc_final: 0.7794 (ttp80) REVERT: E 61 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8777 (tp-100) REVERT: E 65 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8483 (tp30) REVERT: E 142 ASP cc_start: 0.8229 (t0) cc_final: 0.7961 (t0) REVERT: F 40 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6942 (mt-10) REVERT: F 52 ASN cc_start: 0.8725 (m110) cc_final: 0.8490 (m110) REVERT: F 75 GLU cc_start: 0.8018 (pp20) cc_final: 0.7730 (pp20) REVERT: F 79 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8124 (ttp-110) REVERT: F 88 MET cc_start: 0.8704 (ttt) cc_final: 0.8457 (ttt) REVERT: F 98 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7784 (tm-30) REVERT: H 52 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7841 (mm-30) REVERT: H 58 GLU cc_start: 0.7414 (mp0) cc_final: 0.7110 (mp0) REVERT: H 60 GLU cc_start: 0.8085 (tt0) cc_final: 0.7620 (tm-30) REVERT: H 96 MET cc_start: 0.9218 (mtp) cc_final: 0.8722 (ttp) REVERT: H 124 GLU cc_start: 0.8478 (tt0) cc_final: 0.8262 (tt0) REVERT: K 44 TRP cc_start: 0.8207 (p-90) cc_final: 0.7888 (p-90) REVERT: K 83 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6995 (mm-30) REVERT: K 106 ARG cc_start: 0.8323 (ttp80) cc_final: 0.8073 (tmm-80) REVERT: L 47 SER cc_start: 0.8436 (t) cc_final: 0.7522 (t) REVERT: L 62 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7506 (mt-10) REVERT: O 18 ASP cc_start: 0.8370 (m-30) cc_final: 0.8165 (m-30) REVERT: O 26 GLU cc_start: 0.8842 (mp0) cc_final: 0.8295 (mp0) REVERT: O 68 ASP cc_start: 0.8032 (m-30) cc_final: 0.7721 (m-30) REVERT: O 71 LYS cc_start: 0.8711 (tmmt) cc_final: 0.8452 (ptmm) REVERT: O 82 ILE cc_start: 0.9066 (pt) cc_final: 0.8450 (pp) REVERT: O 88 ARG cc_start: 0.8102 (mmm160) cc_final: 0.7831 (mmm160) REVERT: P 76 LYS cc_start: 0.8985 (ttmm) cc_final: 0.8716 (ttmt) REVERT: P 80 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8489 (ttmm) REVERT: Q 52 GLU cc_start: 0.8684 (tt0) cc_final: 0.8412 (tt0) REVERT: R 20 GLU cc_start: 0.7496 (tp30) cc_final: 0.7100 (tp30) REVERT: R 25 ASP cc_start: 0.8756 (t0) cc_final: 0.8225 (t0) REVERT: T 24 ARG cc_start: 0.8246 (mmt180) cc_final: 0.7542 (mmm160) outliers start: 0 outliers final: 1 residues processed: 379 average time/residue: 0.7961 time to fit residues: 350.9241 Evaluate side-chains 311 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 0.4980 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 100 ASN D 126 ASN D 136 GLN D 164 GLN E 73 ASN E 83 HIS E 89 HIS E 97 GLN E 135 ASN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 28 ASN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 6 GLN O 46 HIS Q 51 ASN R 74 HIS T 13 GLN T 61 GLN T 70 ASN T 78 ASN T 84 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.049637 restraints weight = 88067.633| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 1.08 r_work: 0.2630 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9150 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 35577 Z= 0.300 Angle : 1.321 23.313 53344 Z= 0.529 Chirality : 0.114 1.260 6822 Planarity : 0.005 0.055 2783 Dihedral : 18.914 172.269 14239 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.94 % Allowed : 18.42 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.24), residues: 1213 helix: 0.49 (0.23), residues: 477 sheet: -1.92 (0.30), residues: 245 loop : -1.19 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 29 TYR 0.010 0.002 TYR F 4 PHE 0.016 0.002 PHE K 61 TRP 0.004 0.001 TRP P 60 HIS 0.005 0.001 HIS F 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.30 (35577) covalent geometry : angle 1.32073 / 0.53 (53344) hydrogen bonds : bond 0.07536 / 3.83 ( 1379) hydrogen bonds : angle 3.64277 / 1.52 ( 2783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 351 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 ARG cc_start: 0.8019 (tmm160) cc_final: 0.7659 (ttp80) REVERT: D 141 ASP cc_start: 0.8192 (m-30) cc_final: 0.7956 (m-30) REVERT: E 23 LYS cc_start: 0.8685 (ttpt) cc_final: 0.7084 (mptt) REVERT: E 65 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8620 (tp30) REVERT: E 142 ASP cc_start: 0.8302 (t0) cc_final: 0.8026 (t0) REVERT: F 73 GLU cc_start: 0.8834 (tp30) cc_final: 0.8591 (tp30) REVERT: F 75 GLU cc_start: 0.8145 (pp20) cc_final: 0.7793 (pp20) REVERT: F 79 ARG cc_start: 0.8652 (ttm110) cc_final: 0.8130 (ttp-110) REVERT: F 90 MET cc_start: 0.8575 (ptm) cc_final: 0.8305 (ptm) REVERT: H 52 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8159 (mm-30) REVERT: H 58 GLU cc_start: 0.8141 (mp0) cc_final: 0.7886 (mp0) REVERT: H 96 MET cc_start: 0.9361 (mtp) cc_final: 0.9082 (ttp) REVERT: K 69 ARG cc_start: 0.7174 (ttp-110) cc_final: 0.6795 (ttp-110) REVERT: K 77 TYR cc_start: 0.8218 (m-80) cc_final: 0.7662 (m-10) REVERT: K 83 GLU cc_start: 0.6506 (mm-30) cc_final: 0.5860 (mm-30) REVERT: K 106 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8153 (tmm-80) REVERT: L 15 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.8100 (mptp) REVERT: L 47 SER cc_start: 0.9098 (t) cc_final: 0.8850 (t) REVERT: O 10 LYS cc_start: 0.9302 (tppp) cc_final: 0.9052 (tptm) REVERT: O 14 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: O 26 GLU cc_start: 0.9012 (mp0) cc_final: 0.8706 (mp0) REVERT: O 62 GLN cc_start: 0.9031 (OUTLIER) cc_final: 0.8822 (tp40) REVERT: O 68 ASP cc_start: 0.8463 (m-30) cc_final: 0.8165 (m-30) REVERT: O 82 ILE cc_start: 0.9086 (pt) cc_final: 0.8553 (pp) REVERT: O 83 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8263 (mm-30) REVERT: O 88 ARG cc_start: 0.8180 (mmm160) cc_final: 0.7889 (mmm160) REVERT: P 80 LYS cc_start: 0.9077 (ttpp) cc_final: 0.8737 (ttmm) REVERT: R 25 ASP cc_start: 0.8850 (t0) cc_final: 0.8493 (t0) REVERT: R 67 LEU cc_start: 0.9413 (mt) cc_final: 0.9208 (mt) REVERT: T 24 ARG cc_start: 0.8585 (mmt180) cc_final: 0.8150 (mmm160) outliers start: 40 outliers final: 21 residues processed: 360 average time/residue: 0.7439 time to fit residues: 313.6530 Evaluate side-chains 349 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 325 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 53 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [83, 49, 99, 142, 161, 39, 143, 119, 12, 34, 164] chunk 83 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 164 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN T 20 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.072621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.049852 restraints weight = 87575.790| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 1.08 r_work: 0.2631 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9148 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 35577 Z= 0.307 Angle : 1.169 21.390 53344 Z= 0.474 Chirality : 0.096 1.045 6822 Planarity : 0.005 0.042 2783 Dihedral : 19.150 176.559 14237 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.12 % Allowed : 21.38 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.24), residues: 1213 helix: 0.87 (0.24), residues: 477 sheet: -1.53 (0.32), residues: 234 loop : -0.75 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 127 TYR 0.011 0.002 TYR R 51 PHE 0.010 0.002 PHE O 43 TRP 0.006 0.001 TRP K 44 HIS 0.004 0.001 HIS O 42 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.31 (35577) covalent geometry : angle 1.16893 / 0.47 (53344) hydrogen bonds : bond 0.06966 / 3.54 ( 1379) hydrogen bonds : angle 3.49817 / 1.46 ( 2783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 164 GLN cc_start: 0.9247 (mm110) cc_final: 0.8995 (mm110) REVERT: E 20 ARG cc_start: 0.9156 (ttp-170) cc_final: 0.8775 (ttp-170) REVERT: E 23 LYS cc_start: 0.9093 (ttpt) cc_final: 0.7298 (mptt) REVERT: E 142 ASP cc_start: 0.8309 (t0) cc_final: 0.8101 (t0) REVERT: F 41 ASP cc_start: 0.8295 (t0) cc_final: 0.8034 (t0) REVERT: F 65 GLU cc_start: 0.8724 (tt0) cc_final: 0.8469 (tt0) REVERT: F 73 GLU cc_start: 0.8900 (tp30) cc_final: 0.8513 (tp30) REVERT: F 75 GLU cc_start: 0.8180 (pp20) cc_final: 0.7901 (pp20) REVERT: F 79 ARG cc_start: 0.8614 (ttm110) cc_final: 0.8137 (ttp-170) REVERT: H 52 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8185 (mm-30) REVERT: H 58 GLU cc_start: 0.8116 (mp0) cc_final: 0.7839 (mp0) REVERT: K 35 THR cc_start: 0.8443 (t) cc_final: 0.8175 (m) REVERT: K 77 TYR cc_start: 0.8131 (m-80) cc_final: 0.7762 (m-10) REVERT: K 80 LYS cc_start: 0.8709 (mppt) cc_final: 0.8491 (mptt) REVERT: L 47 SER cc_start: 0.8963 (t) cc_final: 0.8672 (t) REVERT: O 10 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9049 (tptm) REVERT: O 14 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: O 26 GLU cc_start: 0.9040 (mp0) cc_final: 0.8682 (mp0) REVERT: O 62 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8804 (tp40) REVERT: O 68 ASP cc_start: 0.8495 (m-30) cc_final: 0.8209 (m-30) REVERT: O 82 ILE cc_start: 0.9062 (pt) cc_final: 0.8509 (pp) REVERT: O 83 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8342 (mm-30) REVERT: O 88 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7857 (mmm160) REVERT: P 80 LYS cc_start: 0.9075 (ttpp) cc_final: 0.8775 (ttmm) REVERT: R 25 ASP cc_start: 0.8892 (t0) cc_final: 0.8521 (t0) REVERT: T 24 ARG cc_start: 0.8580 (mmt180) cc_final: 0.8163 (mmm160) outliers start: 52 outliers final: 29 residues processed: 347 average time/residue: 0.7287 time to fit residues: 297.8615 Evaluate side-chains 342 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 35 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [103, 62, 197, 102, 188, 113, 194, 165, 0, 76, 224] chunk 103 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 194 optimal weight: 4.9990 chunk 165 optimal weight: 0.0670 chunk 0 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 224 optimal weight: 0.8980 overall best weight: 2.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 GLN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN T 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.073642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.051055 restraints weight = 88001.687| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 1.08 r_work: 0.2659 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9137 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35577 Z= 0.247 Angle : 1.101 18.586 53344 Z= 0.447 Chirality : 0.089 0.942 6822 Planarity : 0.005 0.058 2783 Dihedral : 19.140 179.476 14237 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.53 % Allowed : 22.56 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.25), residues: 1213 helix: 1.01 (0.24), residues: 478 sheet: -1.22 (0.33), residues: 239 loop : -0.60 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 6 TYR 0.011 0.001 TYR F 4 PHE 0.016 0.001 PHE K 61 TRP 0.009 0.001 TRP K 44 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.25 (35577) covalent geometry : angle 1.10124 / 0.45 (53344) hydrogen bonds : bond 0.06712 / 3.41 ( 1379) hydrogen bonds : angle 3.37417 / 1.42 ( 2783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 326 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 164 GLN cc_start: 0.9200 (mm110) cc_final: 0.8921 (mm110) REVERT: E 10 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8114 (tm-30) REVERT: E 11 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8542 (pp) REVERT: E 20 ARG cc_start: 0.9162 (ttp-170) cc_final: 0.8812 (ttp-170) REVERT: E 23 LYS cc_start: 0.9077 (ttpt) cc_final: 0.7272 (mptt) REVERT: E 54 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8289 (mmm160) REVERT: F 73 GLU cc_start: 0.8862 (tp30) cc_final: 0.8460 (tp30) REVERT: F 75 GLU cc_start: 0.8174 (pp20) cc_final: 0.7886 (pp20) REVERT: F 79 ARG cc_start: 0.8559 (ttm110) cc_final: 0.8109 (ttp-170) REVERT: F 90 MET cc_start: 0.8469 (ptm) cc_final: 0.8138 (ptm) REVERT: H 52 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8133 (mm-30) REVERT: H 58 GLU cc_start: 0.8128 (mp0) cc_final: 0.7864 (mp0) REVERT: K 35 THR cc_start: 0.8313 (t) cc_final: 0.8034 (m) REVERT: K 77 TYR cc_start: 0.8173 (m-80) cc_final: 0.7885 (m-10) REVERT: K 85 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8130 (mmm) REVERT: L 15 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8041 (mptp) REVERT: L 73 ASN cc_start: 0.8906 (p0) cc_final: 0.8671 (p0) REVERT: O 10 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9058 (tptm) REVERT: O 14 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: O 58 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8302 (ttt90) REVERT: O 62 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8795 (tp40) REVERT: O 68 ASP cc_start: 0.8464 (m-30) cc_final: 0.8164 (m-30) REVERT: O 82 ILE cc_start: 0.9024 (pt) cc_final: 0.8446 (pp) REVERT: O 83 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8281 (mm-30) REVERT: O 88 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7823 (mmm160) REVERT: P 80 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8750 (ttmm) REVERT: Q 6 ARG cc_start: 0.8370 (ttm110) cc_final: 0.8095 (ttm-80) REVERT: Q 26 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: T 24 ARG cc_start: 0.8541 (mmt180) cc_final: 0.8162 (mmm160) outliers start: 46 outliers final: 26 residues processed: 342 average time/residue: 0.7203 time to fit residues: 291.0157 Evaluate side-chains 345 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 310 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [67, 194, 12, 196, 159, 209, 1, 88, 24, 31, 47] chunk 67 optimal weight: 6.9990 chunk 194 optimal weight: 0.7980 chunk 12 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN O 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.072948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.050194 restraints weight = 87425.687| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 1.08 r_work: 0.2636 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 35577 Z= 0.297 Angle : 1.125 16.606 53344 Z= 0.457 Chirality : 0.091 1.017 6822 Planarity : 0.005 0.056 2783 Dihedral : 19.155 179.644 14237 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.52 % Allowed : 24.24 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1213 helix: 1.13 (0.24), residues: 472 sheet: -1.09 (0.33), residues: 232 loop : -0.52 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 6 TYR 0.011 0.002 TYR R 51 PHE 0.013 0.002 PHE F 8 TRP 0.006 0.001 TRP K 44 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.30 (35577) covalent geometry : angle 1.12510 / 0.46 (53344) hydrogen bonds : bond 0.06784 / 3.46 ( 1379) hydrogen bonds : angle 3.35733 / 1.40 ( 2783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 323 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 ARG cc_start: 0.8710 (ptp-170) cc_final: 0.8444 (ptp-170) REVERT: D 164 GLN cc_start: 0.9242 (mm110) cc_final: 0.9011 (mm110) REVERT: E 11 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8546 (pp) REVERT: E 20 ARG cc_start: 0.9201 (ttp-170) cc_final: 0.8836 (ttp-170) REVERT: E 23 LYS cc_start: 0.9164 (ttpt) cc_final: 0.7252 (mptt) REVERT: E 54 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8283 (mmm160) REVERT: F 41 ASP cc_start: 0.8272 (t0) cc_final: 0.8066 (t0) REVERT: F 65 GLU cc_start: 0.8609 (tt0) cc_final: 0.8219 (tp30) REVERT: F 73 GLU cc_start: 0.8927 (tp30) cc_final: 0.8652 (tp30) REVERT: F 75 GLU cc_start: 0.8140 (pp20) cc_final: 0.7847 (pp20) REVERT: F 79 ARG cc_start: 0.8526 (ttm110) cc_final: 0.8081 (ttp-170) REVERT: F 80 PHE cc_start: 0.8037 (m-10) cc_final: 0.7805 (m-10) REVERT: H 52 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8161 (mm-30) REVERT: H 58 GLU cc_start: 0.8135 (mp0) cc_final: 0.7837 (mp0) REVERT: K 35 THR cc_start: 0.8390 (t) cc_final: 0.8178 (m) REVERT: K 77 TYR cc_start: 0.8058 (m-80) cc_final: 0.7786 (m-10) REVERT: L 15 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8095 (mptp) REVERT: L 44 LYS cc_start: 0.8194 (tttm) cc_final: 0.7966 (tptt) REVERT: O 10 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.9061 (tptm) REVERT: O 14 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: O 58 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8364 (ttt90) REVERT: O 62 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8784 (tt0) REVERT: O 68 ASP cc_start: 0.8504 (m-30) cc_final: 0.8231 (m-30) REVERT: O 82 ILE cc_start: 0.9080 (pt) cc_final: 0.8550 (pp) REVERT: O 83 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8433 (mm-30) REVERT: P 77 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8452 (pp20) REVERT: P 80 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8746 (ttmm) REVERT: Q 26 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7972 (mm-30) REVERT: R 25 ASP cc_start: 0.8835 (t0) cc_final: 0.8575 (t70) REVERT: T 24 ARG cc_start: 0.8594 (mmt180) cc_final: 0.8173 (mmm160) outliers start: 56 outliers final: 33 residues processed: 344 average time/residue: 0.7083 time to fit residues: 288.6860 Evaluate side-chains 353 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 311 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 11 ILE Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [151, 138, 209, 220, 93, 162, 104, 24, 181, 49, 215] chunk 151 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 93 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 181 optimal weight: 0.0030 chunk 49 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 GLN ** K 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 80 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.074057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.051390 restraints weight = 87728.141| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.08 r_work: 0.2666 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 35577 Z= 0.234 Angle : 1.076 14.888 53344 Z= 0.438 Chirality : 0.087 0.930 6822 Planarity : 0.004 0.048 2783 Dihedral : 19.190 179.287 14237 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.43 % Allowed : 26.60 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.25), residues: 1213 helix: 1.12 (0.23), residues: 478 sheet: -0.98 (0.33), residues: 239 loop : -0.45 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Q 11 TYR 0.012 0.001 TYR F 4 PHE 0.013 0.001 PHE F 78 TRP 0.004 0.001 TRP P 60 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.23 (35577) covalent geometry : angle 1.07644 / 0.44 (53344) hydrogen bonds : bond 0.06621 / 3.38 ( 1379) hydrogen bonds : angle 3.29915 / 1.39 ( 2783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 321 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 ARG cc_start: 0.8700 (ptp-170) cc_final: 0.8376 (ptp-170) REVERT: D 164 GLN cc_start: 0.9224 (mm110) cc_final: 0.8977 (mm110) REVERT: D 174 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7568 (p0) REVERT: E 20 ARG cc_start: 0.9184 (ttp-170) cc_final: 0.8860 (ttp-170) REVERT: E 23 LYS cc_start: 0.9153 (ttpt) cc_final: 0.7214 (mptt) REVERT: E 54 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8296 (mmm160) REVERT: F 41 ASP cc_start: 0.8234 (t0) cc_final: 0.8016 (t0) REVERT: F 53 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8543 (mtpp) REVERT: F 65 GLU cc_start: 0.8625 (tt0) cc_final: 0.8235 (tt0) REVERT: F 73 GLU cc_start: 0.8888 (tp30) cc_final: 0.8485 (tp30) REVERT: F 75 GLU cc_start: 0.8200 (pp20) cc_final: 0.7881 (pp20) REVERT: F 79 ARG cc_start: 0.8559 (ttm110) cc_final: 0.8051 (ttp-170) REVERT: F 80 PHE cc_start: 0.8028 (m-10) cc_final: 0.7782 (m-10) REVERT: F 90 MET cc_start: 0.8526 (ptm) cc_final: 0.8229 (ptm) REVERT: H 52 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8218 (mm-30) REVERT: H 58 GLU cc_start: 0.8126 (mp0) cc_final: 0.7822 (mp0) REVERT: K 77 TYR cc_start: 0.8107 (m-80) cc_final: 0.7886 (m-10) REVERT: K 85 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7972 (mmm) REVERT: L 15 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8132 (mptp) REVERT: L 44 LYS cc_start: 0.8170 (tttm) cc_final: 0.7949 (tptt) REVERT: O 10 LYS cc_start: 0.9329 (OUTLIER) cc_final: 0.9060 (tptm) REVERT: O 14 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: O 58 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8373 (ttt90) REVERT: O 62 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8817 (tp40) REVERT: O 68 ASP cc_start: 0.8483 (m-30) cc_final: 0.8192 (m-30) REVERT: O 82 ILE cc_start: 0.9019 (pt) cc_final: 0.8433 (pp) REVERT: O 83 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8369 (mm-30) REVERT: P 80 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8751 (ttmm) REVERT: Q 26 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7981 (mm-30) REVERT: R 25 ASP cc_start: 0.8775 (t0) cc_final: 0.8474 (t70) REVERT: T 24 ARG cc_start: 0.8576 (mmt180) cc_final: 0.8152 (mmm160) outliers start: 45 outliers final: 28 residues processed: 335 average time/residue: 0.6962 time to fit residues: 275.8188 Evaluate side-chains 349 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 312 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 76 VAL Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [119, 137, 54, 125, 189, 122, 38, 94, 57, 111, 128] chunk 119 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 57 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 22 HIS K 38 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** P 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.072856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.050051 restraints weight = 88084.228| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 1.09 r_work: 0.2631 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9145 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 35577 Z= 0.313 Angle : 1.125 16.706 53344 Z= 0.459 Chirality : 0.091 1.016 6822 Planarity : 0.005 0.078 2783 Dihedral : 19.222 179.051 14237 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 5.22 % Allowed : 27.49 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.24), residues: 1213 helix: 1.09 (0.23), residues: 477 sheet: -1.03 (0.33), residues: 239 loop : -0.45 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 6 TYR 0.020 0.002 TYR D 51 PHE 0.022 0.002 PHE K 61 TRP 0.006 0.001 TRP Q 73 HIS 0.004 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.31 (35577) covalent geometry : angle 1.12497 / 0.46 (53344) hydrogen bonds : bond 0.06758 / 3.45 ( 1379) hydrogen bonds : angle 3.33247 / 1.40 ( 2783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 310 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 ARG cc_start: 0.8715 (ptp-170) cc_final: 0.8359 (ptp-170) REVERT: E 10 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8266 (tm-30) REVERT: E 11 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8530 (pp) REVERT: E 23 LYS cc_start: 0.9152 (ttpt) cc_final: 0.7214 (mptt) REVERT: E 54 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8304 (mmm160) REVERT: F 2 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8278 (ptp90) REVERT: F 53 LYS cc_start: 0.8848 (mtpp) cc_final: 0.8561 (mtpp) REVERT: F 65 GLU cc_start: 0.8549 (tt0) cc_final: 0.8247 (tt0) REVERT: F 73 GLU cc_start: 0.8880 (tp30) cc_final: 0.8452 (tp30) REVERT: F 75 GLU cc_start: 0.8154 (pp20) cc_final: 0.7862 (pp20) REVERT: F 79 ARG cc_start: 0.8532 (ttm110) cc_final: 0.8111 (ttp-170) REVERT: F 80 PHE cc_start: 0.8067 (m-10) cc_final: 0.7780 (m-10) REVERT: F 90 MET cc_start: 0.8537 (ptm) cc_final: 0.8265 (ptm) REVERT: H 52 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8211 (mm-30) REVERT: H 58 GLU cc_start: 0.8152 (mp0) cc_final: 0.7822 (mp0) REVERT: K 77 TYR cc_start: 0.8108 (m-80) cc_final: 0.7858 (m-10) REVERT: K 85 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7994 (mmm) REVERT: L 15 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8117 (mptp) REVERT: L 56 ARG cc_start: 0.8364 (ttm-80) cc_final: 0.8037 (ttm170) REVERT: L 73 ASN cc_start: 0.8918 (p0) cc_final: 0.8705 (p0) REVERT: O 10 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.9070 (tptm) REVERT: O 14 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: O 58 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8380 (ttt90) REVERT: O 62 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8798 (tt0) REVERT: O 68 ASP cc_start: 0.8488 (m-30) cc_final: 0.8175 (m-30) REVERT: O 82 ILE cc_start: 0.9077 (pt) cc_final: 0.8499 (pp) REVERT: O 83 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8418 (mm-30) REVERT: P 77 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8471 (pp20) REVERT: P 80 LYS cc_start: 0.9041 (ttpp) cc_final: 0.8752 (ttmm) REVERT: R 25 ASP cc_start: 0.8798 (t0) cc_final: 0.8479 (t70) REVERT: T 24 ARG cc_start: 0.8600 (mmt180) cc_final: 0.8167 (mmm160) outliers start: 53 outliers final: 31 residues processed: 332 average time/residue: 0.7087 time to fit residues: 277.6437 Evaluate side-chains 345 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 304 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [0, 144, 191, 113, 100, 135, 48, 101, 79, 81, 168] chunk 0 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 191 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 GLN ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 6 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.049731 restraints weight = 87996.912| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 1.08 r_work: 0.2623 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9147 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 35577 Z= 0.332 Angle : 1.140 17.036 53344 Z= 0.465 Chirality : 0.093 1.047 6822 Planarity : 0.005 0.054 2783 Dihedral : 19.226 179.149 14237 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 5.22 % Allowed : 28.28 % Favored : 66.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.24), residues: 1213 helix: 1.11 (0.23), residues: 473 sheet: -1.02 (0.33), residues: 239 loop : -0.38 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 45 TYR 0.011 0.002 TYR F 59 PHE 0.010 0.002 PHE T 31 TRP 0.006 0.001 TRP Q 73 HIS 0.005 0.001 HIS K 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.33 (35577) covalent geometry : angle 1.14016 / 0.47 (53344) hydrogen bonds : bond 0.06788 / 3.47 ( 1379) hydrogen bonds : angle 3.34131 / 1.40 ( 2783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 164 GLN cc_start: 0.9113 (mm110) cc_final: 0.8875 (mm110) REVERT: E 11 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8530 (pp) REVERT: E 20 ARG cc_start: 0.9133 (ttp-170) cc_final: 0.8805 (ttp-170) REVERT: E 23 LYS cc_start: 0.9156 (ttpt) cc_final: 0.7208 (mptt) REVERT: E 54 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8295 (mmm160) REVERT: F 2 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8320 (ptp90) REVERT: F 53 LYS cc_start: 0.8908 (mtpp) cc_final: 0.8637 (mtpp) REVERT: F 65 GLU cc_start: 0.8616 (tt0) cc_final: 0.8266 (tt0) REVERT: F 73 GLU cc_start: 0.8878 (tp30) cc_final: 0.8462 (tp30) REVERT: F 75 GLU cc_start: 0.8148 (pp20) cc_final: 0.7840 (pp20) REVERT: F 79 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8107 (ttp-170) REVERT: F 80 PHE cc_start: 0.8181 (m-10) cc_final: 0.7888 (m-10) REVERT: H 52 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8164 (mm-30) REVERT: H 58 GLU cc_start: 0.8197 (mp0) cc_final: 0.7864 (mp0) REVERT: K 77 TYR cc_start: 0.8072 (m-80) cc_final: 0.7785 (m-10) REVERT: K 85 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7972 (mmm) REVERT: L 15 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8177 (mptp) REVERT: L 56 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.8028 (ttm170) REVERT: L 73 ASN cc_start: 0.8949 (p0) cc_final: 0.8742 (p0) REVERT: O 10 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.9066 (tptm) REVERT: O 14 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: O 48 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8573 (mtpp) REVERT: O 58 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8389 (ttt90) REVERT: O 62 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8801 (tt0) REVERT: O 68 ASP cc_start: 0.8506 (m-30) cc_final: 0.8192 (m-30) REVERT: O 82 ILE cc_start: 0.9062 (pt) cc_final: 0.8588 (pp) REVERT: P 77 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8459 (pp20) REVERT: P 80 LYS cc_start: 0.9027 (ttpp) cc_final: 0.8744 (ttmm) REVERT: Q 26 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7981 (mm-30) REVERT: R 25 ASP cc_start: 0.8770 (t0) cc_final: 0.8440 (t70) REVERT: T 24 ARG cc_start: 0.8622 (mmt180) cc_final: 0.8168 (mmm160) outliers start: 53 outliers final: 35 residues processed: 325 average time/residue: 0.7183 time to fit residues: 276.1464 Evaluate side-chains 349 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 302 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 54 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 7 THR Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [137, 45, 165, 172, 23, 96, 136, 159, 34, 126, 100] chunk 137 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 34 optimal weight: 8.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 5 ASN L 6 GLN ** P 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.073567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.050871 restraints weight = 87542.235| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 1.08 r_work: 0.2652 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9128 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 35577 Z= 0.234 Angle : 1.102 15.729 53344 Z= 0.451 Chirality : 0.089 0.988 6822 Planarity : 0.005 0.059 2783 Dihedral : 19.248 178.637 14237 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.24 % Allowed : 29.95 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1213 helix: 1.13 (0.23), residues: 473 sheet: -1.03 (0.34), residues: 243 loop : -0.33 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG Q 6 TYR 0.011 0.001 TYR F 59 PHE 0.024 0.002 PHE K 61 TRP 0.005 0.001 TRP P 60 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.23 (35577) covalent geometry : angle 1.10193 / 0.45 (53344) hydrogen bonds : bond 0.06678 / 3.41 ( 1379) hydrogen bonds : angle 3.31929 / 1.40 ( 2783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 312 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 ARG cc_start: 0.8610 (mtt180) cc_final: 0.8314 (ptp-170) REVERT: D 164 GLN cc_start: 0.9130 (mm110) cc_final: 0.8872 (mm110) REVERT: E 11 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8542 (pp) REVERT: E 20 ARG cc_start: 0.9120 (ttp-170) cc_final: 0.8804 (ttp-170) REVERT: E 23 LYS cc_start: 0.9157 (ttpt) cc_final: 0.7225 (mptt) REVERT: E 54 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8289 (mmm160) REVERT: E 162 GLU cc_start: 0.8634 (pm20) cc_final: 0.8358 (pm20) REVERT: F 17 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8845 (mm-40) REVERT: F 53 LYS cc_start: 0.8886 (mtpp) cc_final: 0.8602 (mtpp) REVERT: F 65 GLU cc_start: 0.8615 (tt0) cc_final: 0.8273 (tt0) REVERT: F 73 GLU cc_start: 0.8859 (tp30) cc_final: 0.8443 (tp30) REVERT: F 75 GLU cc_start: 0.8152 (pp20) cc_final: 0.7847 (pp20) REVERT: F 79 ARG cc_start: 0.8525 (ttm110) cc_final: 0.8110 (ttp-170) REVERT: F 80 PHE cc_start: 0.8113 (m-10) cc_final: 0.7826 (m-10) REVERT: F 90 MET cc_start: 0.8489 (ptm) cc_final: 0.8244 (ptm) REVERT: H 52 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8154 (mm-30) REVERT: H 58 GLU cc_start: 0.8192 (mp0) cc_final: 0.7877 (mp0) REVERT: K 77 TYR cc_start: 0.8078 (m-80) cc_final: 0.7779 (m-10) REVERT: K 85 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.7954 (mmm) REVERT: L 15 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8182 (mptp) REVERT: L 56 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.8021 (ttm170) REVERT: O 10 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.9065 (tptm) REVERT: O 14 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7872 (tm-30) REVERT: O 48 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8577 (mtpp) REVERT: O 58 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8392 (ttt90) REVERT: O 62 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8806 (tp40) REVERT: O 68 ASP cc_start: 0.8485 (m-30) cc_final: 0.8171 (m-30) REVERT: O 82 ILE cc_start: 0.9069 (pt) cc_final: 0.8807 (pp) REVERT: P 80 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8753 (ttmm) REVERT: R 25 ASP cc_start: 0.8772 (t0) cc_final: 0.8439 (t70) REVERT: T 24 ARG cc_start: 0.8607 (mmt180) cc_final: 0.8163 (mmm160) outliers start: 43 outliers final: 29 residues processed: 327 average time/residue: 0.6929 time to fit residues: 268.4707 Evaluate side-chains 345 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 306 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain H residue 62 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 58 ARG Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 14 SER Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [39, 194, 57, 93, 130, 88, 47, 99, 224, 122, 202] chunk 39 optimal weight: 4.9990 chunk 194 optimal weight: 0.0170 chunk 57 optimal weight: 4.9990 chunk 93 optimal weight: 20.0000 chunk 130 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 5 ASN ** Q 31 HIS ** 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 = 0.3355 r_free = 0.3355 target = 0.074615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.052028 restraints weight = 88170.673| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.08 r_work: 0.2686 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 35577 Z= 0.189 Angle : 1.069 14.516 53344 Z= 0.439 Chirality : 0.086 0.914 6822 Planarity : 0.005 0.048 2783 Dihedral : 19.252 178.858 14237 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.74 % Allowed : 30.25 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.25), residues: 1213 helix: 1.12 (0.24), residues: 474 sheet: -0.95 (0.34), residues: 241 loop : -0.26 (0.30), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 11 TYR 0.011 0.001 TYR F 59 PHE 0.012 0.001 PHE F 8 TRP 0.004 0.001 TRP K 44 HIS 0.006 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (35577) covalent geometry : angle 1.06894 / 0.44 (53344) hydrogen bonds : bond 0.06615 / 3.37 ( 1379) hydrogen bonds : angle 3.29253 / 1.39 ( 2783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2426 Ramachandran restraints generated. 1213 Oldfield, 0 Emsley, 1213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 319 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 47 ARG cc_start: 0.8586 (mtt180) cc_final: 0.8273 (ptp-170) REVERT: D 164 GLN cc_start: 0.9132 (mm110) cc_final: 0.8862 (mm110) REVERT: D 174 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7553 (p0) REVERT: E 11 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8555 (pp) REVERT: E 20 ARG cc_start: 0.9092 (ttp-170) cc_final: 0.8778 (ttp-170) REVERT: E 23 LYS cc_start: 0.9155 (ttpt) cc_final: 0.7236 (mptt) REVERT: E 54 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8280 (mmm160) REVERT: E 162 GLU cc_start: 0.8642 (pm20) cc_final: 0.8345 (pm20) REVERT: F 17 GLN cc_start: 0.9090 (OUTLIER) cc_final: 0.8816 (mm-40) REVERT: F 53 LYS cc_start: 0.8878 (mtpp) cc_final: 0.8588 (mtpp) REVERT: F 65 GLU cc_start: 0.8623 (tt0) cc_final: 0.8281 (tt0) REVERT: F 73 GLU cc_start: 0.8842 (tp30) cc_final: 0.8566 (tp30) REVERT: F 75 GLU cc_start: 0.8137 (pp20) cc_final: 0.7802 (pp20) REVERT: F 79 ARG cc_start: 0.8528 (ttm110) cc_final: 0.8044 (ttp-170) REVERT: F 80 PHE cc_start: 0.8111 (m-10) cc_final: 0.7886 (m-10) REVERT: F 90 MET cc_start: 0.8463 (ptm) cc_final: 0.8212 (ptm) REVERT: H 52 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8183 (mm-30) REVERT: H 58 GLU cc_start: 0.8192 (mp0) cc_final: 0.7851 (mp0) REVERT: K 77 TYR cc_start: 0.8031 (m-80) cc_final: 0.7750 (m-10) REVERT: K 85 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7927 (mmm) REVERT: L 5 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8581 (m-40) REVERT: L 15 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8163 (mptp) REVERT: L 56 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8000 (ttm170) REVERT: L 62 GLU cc_start: 0.8248 (mm-30) cc_final: 0.8000 (mm-30) REVERT: O 10 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.9054 (tptm) REVERT: O 14 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: O 18 ASP cc_start: 0.8468 (m-30) cc_final: 0.8058 (m-30) REVERT: O 21 ASP cc_start: 0.9058 (t0) cc_final: 0.8823 (t0) REVERT: O 48 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8566 (mtpp) REVERT: O 62 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8807 (tp40) REVERT: O 68 ASP cc_start: 0.8479 (m-30) cc_final: 0.8181 (m-30) REVERT: O 82 ILE cc_start: 0.9033 (pt) cc_final: 0.8782 (pp) REVERT: P 80 LYS cc_start: 0.9038 (ttpp) cc_final: 0.8751 (ttmm) REVERT: R 25 ASP cc_start: 0.8742 (t0) cc_final: 0.8377 (t70) REVERT: T 24 ARG cc_start: 0.8594 (mmt180) cc_final: 0.8152 (mmm160) outliers start: 38 outliers final: 22 residues processed: 331 average time/residue: 0.6903 time to fit residues: 270.7312 Evaluate side-chains 342 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 54 ARG Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 9 MET Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 85 MET Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 5 ASN Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 75 GLN Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain O residue 10 LYS Chi-restraints excluded: chain O residue 14 GLU Chi-restraints excluded: chain O residue 40 GLN Chi-restraints excluded: chain O residue 48 LYS Chi-restraints excluded: chain O residue 62 GLN Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 80 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: [46, 112, 87, 80, 22, 166, 184, 211, 111, 199, 51] chunk 46 optimal weight: 9.9990 chunk 112 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 184 optimal weight: 0.0370 chunk 211 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 97 GLN L 5 ASN L 6 GLN ** Q 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.074656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.052111 restraints weight = 87969.793| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.08 r_work: 0.2682 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 35577 Z= 0.220 Angle : 1.066 14.536 53344 Z= 0.437 Chirality : 0.085 0.883 6822 Planarity : 0.004 0.051 2783 Dihedral : 19.194 179.881 14237 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.55 % Allowed : 31.23 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.25), residues: 1213 helix: 1.12 (0.23), residues: 479 sheet: -0.89 (0.34), residues: 240 loop : -0.23 (0.30), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 45 TYR 0.011 0.001 TYR Q 34 PHE 0.027 0.002 PHE K 61 TRP 0.004 0.001 TRP Q 73 HIS 0.005 0.001 HIS K 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (35577) covalent geometry : angle 1.06600 / 0.44 (53344) hydrogen bonds : bond 0.06539 / 3.34 ( 1379) hydrogen bonds : angle 3.26698 / 1.38 ( 2783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11774.74 seconds wall clock time: 200 minutes 52.06 seconds (12052.06 seconds total)