Starting phenix.real_space_refine on Wed Aug 5 04:08:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pop_17794/08_2026/8pop_17794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pop_17794/08_2026/8pop_17794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pop_17794/08_2026/8pop_17794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pop_17794/08_2026/8pop_17794.map" model { file = "/net/cci-nas-00/data/ceres_data/8pop_17794/08_2026/8pop_17794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pop_17794/08_2026/8pop_17794.cif" } resolution = 3.0 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 55 5.49 5 S 1 5.16 5 C 5374 2.51 5 N 1692 2.21 5 O 1807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8929 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "B" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1003 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "D" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "F" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "G" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "I" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 827 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "J" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 577 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "K" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 568 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Time building chain proxies: 1.42, per 1000 atoms: 0.16 Number of scatterers: 8929 At special positions: 0 Unit cell: (96.3001, 103.433, 105.811, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 1 16.00 P 55 15.00 O 1807 8.00 N 1692 7.00 C 5374 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: 0.50 Conformation dependent library (CDL) restraints added in 256.7 milliseconds 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 81.8% alpha, 0.0% beta 28 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 removed outlier: 3.555A pdb=" N ALA A 14 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 38 through 47 Processing helix chain 'A' and resid 48 through 49 No H-bonds generated for 'chain 'A' and resid 48 through 49' Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 55 through 85 removed outlier: 3.597A pdb=" N GLU A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N THR A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 116 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 48 through 49 No H-bonds generated for 'chain 'B' and resid 48 through 49' Processing helix chain 'B' and resid 50 through 54 Processing helix chain 'B' and resid 55 through 85 removed outlier: 3.599A pdb=" N GLU B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 116 Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 126 through 129 Processing helix chain 'B' and resid 130 through 145 removed outlier: 3.972A pdb=" N ASN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'C' and resid 38 through 47 Processing helix chain 'C' and resid 48 through 49 No H-bonds generated for 'chain 'C' and resid 48 through 49' Processing helix chain 'C' and resid 50 through 54 Processing helix chain 'C' and resid 55 through 85 removed outlier: 3.597A pdb=" N GLU C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 116 Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'D' and resid 35 through 37 No H-bonds generated for 'chain 'D' and resid 35 through 37' Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 48 through 49 No H-bonds generated for 'chain 'D' and resid 48 through 49' Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 55 through 85 removed outlier: 3.585A pdb=" N GLU D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR D 73 " --> pdb=" O GLN D 69 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 116 Processing helix chain 'D' and resid 119 through 123 Processing helix chain 'E' and resid 35 through 37 No H-bonds generated for 'chain 'E' and resid 35 through 37' Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 48 through 49 No H-bonds generated for 'chain 'E' and resid 48 through 49' Processing helix chain 'E' and resid 50 through 54 Processing helix chain 'E' and resid 55 through 85 removed outlier: 3.598A pdb=" N GLU E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR E 73 " --> pdb=" O GLN E 69 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE E 85 " --> pdb=" O LYS E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 116 Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'F' and resid 35 through 37 No H-bonds generated for 'chain 'F' and resid 35 through 37' Processing helix chain 'F' and resid 38 through 47 Processing helix chain 'F' and resid 48 through 49 No H-bonds generated for 'chain 'F' and resid 48 through 49' Processing helix chain 'F' and resid 50 through 54 Processing helix chain 'F' and resid 55 through 85 removed outlier: 3.601A pdb=" N GLU F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR F 73 " --> pdb=" O GLN F 69 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 116 Processing helix chain 'F' and resid 119 through 124 Processing helix chain 'G' and resid 35 through 37 No H-bonds generated for 'chain 'G' and resid 35 through 37' Processing helix chain 'G' and resid 38 through 47 Processing helix chain 'G' and resid 48 through 49 No H-bonds generated for 'chain 'G' and resid 48 through 49' Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 55 through 85 removed outlier: 3.594A pdb=" N GLU G 64 " --> pdb=" O LEU G 60 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR G 73 " --> pdb=" O GLN G 69 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE G 85 " --> pdb=" O LYS G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 116 Processing helix chain 'G' and resid 119 through 124 Processing helix chain 'H' and resid 35 through 37 No H-bonds generated for 'chain 'H' and resid 35 through 37' Processing helix chain 'H' and resid 38 through 47 Processing helix chain 'H' and resid 48 through 49 No H-bonds generated for 'chain 'H' and resid 48 through 49' Processing helix chain 'H' and resid 50 through 54 Processing helix chain 'H' and resid 55 through 85 removed outlier: 3.587A pdb=" N GLU H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR H 73 " --> pdb=" O GLN H 69 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE H 85 " --> pdb=" O LYS H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 116 Processing helix chain 'H' and resid 119 through 124 Processing helix chain 'I' and resid 35 through 37 No H-bonds generated for 'chain 'I' and resid 35 through 37' Processing helix chain 'I' and resid 38 through 47 Processing helix chain 'I' and resid 48 through 49 No H-bonds generated for 'chain 'I' and resid 48 through 49' Processing helix chain 'I' and resid 50 through 54 Processing helix chain 'I' and resid 55 through 85 removed outlier: 3.619A pdb=" N GLU I 64 " --> pdb=" O LEU I 60 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR I 73 " --> pdb=" O GLN I 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE I 85 " --> pdb=" O LYS I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 116 Processing helix chain 'I' and resid 119 through 124 525 hydrogen bonds defined for protein. 1506 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1862 1.33 - 1.45: 2434 1.45 - 1.58: 4777 1.58 - 1.70: 109 1.70 - 1.82: 2 Bond restraints: 9184 Sorted by residual: bond pdb=" C4 DT J 24 " pdb=" C5 DT J 24 " ideal model delta sigma weight residual 1.445 1.409 0.036 9.00e-03 1.23e+04 1.56e+01 bond pdb=" N3 DA J 23 " pdb=" C4 DA J 23 " ideal model delta sigma weight residual 1.344 1.323 0.021 6.00e-03 2.78e+04 1.27e+01 bond pdb=" CE1 HIS I 119 " pdb=" NE2 HIS I 119 " ideal model delta sigma weight residual 1.321 1.288 0.033 1.00e-02 1.00e+04 1.12e+01 bond pdb=" C5 DT J 24 " pdb=" C6 DT J 24 " ideal model delta sigma weight residual 1.339 1.316 0.023 7.00e-03 2.04e+04 1.09e+01 bond pdb=" N1 DT J 24 " pdb=" C6 DT J 24 " ideal model delta sigma weight residual 1.378 1.356 0.022 7.00e-03 2.04e+04 9.72e+00 ... (remaining 9179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 11900 2.66 - 5.33: 635 5.33 - 7.99: 78 7.99 - 10.65: 18 10.65 - 13.31: 5 Bond angle restraints: 12636 Sorted by residual: angle pdb=" O4' DT K 25 " pdb=" C1' DT K 25 " pdb=" N1 DT K 25 " ideal model delta sigma weight residual 108.00 101.13 6.87 7.00e-01 2.04e+00 9.64e+01 angle pdb=" O4' DT K 29 " pdb=" C1' DT K 29 " pdb=" N1 DT K 29 " ideal model delta sigma weight residual 108.00 102.30 5.70 7.00e-01 2.04e+00 6.63e+01 angle pdb=" O5' DT K 26 " pdb=" C5' DT K 26 " pdb=" C4' DT K 26 " ideal model delta sigma weight residual 109.40 115.22 -5.82 8.00e-01 1.56e+00 5.29e+01 angle pdb=" O4' DG J 27 " pdb=" C1' DG J 27 " pdb=" N9 DG J 27 " ideal model delta sigma weight residual 108.00 112.76 -4.76 7.00e-01 2.04e+00 4.63e+01 angle pdb=" O4' DT K 35 " pdb=" C1' DT K 35 " pdb=" N1 DT K 35 " ideal model delta sigma weight residual 108.00 103.28 4.72 7.00e-01 2.04e+00 4.55e+01 ... (remaining 12631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.10: 5151 33.10 - 66.21: 422 66.21 - 99.31: 10 99.31 - 132.41: 0 132.41 - 165.51: 1 Dihedral angle restraints: 5584 sinusoidal: 2781 harmonic: 2803 Sorted by residual: dihedral pdb=" CA ALA A 22 " pdb=" C ALA A 22 " pdb=" N VAL A 23 " pdb=" CA VAL A 23 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DT K 10 " pdb=" C3' DT K 10 " pdb=" O3' DT K 10 " pdb=" P DA K 11 " ideal model delta sinusoidal sigma weight residual 220.00 54.49 165.51 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" CA ASP H 24 " pdb=" C ASP H 24 " pdb=" N THR H 25 " pdb=" CA THR H 25 " ideal model delta harmonic sigma weight residual -180.00 -160.50 -19.50 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1291 0.128 - 0.257: 117 0.257 - 0.385: 6 0.385 - 0.514: 0 0.514 - 0.642: 1 Chirality restraints: 1415 Sorted by residual: chirality pdb=" P DT K 10 " pdb=" OP1 DT K 10 " pdb=" OP2 DT K 10 " pdb=" O5' DT K 10 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CB VAL C 103 " pdb=" CA VAL C 103 " pdb=" CG1 VAL C 103 " pdb=" CG2 VAL C 103 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C4' DT J 24 " pdb=" C5' DT J 24 " pdb=" O4' DT J 24 " pdb=" C3' DT J 24 " both_signs ideal model delta sigma weight residual False -2.53 -2.24 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 1412 not shown) Planarity restraints: 1461 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 26 " -0.105 2.00e-02 2.50e+03 4.69e-02 5.50e+01 pdb=" N1 DT K 26 " 0.070 2.00e-02 2.50e+03 pdb=" C2 DT K 26 " 0.026 2.00e-02 2.50e+03 pdb=" O2 DT K 26 " 0.021 2.00e-02 2.50e+03 pdb=" N3 DT K 26 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT K 26 " -0.037 2.00e-02 2.50e+03 pdb=" O4 DT K 26 " -0.044 2.00e-02 2.50e+03 pdb=" C5 DT K 26 " 0.008 2.00e-02 2.50e+03 pdb=" C7 DT K 26 " 0.016 2.00e-02 2.50e+03 pdb=" C6 DT K 26 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K 29 " -0.090 2.00e-02 2.50e+03 4.27e-02 4.56e+01 pdb=" N1 DT K 29 " 0.083 2.00e-02 2.50e+03 pdb=" C2 DT K 29 " 0.031 2.00e-02 2.50e+03 pdb=" O2 DT K 29 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT K 29 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DT K 29 " -0.024 2.00e-02 2.50e+03 pdb=" O4 DT K 29 " -0.035 2.00e-02 2.50e+03 pdb=" C5 DT K 29 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT K 29 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT K 29 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K 25 " -0.076 2.00e-02 2.50e+03 3.83e-02 3.67e+01 pdb=" N1 DT K 25 " 0.077 2.00e-02 2.50e+03 pdb=" C2 DT K 25 " 0.024 2.00e-02 2.50e+03 pdb=" O2 DT K 25 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DT K 25 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DT K 25 " -0.003 2.00e-02 2.50e+03 pdb=" O4 DT K 25 " -0.045 2.00e-02 2.50e+03 pdb=" C5 DT K 25 " 0.009 2.00e-02 2.50e+03 pdb=" C7 DT K 25 " 0.014 2.00e-02 2.50e+03 pdb=" C6 DT K 25 " -0.011 2.00e-02 2.50e+03 ... (remaining 1458 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2015 2.80 - 3.33: 8523 3.33 - 3.85: 15099 3.85 - 4.38: 18959 4.38 - 4.90: 28441 Nonbonded interactions: 73037 Sorted by model distance: nonbonded pdb=" O ASN A 20 " pdb=" O VAL A 23 " model vdw 2.277 3.040 nonbonded pdb=" OH TYR C 71 " pdb=" OE2 GLU D 83 " model vdw 2.389 3.040 nonbonded pdb=" N GLU E 89 " pdb=" OE1 GLU E 89 " model vdw 2.405 3.120 nonbonded pdb=" O ALA A 50 " pdb=" OG SER A 53 " model vdw 2.409 3.040 nonbonded pdb=" OG SER F 120 " pdb=" OD1 ASN F 124 " model vdw 2.410 3.040 ... (remaining 73032 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 24 through 124) selection = chain 'G' selection = (chain 'H' and resid 24 through 124) selection = chain 'I' } 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.210 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:5.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.009 0.058 9184 Z= 0.606 Angle : 1.445 13.313 12636 Z= 0.996 Chirality : 0.076 0.642 1415 Planarity : 0.015 0.236 1461 Dihedral : 20.033 165.513 3734 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 0.12 % Allowed : 1.19 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.23), residues: 935 helix: -0.39 (0.17), residues: 686 sheet: None (None), residues: 0 loop : 0.37 (0.35), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.003 ARG H 114 TYR 0.024 0.008 TYR G 71 PHE 0.039 0.009 PHE H 41 TRP 0.028 0.007 TRP A 42 HIS 0.024 0.005 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.61 ( 9184) covalent geometry : angle 1.44480 / 1.00 (12636) hydrogen bonds : bond 0.26673 / 18.08 ( 589) hydrogen bonds : angle 6.56117 / 4.76 ( 1634) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8107 (mtpt) REVERT: A 24 ASP cc_start: 0.8444 (t0) cc_final: 0.8135 (t0) REVERT: A 64 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8271 (mt-10) REVERT: A 77 LYS cc_start: 0.8046 (mttt) cc_final: 0.7679 (mptt) REVERT: A 78 ASP cc_start: 0.8275 (t0) cc_final: 0.7883 (t0) REVERT: A 82 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7874 (mp0) REVERT: A 92 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7603 (mm-30) REVERT: A 96 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8114 (ttpt) REVERT: B 47 ARG cc_start: 0.8969 (mtt90) cc_final: 0.8123 (mtp180) REVERT: B 78 ASP cc_start: 0.8375 (m-30) cc_final: 0.8139 (m-30) REVERT: B 82 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8513 (mp0) REVERT: B 96 LYS cc_start: 0.8859 (tttt) cc_final: 0.8533 (ttpp) REVERT: B 135 GLN cc_start: 0.8699 (tp40) cc_final: 0.8436 (tp40) REVERT: C 82 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8154 (mm-30) REVERT: C 121 HIS cc_start: 0.8124 (t-90) cc_final: 0.7845 (t-90) REVERT: D 47 ARG cc_start: 0.8835 (mtm110) cc_final: 0.8027 (mtt90) REVERT: D 82 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8204 (mp0) REVERT: D 97 ASP cc_start: 0.8403 (m-30) cc_final: 0.8151 (m-30) REVERT: D 100 LYS cc_start: 0.8511 (mttt) cc_final: 0.7975 (tptp) REVERT: E 77 LYS cc_start: 0.8395 (tttt) cc_final: 0.8066 (tmtt) REVERT: E 81 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7754 (tttt) REVERT: E 96 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8105 (tttp) REVERT: E 100 LYS cc_start: 0.7858 (mttt) cc_final: 0.7513 (tptp) REVERT: E 115 ASP cc_start: 0.8726 (t70) cc_final: 0.8392 (OUTLIER) REVERT: F 39 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8443 (tm-30) REVERT: F 52 ASP cc_start: 0.8196 (m-30) cc_final: 0.7867 (p0) REVERT: F 64 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8445 (mm-30) REVERT: F 83 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8090 (mt-10) REVERT: F 91 ASP cc_start: 0.7858 (t0) cc_final: 0.7417 (t0) REVERT: F 96 LYS cc_start: 0.8619 (tttt) cc_final: 0.8330 (ttpp) REVERT: G 34 LEU cc_start: 0.7714 (tp) cc_final: 0.7480 (tp) REVERT: G 82 GLU cc_start: 0.8303 (mm-30) cc_final: 0.8006 (mp0) REVERT: G 85 ILE cc_start: 0.7764 (mt) cc_final: 0.7501 (mp) REVERT: H 77 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8123 (mmmt) REVERT: H 78 ASP cc_start: 0.8058 (m-30) cc_final: 0.7822 (m-30) REVERT: I 51 LEU cc_start: 0.8593 (mt) cc_final: 0.8324 (mm) REVERT: I 85 ILE cc_start: 0.7976 (mt) cc_final: 0.7737 (mm) REVERT: I 96 LYS cc_start: 0.8573 (tttt) cc_final: 0.8271 (ttpp) REVERT: I 107 ARG cc_start: 0.8475 (mtt180) cc_final: 0.7602 (mtp85) outliers start: 1 outliers final: 1 residues processed: 295 average time/residue: 0.6247 time to fit residues: 192.6530 Evaluate side-chains 227 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN B 101 GLN C 69 GLN D 43 HIS D 101 GLN E 124 ASN F 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.141947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121788 restraints weight = 11274.391| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.46 r_work: 0.3314 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9184 Z= 0.213 Angle : 0.700 8.916 12636 Z= 0.382 Chirality : 0.047 0.390 1415 Planarity : 0.006 0.036 1461 Dihedral : 22.116 148.478 1682 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.23 % Allowed : 13.38 % Favored : 83.39 % 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: 2.54 (0.25), residues: 935 helix: 2.06 (0.19), residues: 686 sheet: None (None), residues: 0 loop : 0.75 (0.31), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 84 TYR 0.010 0.002 TYR B 71 PHE 0.010 0.002 PHE G 41 TRP 0.007 0.002 TRP D 54 HIS 0.006 0.001 HIS G 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.21 ( 9184) covalent geometry : angle 0.70018 / 0.38 (12636) hydrogen bonds : bond 0.10551 / 7.29 ( 589) hydrogen bonds : angle 4.06035 / 2.90 ( 1634) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7614 (t0) cc_final: 0.7369 (t70) REVERT: A 37 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8506 (mmmt) REVERT: A 64 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8261 (mt-10) REVERT: A 77 LYS cc_start: 0.8409 (mttt) cc_final: 0.8136 (mptt) REVERT: A 80 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7575 (mpt180) REVERT: B 47 ARG cc_start: 0.8798 (mtt90) cc_final: 0.8206 (mtp180) REVERT: B 96 LYS cc_start: 0.8731 (tttt) cc_final: 0.8528 (ttpp) REVERT: B 135 GLN cc_start: 0.8826 (tp40) cc_final: 0.8609 (tp40) REVERT: C 64 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7915 (mm-30) REVERT: C 100 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8240 (mtpt) REVERT: D 81 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7736 (ttmm) REVERT: E 77 LYS cc_start: 0.8681 (tttt) cc_final: 0.8449 (tmtt) REVERT: E 96 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7892 (tttp) REVERT: E 117 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8416 (mt0) REVERT: F 64 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7809 (mm-30) REVERT: F 82 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7668 (mp0) REVERT: F 91 ASP cc_start: 0.8150 (t0) cc_final: 0.7873 (t0) REVERT: G 80 ARG cc_start: 0.8023 (mmt-90) cc_final: 0.7746 (mtt-85) REVERT: G 82 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7957 (mp0) REVERT: G 85 ILE cc_start: 0.8347 (mt) cc_final: 0.8064 (mp) REVERT: H 81 LYS cc_start: 0.8586 (ttmt) cc_final: 0.8201 (tmtm) REVERT: H 84 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7248 (mpp-170) REVERT: H 121 HIS cc_start: 0.8488 (t-90) cc_final: 0.8244 (t70) REVERT: I 107 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7891 (mtp85) outliers start: 27 outliers final: 7 residues processed: 244 average time/residue: 0.6259 time to fit residues: 159.5967 Evaluate side-chains 228 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 220 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 84 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 142 ASN D 101 GLN E 106 GLN F 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119309 restraints weight = 11342.690| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.43 r_work: 0.3274 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9184 Z= 0.173 Angle : 0.641 7.763 12636 Z= 0.343 Chirality : 0.043 0.346 1415 Planarity : 0.004 0.033 1461 Dihedral : 22.129 150.865 1682 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.87 % Allowed : 18.88 % Favored : 78.26 % 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: 3.23 (0.25), residues: 935 helix: 2.68 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 0.89 (0.29), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 113 TYR 0.007 0.001 TYR D 71 PHE 0.011 0.002 PHE G 41 TRP 0.006 0.001 TRP C 42 HIS 0.010 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 ( 9184) covalent geometry : angle 0.64135 / 0.34 (12636) hydrogen bonds : bond 0.08803 / 6.09 ( 589) hydrogen bonds : angle 3.71268 / 2.66 ( 1634) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.204 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8468 (mmmt) REVERT: A 77 LYS cc_start: 0.8313 (mttt) cc_final: 0.8023 (mptt) REVERT: B 47 ARG cc_start: 0.8820 (mtt90) cc_final: 0.8205 (mtp-110) REVERT: B 145 ASN cc_start: 0.7454 (m-40) cc_final: 0.7170 (m-40) REVERT: C 64 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7672 (mm-30) REVERT: C 82 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7467 (tp30) REVERT: C 100 LYS cc_start: 0.8470 (ttmm) cc_final: 0.8204 (mtpt) REVERT: D 81 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7803 (ttmm) REVERT: E 84 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7656 (mtp180) REVERT: E 117 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8614 (mt0) REVERT: F 52 ASP cc_start: 0.7957 (p0) cc_final: 0.7682 (p0) REVERT: F 91 ASP cc_start: 0.8260 (t0) cc_final: 0.7803 (t0) REVERT: G 82 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7683 (mp0) REVERT: G 85 ILE cc_start: 0.7985 (mt) cc_final: 0.7730 (mp) REVERT: G 86 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6408 (ttm170) REVERT: H 81 LYS cc_start: 0.8318 (ttmt) cc_final: 0.8059 (tmtm) REVERT: H 84 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7391 (mpp-170) REVERT: H 121 HIS cc_start: 0.8488 (t-90) cc_final: 0.8233 (t70) REVERT: I 107 ARG cc_start: 0.8297 (mtt180) cc_final: 0.7780 (mtp85) REVERT: I 114 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8103 (tpt170) outliers start: 24 outliers final: 6 residues processed: 228 average time/residue: 0.6369 time to fit residues: 151.5600 Evaluate side-chains 221 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 211 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain I residue 114 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 9.9990 chunk 49 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN B 101 GLN B 135 GLN F 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.120328 restraints weight = 11446.220| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.47 r_work: 0.3289 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9184 Z= 0.160 Angle : 0.613 8.512 12636 Z= 0.323 Chirality : 0.041 0.356 1415 Planarity : 0.005 0.060 1461 Dihedral : 22.052 146.792 1682 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.23 % Allowed : 20.79 % Favored : 75.99 % 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: 3.55 (0.25), residues: 935 helix: 2.90 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 1.08 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 47 TYR 0.006 0.001 TYR D 71 PHE 0.007 0.001 PHE G 41 TRP 0.003 0.001 TRP A 54 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 ( 9184) covalent geometry : angle 0.61268 / 0.32 (12636) hydrogen bonds : bond 0.07677 / 5.30 ( 589) hydrogen bonds : angle 3.51410 / 2.53 ( 1634) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.316 Fit side-chains REVERT: A 37 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8428 (mmmt) REVERT: A 77 LYS cc_start: 0.8331 (mttt) cc_final: 0.8018 (mptt) REVERT: B 47 ARG cc_start: 0.8790 (mtt90) cc_final: 0.8138 (mtp-110) REVERT: C 82 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7553 (tp30) REVERT: C 100 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8081 (mtpt) REVERT: D 27 ASP cc_start: 0.8783 (m-30) cc_final: 0.8549 (m-30) REVERT: E 81 LYS cc_start: 0.8743 (ttmp) cc_final: 0.8378 (tttt) REVERT: E 84 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7520 (mtp180) REVERT: E 117 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8682 (mt0) REVERT: F 52 ASP cc_start: 0.8119 (p0) cc_final: 0.7831 (p0) REVERT: F 83 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7563 (mt-10) REVERT: F 86 ARG cc_start: 0.7090 (mmt180) cc_final: 0.6729 (mmt-90) REVERT: G 85 ILE cc_start: 0.7960 (mt) cc_final: 0.7645 (mp) REVERT: G 86 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.5791 (ttm170) REVERT: H 81 LYS cc_start: 0.8447 (ttmt) cc_final: 0.7958 (tmtm) REVERT: H 84 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7461 (mpp-170) REVERT: H 121 HIS cc_start: 0.8496 (t-90) cc_final: 0.8242 (t70) REVERT: I 107 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7623 (mtp85) REVERT: I 114 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7960 (tpt170) outliers start: 27 outliers final: 11 residues processed: 237 average time/residue: 0.6252 time to fit residues: 155.1885 Evaluate side-chains 230 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 96 LYS Chi-restraints excluded: chain I residue 114 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 0.0000 chunk 77 optimal weight: 0.3980 chunk 92 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN C 43 HIS F 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.143900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122712 restraints weight = 11428.780| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.48 r_work: 0.3323 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9184 Z= 0.144 Angle : 0.580 7.503 12636 Z= 0.309 Chirality : 0.040 0.343 1415 Planarity : 0.004 0.052 1461 Dihedral : 22.033 146.415 1682 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.51 % Allowed : 22.22 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.73 (0.26), residues: 935 helix: 2.91 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.34 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 84 TYR 0.004 0.001 TYR F 71 PHE 0.006 0.001 PHE G 41 TRP 0.003 0.001 TRP A 54 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 9184) covalent geometry : angle 0.58013 / 0.31 (12636) hydrogen bonds : bond 0.06639 / 4.58 ( 589) hydrogen bonds : angle 3.36225 / 2.42 ( 1634) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 221 time to evaluate : 0.288 Fit side-chains REVERT: A 4 LYS cc_start: 0.8162 (mtpt) cc_final: 0.7918 (tttp) REVERT: A 37 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8368 (mmmt) REVERT: A 77 LYS cc_start: 0.8286 (mttt) cc_final: 0.7971 (mptt) REVERT: A 80 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7769 (mpt180) REVERT: B 47 ARG cc_start: 0.8754 (mtt90) cc_final: 0.8127 (mtp-110) REVERT: B 81 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.8023 (ttmt) REVERT: C 81 LYS cc_start: 0.8148 (mppt) cc_final: 0.7766 (mmtp) REVERT: C 82 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7514 (tp30) REVERT: C 100 LYS cc_start: 0.8381 (ttmm) cc_final: 0.8069 (mtpt) REVERT: D 27 ASP cc_start: 0.8794 (m-30) cc_final: 0.8566 (m-30) REVERT: E 35 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7663 (mt-10) REVERT: E 81 LYS cc_start: 0.8706 (ttmp) cc_final: 0.8339 (tmtt) REVERT: E 84 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7450 (ttp-170) REVERT: E 117 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8677 (mt0) REVERT: F 52 ASP cc_start: 0.8145 (p0) cc_final: 0.7837 (p0) REVERT: F 91 ASP cc_start: 0.7889 (t0) cc_final: 0.7632 (t0) REVERT: G 82 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7271 (tp30) REVERT: G 85 ILE cc_start: 0.7905 (mt) cc_final: 0.7601 (mp) REVERT: H 77 LYS cc_start: 0.7788 (mmmt) cc_final: 0.7342 (mppt) REVERT: H 81 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7951 (tmtm) REVERT: H 84 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7394 (mpp-170) REVERT: H 115 ASP cc_start: 0.8818 (t0) cc_final: 0.8613 (t70) REVERT: H 121 HIS cc_start: 0.8371 (t-90) cc_final: 0.8100 (t70) REVERT: I 101 GLN cc_start: 0.8605 (mt0) cc_final: 0.8351 (mt0) REVERT: I 107 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7652 (mtp180) outliers start: 21 outliers final: 4 residues processed: 228 average time/residue: 0.6620 time to fit residues: 157.9039 Evaluate side-chains 213 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 205 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain H residue 84 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 61 optimal weight: 0.0010 chunk 67 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN F 124 ASN G 69 GLN I 69 GLN I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.123527 restraints weight = 11438.463| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.47 r_work: 0.3335 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9184 Z= 0.137 Angle : 0.583 8.211 12636 Z= 0.306 Chirality : 0.039 0.342 1415 Planarity : 0.004 0.053 1461 Dihedral : 21.978 144.927 1682 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.63 % Allowed : 22.10 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.81 (0.26), residues: 935 helix: 2.97 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.38 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 84 TYR 0.003 0.001 TYR F 71 PHE 0.006 0.001 PHE G 41 TRP 0.003 0.001 TRP C 42 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 ( 9184) covalent geometry : angle 0.58293 / 0.31 (12636) hydrogen bonds : bond 0.06269 / 4.31 ( 589) hydrogen bonds : angle 3.28649 / 2.37 ( 1634) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.256 Fit side-chains REVERT: A 4 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7961 (tttp) REVERT: A 37 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8301 (mmmt) REVERT: A 77 LYS cc_start: 0.8264 (mttt) cc_final: 0.7979 (mptt) REVERT: A 101 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8522 (mt0) REVERT: B 47 ARG cc_start: 0.8741 (mtt90) cc_final: 0.8106 (mtp-110) REVERT: C 81 LYS cc_start: 0.8065 (mppt) cc_final: 0.7705 (ttpt) REVERT: C 82 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7522 (tp30) REVERT: C 100 LYS cc_start: 0.8341 (ttmm) cc_final: 0.8121 (mtpt) REVERT: D 27 ASP cc_start: 0.8718 (m-30) cc_final: 0.8511 (m-30) REVERT: E 35 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: E 81 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8245 (tmtt) REVERT: E 84 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7377 (ttp-170) REVERT: E 117 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8682 (mt0) REVERT: F 52 ASP cc_start: 0.8170 (p0) cc_final: 0.7932 (p0) REVERT: G 82 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7265 (tp30) REVERT: G 85 ILE cc_start: 0.7703 (mt) cc_final: 0.7395 (mp) REVERT: H 77 LYS cc_start: 0.7751 (mmmt) cc_final: 0.7279 (mptt) REVERT: H 81 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7906 (tmtm) REVERT: H 84 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7253 (mpp-170) REVERT: H 121 HIS cc_start: 0.8407 (t-90) cc_final: 0.8145 (t70) REVERT: I 101 GLN cc_start: 0.8593 (mt0) cc_final: 0.8279 (mt0) REVERT: I 104 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6783 (tp30) REVERT: I 107 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7723 (mtp180) outliers start: 22 outliers final: 8 residues processed: 216 average time/residue: 0.6682 time to fit residues: 151.3466 Evaluate side-chains 214 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain I residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 9.9990 chunk 71 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 34 optimal weight: 0.0030 chunk 13 optimal weight: 8.9990 chunk 94 optimal weight: 40.0000 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN F 124 ASN H 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122366 restraints weight = 11493.749| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.47 r_work: 0.3320 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9184 Z= 0.146 Angle : 0.584 7.095 12636 Z= 0.309 Chirality : 0.039 0.337 1415 Planarity : 0.004 0.050 1461 Dihedral : 21.958 143.853 1682 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.11 % Allowed : 22.34 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.82 (0.26), residues: 935 helix: 2.98 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.36 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 86 TYR 0.007 0.001 TYR E 71 PHE 0.007 0.001 PHE G 41 TRP 0.005 0.001 TRP F 42 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 ( 9184) covalent geometry : angle 0.58428 / 0.31 (12636) hydrogen bonds : bond 0.06454 / 4.45 ( 589) hydrogen bonds : angle 3.27632 / 2.36 ( 1634) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.224 Fit side-chains REVERT: A 4 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7989 (tttp) REVERT: A 37 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8307 (mmmt) REVERT: A 77 LYS cc_start: 0.8292 (mttt) cc_final: 0.7987 (mptt) REVERT: A 80 ARG cc_start: 0.8257 (tpp80) cc_final: 0.7500 (mpt180) REVERT: A 101 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: B 47 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8124 (mtp-110) REVERT: C 81 LYS cc_start: 0.8024 (mppt) cc_final: 0.7627 (ttpt) REVERT: C 82 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7660 (tp30) REVERT: C 100 LYS cc_start: 0.8371 (ttmm) cc_final: 0.8136 (mtpt) REVERT: D 27 ASP cc_start: 0.8760 (m-30) cc_final: 0.8538 (m-30) REVERT: E 35 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: E 81 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8253 (tmtt) REVERT: E 84 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.7360 (ttp-170) REVERT: E 117 GLN cc_start: 0.8964 (mm-40) cc_final: 0.8716 (mt0) REVERT: F 52 ASP cc_start: 0.8208 (p0) cc_final: 0.7964 (p0) REVERT: G 82 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7329 (tp30) REVERT: G 85 ILE cc_start: 0.7677 (mt) cc_final: 0.7368 (mp) REVERT: H 77 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7444 (mptt) REVERT: H 81 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7924 (tmtm) REVERT: H 121 HIS cc_start: 0.8377 (t-90) cc_final: 0.8112 (t70) REVERT: I 30 SER cc_start: 0.8194 (OUTLIER) cc_final: 0.7820 (p) REVERT: I 83 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6663 (mt-10) REVERT: I 101 GLN cc_start: 0.8617 (mt0) cc_final: 0.8296 (mt0) REVERT: I 104 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6813 (tp30) REVERT: I 107 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7736 (mtp180) outliers start: 26 outliers final: 8 residues processed: 215 average time/residue: 0.7010 time to fit residues: 157.8584 Evaluate side-chains 212 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain G residue 109 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 30 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 64 optimal weight: 0.4980 chunk 18 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN D 101 GLN I 106 GLN I 124 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125449 restraints weight = 11415.306| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.48 r_work: 0.3361 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9184 Z= 0.131 Angle : 0.571 8.808 12636 Z= 0.303 Chirality : 0.038 0.331 1415 Planarity : 0.004 0.044 1461 Dihedral : 21.900 143.569 1682 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.99 % Allowed : 22.82 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.94 (0.26), residues: 935 helix: 3.03 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.53 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 84 TYR 0.004 0.001 TYR G 71 PHE 0.005 0.001 PHE G 41 TRP 0.003 0.000 TRP C 42 HIS 0.002 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 ( 9184) covalent geometry : angle 0.57061 / 0.30 (12636) hydrogen bonds : bond 0.05647 / 3.87 ( 589) hydrogen bonds : angle 3.19502 / 2.30 ( 1634) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.246 Fit side-chains REVERT: A 4 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7961 (tttp) REVERT: A 37 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8210 (mmmt) REVERT: A 77 LYS cc_start: 0.8250 (mttt) cc_final: 0.7944 (mptt) REVERT: A 80 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7513 (mpt180) REVERT: B 47 ARG cc_start: 0.8729 (mtt90) cc_final: 0.8087 (mtp-110) REVERT: C 69 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8117 (mt0) REVERT: C 81 LYS cc_start: 0.7960 (mppt) cc_final: 0.7583 (ttpt) REVERT: C 82 GLU cc_start: 0.8059 (mm-30) cc_final: 0.7729 (tp30) REVERT: C 100 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8185 (mtpt) REVERT: D 78 ASP cc_start: 0.7923 (m-30) cc_final: 0.7681 (m-30) REVERT: E 81 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8090 (ttmm) REVERT: E 84 ARG cc_start: 0.7505 (mtp180) cc_final: 0.7253 (ttp-170) REVERT: E 117 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8695 (mt0) REVERT: F 52 ASP cc_start: 0.8220 (p0) cc_final: 0.8018 (p0) REVERT: F 81 LYS cc_start: 0.7958 (ttmm) cc_final: 0.7412 (ttmm) REVERT: G 82 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7314 (tp30) REVERT: G 85 ILE cc_start: 0.7562 (mt) cc_final: 0.7223 (mp) REVERT: H 77 LYS cc_start: 0.8003 (mmmt) cc_final: 0.7396 (mptt) REVERT: H 81 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7820 (tmtm) REVERT: H 115 ASP cc_start: 0.8804 (t0) cc_final: 0.8574 (t70) REVERT: H 121 HIS cc_start: 0.8406 (t-90) cc_final: 0.8143 (t70) REVERT: I 30 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7873 (p) REVERT: I 83 GLU cc_start: 0.7489 (tm-30) cc_final: 0.6769 (mt-10) REVERT: I 101 GLN cc_start: 0.8528 (mt0) cc_final: 0.8203 (mt0) REVERT: I 104 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6812 (tp30) REVERT: I 107 ARG cc_start: 0.8057 (mtt180) cc_final: 0.7712 (mtp180) outliers start: 25 outliers final: 6 residues processed: 220 average time/residue: 0.6946 time to fit residues: 160.0907 Evaluate side-chains 202 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain I residue 30 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 3 optimal weight: 0.0060 chunk 14 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN I 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.143458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.122354 restraints weight = 11346.083| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.48 r_work: 0.3321 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9184 Z= 0.159 Angle : 0.597 8.478 12636 Z= 0.319 Chirality : 0.039 0.327 1415 Planarity : 0.005 0.042 1461 Dihedral : 21.873 142.209 1682 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 2.39 % Allowed : 23.30 % Favored : 74.31 % 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: 3.78 (0.26), residues: 935 helix: 2.92 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.44 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 114 TYR 0.010 0.001 TYR E 71 PHE 0.008 0.001 PHE G 41 TRP 0.006 0.001 TRP F 42 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 ( 9184) covalent geometry : angle 0.59710 / 0.32 (12636) hydrogen bonds : bond 0.06398 / 4.39 ( 589) hydrogen bonds : angle 3.33584 / 2.39 ( 1634) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.299 Fit side-chains REVERT: A 4 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7992 (tttp) REVERT: A 37 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8332 (mmmt) REVERT: A 77 LYS cc_start: 0.8285 (mttt) cc_final: 0.8047 (mptt) REVERT: B 47 ARG cc_start: 0.8773 (mtt90) cc_final: 0.8120 (mtp-110) REVERT: C 69 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8118 (mt0) REVERT: C 81 LYS cc_start: 0.7990 (mppt) cc_final: 0.7606 (ttpt) REVERT: C 82 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7707 (tp30) REVERT: C 100 LYS cc_start: 0.8385 (ttmm) cc_final: 0.8120 (mtpt) REVERT: D 78 ASP cc_start: 0.7992 (m-30) cc_final: 0.7726 (m-30) REVERT: E 35 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: E 81 LYS cc_start: 0.8576 (ttmp) cc_final: 0.8066 (ttmm) REVERT: E 84 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.7251 (mtm110) REVERT: E 101 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8234 (mm-40) REVERT: E 117 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8701 (mt0) REVERT: F 52 ASP cc_start: 0.8244 (p0) cc_final: 0.7995 (p0) REVERT: F 81 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7635 (ttmm) REVERT: F 97 ASP cc_start: 0.7657 (m-30) cc_final: 0.7374 (t0) REVERT: G 82 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7342 (tp30) REVERT: G 85 ILE cc_start: 0.7607 (mt) cc_final: 0.7263 (mp) REVERT: H 77 LYS cc_start: 0.8040 (mmmt) cc_final: 0.7459 (mppt) REVERT: H 81 LYS cc_start: 0.8326 (ttmt) cc_final: 0.7905 (tmtm) REVERT: H 121 HIS cc_start: 0.8346 (t-90) cc_final: 0.8080 (t70) REVERT: I 30 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7896 (p) REVERT: I 83 GLU cc_start: 0.7535 (tm-30) cc_final: 0.6747 (mt-10) REVERT: I 101 GLN cc_start: 0.8659 (mt0) cc_final: 0.8359 (mt0) REVERT: I 104 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6929 (tp30) REVERT: I 107 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7721 (mtp180) outliers start: 20 outliers final: 11 residues processed: 212 average time/residue: 0.7065 time to fit residues: 157.0797 Evaluate side-chains 216 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 92 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 0.0270 chunk 3 optimal weight: 0.0870 chunk 17 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 64 optimal weight: 0.0670 chunk 18 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN C 124 ASN I 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.127703 restraints weight = 11332.716| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.48 r_work: 0.3392 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9184 Z= 0.134 Angle : 0.579 8.113 12636 Z= 0.309 Chirality : 0.037 0.322 1415 Planarity : 0.004 0.044 1461 Dihedral : 21.809 142.385 1682 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.79 % Allowed : 24.25 % Favored : 73.95 % 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: 3.97 (0.26), residues: 935 helix: 3.02 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.62 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 114 TYR 0.004 0.001 TYR E 71 PHE 0.005 0.001 PHE A 41 TRP 0.004 0.001 TRP A 54 HIS 0.002 0.001 HIS I 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 ( 9184) covalent geometry : angle 0.57915 / 0.31 (12636) hydrogen bonds : bond 0.05211 / 3.55 ( 589) hydrogen bonds : angle 3.23653 / 2.33 ( 1634) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 202 time to evaluate : 0.326 Fit side-chains REVERT: A 4 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7955 (tttp) REVERT: A 37 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8268 (mmmt) REVERT: A 77 LYS cc_start: 0.8239 (mttt) cc_final: 0.8004 (mptt) REVERT: A 80 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7671 (mpt180) REVERT: B 47 ARG cc_start: 0.8696 (mtt90) cc_final: 0.8049 (mtp-110) REVERT: C 27 ASP cc_start: 0.7597 (m-30) cc_final: 0.7178 (m-30) REVERT: C 69 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8125 (mt0) REVERT: C 81 LYS cc_start: 0.7930 (mppt) cc_final: 0.7587 (ttpt) REVERT: C 82 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7731 (tp30) REVERT: C 100 LYS cc_start: 0.8349 (ttmm) cc_final: 0.8145 (mtpt) REVERT: D 78 ASP cc_start: 0.7947 (m-30) cc_final: 0.7703 (m-30) REVERT: E 81 LYS cc_start: 0.8525 (ttmp) cc_final: 0.8108 (tmtt) REVERT: F 81 LYS cc_start: 0.7895 (ttmm) cc_final: 0.7305 (ttmm) REVERT: G 82 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7312 (tp30) REVERT: G 85 ILE cc_start: 0.7447 (mt) cc_final: 0.7087 (mp) REVERT: H 77 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7438 (mppt) REVERT: H 81 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7760 (tmtm) REVERT: H 115 ASP cc_start: 0.8806 (t0) cc_final: 0.8563 (t70) REVERT: H 121 HIS cc_start: 0.8361 (t-90) cc_final: 0.8091 (t70) REVERT: I 30 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7904 (p) REVERT: I 83 GLU cc_start: 0.7511 (tm-30) cc_final: 0.6785 (mt-10) REVERT: I 96 LYS cc_start: 0.7982 (ptpt) cc_final: 0.7700 (ptmm) REVERT: I 101 GLN cc_start: 0.8480 (mt0) cc_final: 0.8179 (mt0) REVERT: I 104 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6832 (tp30) REVERT: I 107 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7588 (mtp180) outliers start: 15 outliers final: 7 residues processed: 212 average time/residue: 0.6689 time to fit residues: 148.8552 Evaluate side-chains 203 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 194 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain I residue 30 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 overall best weight: 2.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 GLN B 142 ASN C 124 ASN E 106 GLN I 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124184 restraints weight = 11362.420| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.48 r_work: 0.3345 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9184 Z= 0.153 Angle : 0.600 8.441 12636 Z= 0.320 Chirality : 0.039 0.317 1415 Planarity : 0.005 0.063 1461 Dihedral : 21.702 140.560 1682 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 2.03 % Allowed : 24.01 % Favored : 73.95 % 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: 3.90 (0.26), residues: 935 helix: 2.98 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.58 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 84 TYR 0.010 0.001 TYR E 71 PHE 0.007 0.001 PHE G 41 TRP 0.004 0.001 TRP C 42 HIS 0.009 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 9184) covalent geometry : angle 0.60042 / 0.32 (12636) hydrogen bonds : bond 0.05999 / 4.11 ( 589) hydrogen bonds : angle 3.29092 / 2.37 ( 1634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3251.92 seconds wall clock time: 55 minutes 50.84 seconds (3350.84 seconds total)