Starting phenix.real_space_refine on Thu Jul 2 11:24:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pop_17794/07_2026/8pop_17794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pop_17794/07_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_17794/07_2026/8pop_17794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pop_17794/07_2026/8pop_17794.map" model { file = "/net/cci-nas-00/data/ceres_data/8pop_17794/07_2026/8pop_17794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pop_17794/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.11, per 1000 atoms: 0.24 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: 0.74 Conformation dependent library (CDL) restraints added in 482.5 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: 1.03 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: 1.42 Time building geometry restraints manager: 1.02 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: 11911 2.66 - 5.33: 625 5.33 - 7.99: 77 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=" O3' DA J 22 " pdb=" P DA J 23 " pdb=" O5' DA J 23 " ideal model delta sigma weight residual 104.00 92.88 11.12 1.50e+00 4.44e-01 5.50e+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=" O3' DT J 16 " pdb=" P DA J 17 " pdb=" O5' DA J 17 " ideal model delta sigma weight residual 104.00 93.58 10.42 1.50e+00 4.44e-01 4.82e+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: 0.200 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.370 Find NCS groups from input model: 0.130 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:7.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.780 ------------------------------------------------------------------------------- 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 : 1.442 13.313 12636 Z= 0.999 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 1.44159 / 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 : 0.325 Fit side-chains revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8314 (mtpt) cc_final: 0.8046 (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: 0.7680 (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: 0.8140 (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: 0.8028 (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: 0.7976 (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: 0.8103 (tttp) REVERT: E 100 LYS cc_start: 0.7858 (mttt) cc_final: 0.7502 (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: 0.7500 (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: 0.8288 time to fit residues: 255.0850 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 : 0.327 ------------------------------------------------------------------------------- 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 = 0.3697 r_free = 0.3697 target = 0.141887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121687 restraints weight = 11272.922| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.46 r_work: 0.3311 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9184 Z= 0.202 Angle : 0.693 8.161 12636 Z= 0.376 Chirality : 0.046 0.366 1415 Planarity : 0.005 0.042 1461 Dihedral : 22.210 149.426 1682 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.11 % Allowed : 13.26 % Favored : 83.63 % 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: 2.51 (0.25), residues: 935 helix: 2.05 (0.19), residues: 686 sheet: None (None), residues: 0 loop : 0.73 (0.31), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 80 TYR 0.010 0.001 TYR B 71 PHE 0.011 0.002 PHE G 41 TRP 0.006 0.001 TRP I 54 HIS 0.005 0.001 HIS F 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.20 ( 9184) covalent geometry : angle 0.69309 / 0.38 (12636) hydrogen bonds : bond 0.10720 / 7.41 ( 589) hydrogen bonds : angle 4.07366 / 2.91 ( 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: 26 poor density : 239 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7620 (t0) cc_final: 0.7373 (t70) REVERT: A 37 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8530 (mmmt) REVERT: A 64 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8240 (mt-10) REVERT: A 77 LYS cc_start: 0.8418 (mttt) cc_final: 0.8157 (mptt) REVERT: A 80 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7816 (mmp80) REVERT: B 47 ARG cc_start: 0.8795 (mtt90) cc_final: 0.8207 (mtp180) REVERT: B 64 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7408 (mm-30) REVERT: B 96 LYS cc_start: 0.8740 (tttt) cc_final: 0.8535 (ttpp) REVERT: B 135 GLN cc_start: 0.8813 (tp40) cc_final: 0.8600 (tp40) REVERT: C 64 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7904 (mm-30) REVERT: C 100 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8251 (mtpt) REVERT: D 81 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7744 (ttmm) REVERT: E 77 LYS cc_start: 0.8686 (tttt) cc_final: 0.8474 (tmtt) REVERT: E 81 LYS cc_start: 0.8525 (ttmt) cc_final: 0.8298 (tttt) REVERT: E 96 LYS cc_start: 0.8173 (ttmt) cc_final: 0.7901 (tttp) REVERT: E 117 GLN cc_start: 0.8675 (mm-40) cc_final: 0.8415 (mt0) REVERT: F 64 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7810 (mm-30) REVERT: F 82 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7685 (mp0) REVERT: F 91 ASP cc_start: 0.8149 (t0) cc_final: 0.7868 (t0) REVERT: G 80 ARG cc_start: 0.8028 (mmt-90) cc_final: 0.7757 (mtt-85) REVERT: G 82 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7897 (mp0) REVERT: G 85 ILE cc_start: 0.8352 (mt) cc_final: 0.8069 (mp) REVERT: H 81 LYS cc_start: 0.8589 (ttmt) cc_final: 0.8204 (tmtm) REVERT: H 84 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7264 (mpp-170) REVERT: H 121 HIS cc_start: 0.8492 (t-90) cc_final: 0.8250 (t70) REVERT: I 51 LEU cc_start: 0.8168 (mt) cc_final: 0.7933 (mm) REVERT: I 107 ARG cc_start: 0.8299 (mtt180) cc_final: 0.7866 (mtp85) outliers start: 26 outliers final: 7 residues processed: 244 average time/residue: 0.8158 time to fit residues: 208.0020 Evaluate side-chains 229 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 221 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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: 2.9990 chunk 16 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 34 optimal weight: 0.3980 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN D 101 GLN E 106 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 = 0.3689 r_free = 0.3689 target = 0.142004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.120872 restraints weight = 11345.863| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.44 r_work: 0.3296 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9184 Z= 0.169 Angle : 0.619 7.135 12636 Z= 0.334 Chirality : 0.042 0.326 1415 Planarity : 0.004 0.033 1461 Dihedral : 22.179 151.393 1682 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.99 % Allowed : 18.04 % Favored : 78.97 % 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: 3.31 (0.25), residues: 935 helix: 2.74 (0.20), residues: 656 sheet: None (None), residues: 0 loop : 0.94 (0.29), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 113 TYR 0.004 0.001 TYR D 71 PHE 0.008 0.001 PHE G 41 TRP 0.006 0.001 TRP C 42 HIS 0.011 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 ( 9184) covalent geometry : angle 0.61857 / 0.33 (12636) hydrogen bonds : bond 0.08394 / 5.80 ( 589) hydrogen bonds : angle 3.67118 / 2.63 ( 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 249 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8466 (mmmt) REVERT: A 77 LYS cc_start: 0.8292 (mttt) cc_final: 0.8021 (mptt) REVERT: B 47 ARG cc_start: 0.8785 (mtt90) cc_final: 0.8196 (mtp-110) REVERT: C 64 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7566 (mm-30) REVERT: C 82 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7466 (tp30) REVERT: C 100 LYS cc_start: 0.8450 (ttmm) cc_final: 0.8185 (mtpt) REVERT: D 81 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7708 (ttmm) REVERT: E 35 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: E 117 GLN cc_start: 0.8836 (mm-40) cc_final: 0.8561 (mt0) REVERT: F 52 ASP cc_start: 0.7955 (p0) cc_final: 0.7651 (p0) REVERT: F 64 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7661 (mm-30) REVERT: F 91 ASP cc_start: 0.8250 (t0) cc_final: 0.7834 (t0) REVERT: F 114 ARG cc_start: 0.7754 (ttm110) cc_final: 0.7499 (ttp80) REVERT: G 82 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7693 (mp0) REVERT: G 85 ILE cc_start: 0.7988 (mt) cc_final: 0.7739 (mp) REVERT: H 81 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8042 (tmtm) REVERT: H 84 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7337 (mpp-170) REVERT: H 121 HIS cc_start: 0.8470 (t-90) cc_final: 0.8198 (t70) REVERT: I 107 ARG cc_start: 0.8243 (mtt180) cc_final: 0.7769 (mtp85) REVERT: I 114 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8101 (tpt170) outliers start: 25 outliers final: 5 residues processed: 230 average time/residue: 0.8650 time to fit residues: 207.4089 Evaluate side-chains 217 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 35 GLU 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: 10.0000 chunk 49 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 124 ASN B 101 GLN B 135 GLN B 142 ASN E 106 GLN F 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120645 restraints weight = 11469.237| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.44 r_work: 0.3292 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9184 Z= 0.161 Angle : 0.608 7.371 12636 Z= 0.324 Chirality : 0.041 0.328 1415 Planarity : 0.005 0.059 1461 Dihedral : 22.140 147.543 1682 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.11 % Allowed : 20.19 % Favored : 76.70 % 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: 3.50 (0.26), residues: 935 helix: 2.75 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.20 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 84 TYR 0.007 0.001 TYR D 71 PHE 0.008 0.001 PHE G 41 TRP 0.003 0.001 TRP F 42 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 ( 9184) covalent geometry : angle 0.60822 / 0.32 (12636) hydrogen bonds : bond 0.07699 / 5.32 ( 589) hydrogen bonds : angle 3.50206 / 2.51 ( 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 246 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 220 time to evaluate : 0.384 Fit side-chains REVERT: A 37 LYS cc_start: 0.8816 (mmtt) cc_final: 0.8456 (mmmt) REVERT: A 77 LYS cc_start: 0.8343 (mttt) cc_final: 0.8072 (mptt) REVERT: B 47 ARG cc_start: 0.8763 (mtt90) cc_final: 0.8174 (mtp-110) REVERT: C 82 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7572 (tp30) REVERT: C 100 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8253 (mtpt) REVERT: E 117 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8674 (mt0) REVERT: F 52 ASP cc_start: 0.8080 (p0) cc_final: 0.7813 (p0) REVERT: F 86 ARG cc_start: 0.7095 (mmt180) cc_final: 0.6760 (mmt-90) REVERT: F 91 ASP cc_start: 0.8278 (t0) cc_final: 0.7886 (t0) REVERT: G 85 ILE cc_start: 0.8017 (mt) cc_final: 0.7715 (mp) REVERT: G 97 ASP cc_start: 0.8084 (m-30) cc_final: 0.7876 (m-30) REVERT: H 81 LYS cc_start: 0.8448 (ttmt) cc_final: 0.8025 (tmtm) REVERT: H 84 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7512 (mpp-170) REVERT: H 121 HIS cc_start: 0.8485 (t-90) cc_final: 0.8229 (t70) REVERT: I 107 ARG cc_start: 0.8206 (mtt180) cc_final: 0.7677 (mtp85) REVERT: I 114 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7963 (tpt170) outliers start: 26 outliers final: 11 residues processed: 229 average time/residue: 0.8263 time to fit residues: 197.5961 Evaluate side-chains 221 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 208 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 H residue 30 SER Chi-restraints excluded: chain H residue 84 ARG 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: 10.0000 chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN C 43 HIS 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 = 0.3667 r_free = 0.3667 target = 0.140458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.119482 restraints weight = 11403.444| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.42 r_work: 0.3279 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9184 Z= 0.174 Angle : 0.618 8.156 12636 Z= 0.328 Chirality : 0.041 0.318 1415 Planarity : 0.005 0.057 1461 Dihedral : 22.148 146.678 1682 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.87 % Allowed : 21.15 % 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: 3.42 (0.25), residues: 935 helix: 2.70 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.14 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 84 TYR 0.007 0.001 TYR E 71 PHE 0.009 0.002 PHE G 41 TRP 0.005 0.001 TRP F 42 HIS 0.005 0.001 HIS F 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 9184) covalent geometry : angle 0.61826 / 0.33 (12636) hydrogen bonds : bond 0.07786 / 5.37 ( 589) hydrogen bonds : angle 3.50238 / 2.52 ( 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: 24 poor density : 218 time to evaluate : 0.362 Fit side-chains REVERT: A 37 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8460 (mmmt) REVERT: A 77 LYS cc_start: 0.8349 (mttt) cc_final: 0.8084 (mptt) REVERT: B 47 ARG cc_start: 0.8774 (mtt90) cc_final: 0.8168 (mtp-110) REVERT: B 81 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: C 81 LYS cc_start: 0.8244 (mppt) cc_final: 0.7840 (mmtp) REVERT: C 82 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7532 (tp30) REVERT: C 100 LYS cc_start: 0.8503 (ttmm) cc_final: 0.8257 (mtpt) REVERT: E 117 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8657 (mt0) REVERT: F 52 ASP cc_start: 0.8143 (p0) cc_final: 0.7855 (p0) REVERT: F 86 ARG cc_start: 0.7174 (mmt180) cc_final: 0.6853 (mmt-90) REVERT: F 97 ASP cc_start: 0.7898 (m-30) cc_final: 0.7657 (t0) REVERT: G 82 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7414 (tp30) REVERT: G 85 ILE cc_start: 0.8018 (mt) cc_final: 0.7707 (mp) REVERT: G 96 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8182 (mtpt) REVERT: G 97 ASP cc_start: 0.8079 (m-30) cc_final: 0.7849 (m-30) REVERT: H 81 LYS cc_start: 0.8382 (ttmt) cc_final: 0.7977 (tmtm) REVERT: H 121 HIS cc_start: 0.8373 (t-90) cc_final: 0.8129 (t70) REVERT: I 101 GLN cc_start: 0.8645 (mt0) cc_final: 0.8358 (mt0) REVERT: I 107 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7691 (mtp85) outliers start: 24 outliers final: 10 residues processed: 226 average time/residue: 0.8213 time to fit residues: 193.9787 Evaluate side-chains 222 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 36 LYS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 96 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 0.0770 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN I 69 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 = 0.3697 r_free = 0.3697 target = 0.142946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.121770 restraints weight = 11433.009| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.47 r_work: 0.3309 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3990 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= 0.146 Angle : 0.584 8.036 12636 Z= 0.310 Chirality : 0.039 0.316 1415 Planarity : 0.004 0.037 1461 Dihedral : 22.091 146.278 1682 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.39 % Allowed : 21.98 % Favored : 75.63 % 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: 3.64 (0.26), residues: 935 helix: 2.86 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.23 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 76 TYR 0.004 0.001 TYR E 71 PHE 0.007 0.001 PHE G 41 TRP 0.004 0.001 TRP C 42 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 ( 9184) covalent geometry : angle 0.58421 / 0.31 (12636) hydrogen bonds : bond 0.06798 / 4.68 ( 589) hydrogen bonds : angle 3.37907 / 2.43 ( 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 237 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 217 time to evaluate : 0.312 Fit side-chains REVERT: A 37 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8324 (mmmt) REVERT: A 77 LYS cc_start: 0.8288 (mttt) cc_final: 0.7994 (mptt) REVERT: A 80 ARG cc_start: 0.8249 (tpp80) cc_final: 0.7574 (mpt180) REVERT: B 47 ARG cc_start: 0.8779 (mtt90) cc_final: 0.8142 (mtp-110) REVERT: C 81 LYS cc_start: 0.8153 (mppt) cc_final: 0.7845 (ttpt) REVERT: C 82 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7742 (tp30) REVERT: C 100 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8074 (mtpt) REVERT: D 27 ASP cc_start: 0.8758 (m-30) cc_final: 0.8505 (m-30) REVERT: E 97 ASP cc_start: 0.7663 (t0) cc_final: 0.7413 (t0) REVERT: E 117 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8694 (mt0) REVERT: F 52 ASP cc_start: 0.8216 (p0) cc_final: 0.8000 (p0) REVERT: F 86 ARG cc_start: 0.7241 (mmt180) cc_final: 0.6913 (mmt90) REVERT: F 96 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8177 (ttpp) REVERT: G 82 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7355 (tp30) REVERT: G 85 ILE cc_start: 0.7844 (mt) cc_final: 0.7513 (mp) REVERT: G 97 ASP cc_start: 0.8061 (m-30) cc_final: 0.7821 (m-30) REVERT: H 81 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7917 (tmtm) REVERT: H 84 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7303 (mpp-170) REVERT: H 121 HIS cc_start: 0.8385 (t-90) cc_final: 0.8114 (t70) REVERT: I 101 GLN cc_start: 0.8618 (mt0) cc_final: 0.8344 (mt0) REVERT: I 107 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7719 (mtp180) outliers start: 20 outliers final: 9 residues processed: 223 average time/residue: 0.7879 time to fit residues: 183.8741 Evaluate side-chains 218 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 39 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain H residue 84 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 33 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 34 optimal weight: 0.0060 chunk 13 optimal weight: 8.9990 chunk 94 optimal weight: 40.0000 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN H 124 ASN I 69 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 = 0.3701 r_free = 0.3701 target = 0.143205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122060 restraints weight = 11485.250| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.48 r_work: 0.3314 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9184 Z= 0.146 Angle : 0.588 8.455 12636 Z= 0.311 Chirality : 0.039 0.310 1415 Planarity : 0.004 0.030 1461 Dihedral : 22.085 145.100 1682 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.87 % Allowed : 22.46 % Favored : 74.67 % 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: 3.72 (0.26), residues: 935 helix: 2.91 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.30 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 76 TYR 0.005 0.001 TYR E 71 PHE 0.006 0.001 PHE G 41 TRP 0.004 0.001 TRP C 42 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 ( 9184) covalent geometry : angle 0.58826 / 0.31 (12636) hydrogen bonds : bond 0.06549 / 4.51 ( 589) hydrogen bonds : angle 3.31648 / 2.39 ( 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 235 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.326 Fit side-chains REVERT: A 37 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8276 (mmmt) REVERT: A 77 LYS cc_start: 0.8299 (mttt) cc_final: 0.8012 (mptt) REVERT: B 47 ARG cc_start: 0.8780 (mtt90) cc_final: 0.8140 (mtp-110) REVERT: C 81 LYS cc_start: 0.8080 (mppt) cc_final: 0.7731 (ttpt) REVERT: C 82 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7702 (tp30) REVERT: C 100 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8144 (mtpt) REVERT: D 27 ASP cc_start: 0.8748 (m-30) cc_final: 0.8520 (m-30) REVERT: E 35 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: E 97 ASP cc_start: 0.7723 (t0) cc_final: 0.7403 (t0) REVERT: E 117 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8717 (mt0) REVERT: F 52 ASP cc_start: 0.8187 (p0) cc_final: 0.7946 (p0) REVERT: F 64 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7690 (mm-30) REVERT: F 81 LYS cc_start: 0.8137 (ttmm) cc_final: 0.7614 (ttmm) REVERT: F 86 ARG cc_start: 0.7239 (mmt180) cc_final: 0.6993 (mmt90) REVERT: F 96 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7913 (ttpp) REVERT: G 82 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7312 (tp30) REVERT: G 85 ILE cc_start: 0.7685 (mt) cc_final: 0.7369 (mp) REVERT: G 97 ASP cc_start: 0.7986 (m-30) cc_final: 0.7729 (m-30) REVERT: H 77 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7306 (mppt) REVERT: H 81 LYS cc_start: 0.8294 (ttmt) cc_final: 0.7909 (tmtm) REVERT: H 121 HIS cc_start: 0.8340 (t-90) cc_final: 0.8096 (t70) REVERT: I 101 GLN cc_start: 0.8605 (mt0) cc_final: 0.8311 (mt0) REVERT: I 107 ARG cc_start: 0.8089 (mtt180) cc_final: 0.7721 (mtp180) outliers start: 24 outliers final: 11 residues processed: 221 average time/residue: 0.7926 time to fit residues: 183.2909 Evaluate side-chains 218 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 144 LYS Chi-restraints excluded: chain C residue 30 SER 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 36 LYS Chi-restraints excluded: chain G residue 84 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 59 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN C 43 HIS I 69 GLN I 106 GLN I 124 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.145263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124146 restraints weight = 11414.227| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.47 r_work: 0.3344 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9184 Z= 0.136 Angle : 0.574 7.791 12636 Z= 0.305 Chirality : 0.038 0.306 1415 Planarity : 0.004 0.029 1461 Dihedral : 22.010 144.464 1682 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.51 % Allowed : 23.42 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.85 (0.26), residues: 935 helix: 2.98 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.40 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 84 TYR 0.006 0.001 TYR E 71 PHE 0.005 0.001 PHE G 41 TRP 0.003 0.001 TRP C 42 HIS 0.009 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 ( 9184) covalent geometry : angle 0.57404 / 0.31 (12636) hydrogen bonds : bond 0.05949 / 4.08 ( 589) hydrogen bonds : angle 3.23957 / 2.34 ( 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 232 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8243 (mmmt) REVERT: A 77 LYS cc_start: 0.8269 (mttt) cc_final: 0.7971 (mptt) REVERT: A 80 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7478 (mpt180) REVERT: B 47 ARG cc_start: 0.8766 (mtt90) cc_final: 0.8132 (mtp-110) REVERT: C 39 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7902 (tm-30) REVERT: C 81 LYS cc_start: 0.8002 (mppt) cc_final: 0.7646 (ttpt) REVERT: C 82 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7656 (tp30) REVERT: C 100 LYS cc_start: 0.8362 (ttmm) cc_final: 0.8021 (mtpt) REVERT: E 35 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: E 97 ASP cc_start: 0.7631 (t0) cc_final: 0.7271 (t0) REVERT: E 117 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8711 (mt0) REVERT: F 52 ASP cc_start: 0.8253 (p0) cc_final: 0.8046 (p0) REVERT: F 64 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7735 (mm-30) REVERT: F 81 LYS cc_start: 0.8048 (ttmm) cc_final: 0.7574 (ttmm) REVERT: F 96 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7701 (ttpp) REVERT: G 82 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7340 (tp30) REVERT: G 85 ILE cc_start: 0.7630 (mt) cc_final: 0.7292 (mp) REVERT: G 97 ASP cc_start: 0.8032 (m-30) cc_final: 0.7682 (m-30) REVERT: H 77 LYS cc_start: 0.7748 (mmmt) cc_final: 0.7298 (mppt) REVERT: H 81 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7881 (tmtm) REVERT: H 121 HIS cc_start: 0.8369 (t-90) cc_final: 0.8115 (t70) REVERT: I 83 GLU cc_start: 0.7448 (tm-30) cc_final: 0.6776 (mt-10) REVERT: I 101 GLN cc_start: 0.8571 (mt0) cc_final: 0.8271 (mt0) REVERT: I 104 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6770 (tp30) REVERT: I 107 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7734 (mtp180) outliers start: 21 outliers final: 9 residues processed: 220 average time/residue: 0.7886 time to fit residues: 181.7479 Evaluate side-chains 212 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 G residue 109 ILE Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain I residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 25 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 3 optimal weight: 0.0470 chunk 14 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN C 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 = 0.3724 r_free = 0.3724 target = 0.145268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.124086 restraints weight = 11356.223| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.47 r_work: 0.3342 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9184 Z= 0.137 Angle : 0.574 8.785 12636 Z= 0.307 Chirality : 0.038 0.301 1415 Planarity : 0.005 0.066 1461 Dihedral : 21.995 143.414 1682 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.67 % Allowed : 24.37 % 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: 3.07 (0.19), residues: 679 sheet: None (None), residues: 0 loop : 1.51 (0.33), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 84 TYR 0.007 0.001 TYR E 71 PHE 0.006 0.001 PHE G 41 TRP 0.004 0.001 TRP C 42 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 ( 9184) covalent geometry : angle 0.57361 / 0.31 (12636) hydrogen bonds : bond 0.05887 / 4.04 ( 589) hydrogen bonds : angle 3.22504 / 2.33 ( 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 221 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 207 time to evaluate : 0.333 Fit side-chains REVERT: A 4 LYS cc_start: 0.7631 (tttp) cc_final: 0.7421 (tttt) REVERT: A 37 LYS cc_start: 0.8708 (mmtt) cc_final: 0.8277 (mmmt) REVERT: A 77 LYS cc_start: 0.8265 (mttt) cc_final: 0.8030 (mptt) REVERT: A 80 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7496 (mpt180) REVERT: B 47 ARG cc_start: 0.8782 (mtt90) cc_final: 0.8127 (mtp-110) REVERT: C 81 LYS cc_start: 0.7974 (mppt) cc_final: 0.7612 (ttpt) REVERT: C 82 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7718 (tp30) REVERT: C 100 LYS cc_start: 0.8315 (ttmm) cc_final: 0.8090 (mtpt) REVERT: E 35 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: E 97 ASP cc_start: 0.7680 (t0) cc_final: 0.7282 (t0) REVERT: E 101 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8201 (mm-40) REVERT: E 117 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8728 (mt0) REVERT: F 52 ASP cc_start: 0.8211 (p0) cc_final: 0.7988 (p0) REVERT: F 64 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7706 (mm-30) REVERT: F 81 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7605 (ttmm) REVERT: F 96 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7714 (ttpp) REVERT: F 114 ARG cc_start: 0.7603 (ttp80) cc_final: 0.7197 (ttp80) REVERT: G 82 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7338 (tp30) REVERT: G 85 ILE cc_start: 0.7547 (mt) cc_final: 0.7197 (mp) REVERT: G 97 ASP cc_start: 0.7984 (m-30) cc_final: 0.7643 (m-30) REVERT: H 77 LYS cc_start: 0.7737 (mmmt) cc_final: 0.7323 (mppt) REVERT: H 81 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7859 (tmtm) REVERT: H 121 HIS cc_start: 0.8382 (t-90) cc_final: 0.8125 (t70) REVERT: I 83 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6670 (mt-10) REVERT: I 101 GLN cc_start: 0.8564 (mt0) cc_final: 0.8249 (mt0) REVERT: I 104 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6839 (tp30) REVERT: I 107 ARG cc_start: 0.8039 (mtt180) cc_final: 0.7665 (mtp180) outliers start: 14 outliers final: 10 residues processed: 213 average time/residue: 0.7240 time to fit residues: 161.5059 Evaluate side-chains 215 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 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 H residue 48 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: 3.9990 chunk 43 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 3 optimal weight: 0.0070 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 64 optimal weight: 0.0980 chunk 18 optimal weight: 20.0000 chunk 66 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 101 GLN B 135 GLN B 142 ASN C 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 = 0.3777 r_free = 0.3777 target = 0.149769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128832 restraints weight = 11377.408| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.47 r_work: 0.3407 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.4662 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= 0.131 Angle : 0.573 8.564 12636 Z= 0.306 Chirality : 0.037 0.297 1415 Planarity : 0.004 0.064 1461 Dihedral : 21.931 143.008 1682 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.03 % Allowed : 24.25 % Favored : 73.72 % 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: 4.15 (0.26), residues: 935 helix: 3.15 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.71 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 84 TYR 0.005 0.001 TYR E 71 PHE 0.004 0.001 PHE A 41 TRP 0.005 0.000 TRP F 42 HIS 0.003 0.001 HIS F 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 ( 9184) covalent geometry : angle 0.57342 / 0.31 (12636) hydrogen bonds : bond 0.04954 / 3.37 ( 589) hydrogen bonds : angle 3.13754 / 2.27 ( 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 225 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.321 Fit side-chains REVERT: A 37 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8255 (mmmt) REVERT: A 77 LYS cc_start: 0.8303 (mttt) cc_final: 0.8061 (mptt) REVERT: A 80 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7467 (mpt180) REVERT: B 47 ARG cc_start: 0.8729 (mtt90) cc_final: 0.8080 (mtp-110) REVERT: C 27 ASP cc_start: 0.7570 (m-30) cc_final: 0.7173 (m-30) REVERT: C 81 LYS cc_start: 0.7889 (mppt) cc_final: 0.7561 (ttpt) REVERT: C 82 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7708 (tp30) REVERT: C 100 LYS cc_start: 0.8303 (ttmm) cc_final: 0.8092 (mtpt) REVERT: E 81 LYS cc_start: 0.8568 (tmtt) cc_final: 0.8038 (tptt) REVERT: E 84 ARG cc_start: 0.7615 (ttp-170) cc_final: 0.7313 (mtm110) REVERT: E 97 ASP cc_start: 0.7501 (t0) cc_final: 0.7130 (t0) REVERT: F 81 LYS cc_start: 0.7808 (ttmm) cc_final: 0.7322 (ttmm) REVERT: F 83 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7204 (mt-10) REVERT: F 86 ARG cc_start: 0.7276 (mmt90) cc_final: 0.7064 (mmt90) REVERT: F 96 LYS cc_start: 0.8002 (ttpt) cc_final: 0.7801 (ttpp) REVERT: G 82 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7286 (tp30) REVERT: G 85 ILE cc_start: 0.7414 (mt) cc_final: 0.7054 (mp) REVERT: G 97 ASP cc_start: 0.8060 (m-30) cc_final: 0.7678 (m-30) REVERT: H 77 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7487 (mppt) REVERT: H 81 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7769 (tmtm) REVERT: H 115 ASP cc_start: 0.8777 (t0) cc_final: 0.8527 (t70) REVERT: H 121 HIS cc_start: 0.8343 (t-90) cc_final: 0.8095 (t70) REVERT: I 83 GLU cc_start: 0.7395 (tm-30) cc_final: 0.6746 (mt-10) REVERT: I 96 LYS cc_start: 0.7946 (ptpt) cc_final: 0.7665 (ptmm) REVERT: I 101 GLN cc_start: 0.8485 (mt0) cc_final: 0.8167 (mt0) REVERT: I 107 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7578 (mtp180) REVERT: I 109 ILE cc_start: 0.8909 (mt) cc_final: 0.8686 (mt) outliers start: 17 outliers final: 6 residues processed: 215 average time/residue: 0.7100 time to fit residues: 159.9787 Evaluate side-chains 204 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 198 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 H residue 48 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 79 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 12 optimal weight: 0.0010 overall best weight: 1.9590 ------------------------------------------------------------------------------- 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 D 101 GLN G 69 GLN 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 = 0.3744 r_free = 0.3744 target = 0.146962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125933 restraints weight = 11352.290| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.47 r_work: 0.3369 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9184 Z= 0.141 Angle : 0.580 8.532 12636 Z= 0.311 Chirality : 0.037 0.294 1415 Planarity : 0.004 0.061 1461 Dihedral : 21.876 141.504 1682 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.43 % Allowed : 25.45 % Favored : 73.12 % 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: 4.12 (0.26), residues: 935 helix: 3.13 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.69 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 84 TYR 0.010 0.001 TYR E 71 PHE 0.006 0.001 PHE G 41 TRP 0.004 0.001 TRP A 42 HIS 0.004 0.001 HIS F 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9184) covalent geometry : angle 0.57974 / 0.31 (12636) hydrogen bonds : bond 0.05487 / 3.76 ( 589) hydrogen bonds : angle 3.16735 / 2.29 ( 1634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3816.26 seconds wall clock time: 65 minutes 42.25 seconds (3942.25 seconds total)