Starting phenix.real_space_refine on Fri Aug 22 23:15:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pop_17794/08_2025/8pop_17794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pop_17794/08_2025/8pop_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_2025/8pop_17794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pop_17794/08_2025/8pop_17794.map" model { file = "/net/cci-nas-00/data/ceres_data/8pop_17794/08_2025/8pop_17794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pop_17794/08_2025/8pop_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-2.0-5787/lib/python3.9/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: 2.32, per 1000 atoms: 0.26 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: 1.04 Conformation dependent library (CDL) restraints added in 248.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.21 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: 1.32 Time building geometry restraints manager: 1.29 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=" 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=" CG HIS I 119 " pdb=" CD2 HIS I 119 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.71e+00 bond pdb=" CA SER A 48 " pdb=" CB SER A 48 " ideal model delta sigma weight residual 1.530 1.482 0.048 1.64e-02 3.72e+03 8.40e+00 bond pdb=" C ASN A 124 " pdb=" O ASN A 124 " ideal model delta sigma weight residual 1.231 1.289 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" CG HIS H 119 " pdb=" CD2 HIS H 119 " ideal model delta sigma weight residual 1.354 1.322 0.032 1.10e-02 8.26e+03 8.33e+00 ... (remaining 9179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 11907 2.66 - 5.33: 624 5.33 - 7.99: 82 7.99 - 10.65: 18 10.65 - 13.31: 5 Bond angle restraints: 12636 Sorted by residual: angle pdb=" C4' DT K 29 " pdb=" C3' DT K 29 " pdb=" O3' DT K 29 " ideal model delta sigma weight residual 110.00 98.67 11.33 1.50e+00 4.44e-01 5.70e+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=" 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 angle pdb=" O3' DT K 24 " pdb=" C3' DT K 24 " pdb=" C2' DT K 24 " ideal model delta sigma weight residual 111.50 101.26 10.24 1.50e+00 4.44e-01 4.66e+01 angle pdb=" O3' DG K 14 " pdb=" P DC K 15 " pdb=" O5' DC K 15 " ideal model delta sigma weight residual 104.00 94.21 9.79 1.50e+00 4.44e-01 4.26e+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 - 0.126: 1292 0.126 - 0.253: 117 0.253 - 0.379: 5 0.379 - 0.506: 0 0.506 - 0.632: 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 2.35 -2.98 -0.63 2.00e-01 2.50e+01 9.99e+00 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=" CA SER A 120 " pdb=" N SER A 120 " pdb=" C SER A 120 " pdb=" CB SER A 120 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+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: 0.140 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.020 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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= 0.538 Angle : 1.443 13.313 12636 Z= 0.945 Chirality : 0.075 0.632 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 aren 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 covalent geometry : bond 0.00862 ( 9184) covalent geometry : angle 1.44328 (12636) hydrogen bonds : bond 0.26673 ( 589) hydrogen bonds : angle 6.56117 ( 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 : 0.358 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: 0.8698 (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: 0.7416 (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: 0.8649 time to fit residues: 265.8691 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 : 0.337 ------------------------------------------------------------------------------- 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: 7.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3725 r_free = 0.3725 target = 0.144050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124342 restraints weight = 11268.258| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.43 r_work: 0.3341 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9184 Z= 0.193 Angle : 0.622 7.067 12636 Z= 0.346 Chirality : 0.039 0.131 1415 Planarity : 0.004 0.031 1461 Dihedral : 21.810 147.924 1682 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.87 % Allowed : 12.90 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.26), residues: 935 helix: 2.38 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.12 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 113 TYR 0.008 0.001 TYR D 71 PHE 0.007 0.001 PHE C 41 TRP 0.005 0.001 TRP D 54 HIS 0.005 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 9184) covalent geometry : angle 0.62237 (12636) hydrogen bonds : bond 0.08920 ( 589) hydrogen bonds : angle 3.74085 ( 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 248 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8464 (mmmt) REVERT: A 64 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8167 (mt-10) REVERT: A 77 LYS cc_start: 0.8307 (mttt) cc_final: 0.8047 (mptt) REVERT: B 47 ARG cc_start: 0.8734 (mtt90) cc_final: 0.8160 (mtp-110) REVERT: B 100 LYS cc_start: 0.8668 (tptt) cc_final: 0.8339 (mmtm) REVERT: C 64 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7665 (mm-30) REVERT: C 81 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7915 (mppt) REVERT: C 100 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8194 (mtpt) REVERT: D 81 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7442 (ttmm) REVERT: D 82 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7736 (mp0) REVERT: D 100 LYS cc_start: 0.8583 (mttt) cc_final: 0.8345 (tptp) REVERT: E 71 TYR cc_start: 0.9200 (t80) cc_final: 0.8860 (t80) REVERT: E 81 LYS cc_start: 0.8584 (ttmt) cc_final: 0.8352 (tmtt) REVERT: E 117 GLN cc_start: 0.8709 (mm-40) cc_final: 0.8487 (mt0) REVERT: F 91 ASP cc_start: 0.8289 (t0) cc_final: 0.7795 (t0) REVERT: F 115 ASP cc_start: 0.7781 (t70) cc_final: 0.7548 (t0) REVERT: G 82 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7916 (mp0) REVERT: G 85 ILE cc_start: 0.8216 (mt) cc_final: 0.7999 (mp) REVERT: H 84 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7239 (mpp-170) REVERT: H 121 HIS cc_start: 0.8484 (t-90) cc_final: 0.8226 (t70) REVERT: I 107 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7845 (mtp85) REVERT: I 114 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.8030 (tpt170) outliers start: 24 outliers final: 5 residues processed: 231 average time/residue: 0.9613 time to fit residues: 231.1359 Evaluate side-chains 217 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 210 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 72 ILE Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain I residue 114 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: 20.0000 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.0010 chunk 10 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 135 GLN D 101 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 = 0.3693 r_free = 0.3693 target = 0.142637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.121577 restraints weight = 11377.839| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.46 r_work: 0.3307 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9184 Z= 0.161 Angle : 0.567 8.318 12636 Z= 0.312 Chirality : 0.036 0.120 1415 Planarity : 0.004 0.053 1461 Dihedral : 21.896 148.147 1682 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 3.23 % Allowed : 18.16 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.65 (0.26), residues: 935 helix: 2.83 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.37 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 76 TYR 0.009 0.001 TYR D 71 PHE 0.008 0.001 PHE G 41 TRP 0.004 0.001 TRP H 54 HIS 0.007 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9184) covalent geometry : angle 0.56662 (12636) hydrogen bonds : bond 0.07231 ( 589) hydrogen bonds : angle 3.36543 ( 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 253 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 0.361 Fit side-chains REVERT: A 37 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8484 (mmmt) REVERT: A 77 LYS cc_start: 0.8330 (mttt) cc_final: 0.7990 (mptt) REVERT: A 80 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7813 (mpt180) REVERT: B 47 ARG cc_start: 0.8773 (mtt90) cc_final: 0.8122 (mtp-110) REVERT: C 82 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7674 (tp30) REVERT: C 100 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8220 (mtpt) REVERT: D 81 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7482 (tptp) REVERT: D 82 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7628 (mp0) REVERT: D 100 LYS cc_start: 0.8380 (mttt) cc_final: 0.8154 (tptp) REVERT: E 81 LYS cc_start: 0.8619 (ttmt) cc_final: 0.8398 (tttt) REVERT: E 84 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7541 (ttp-170) REVERT: E 117 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8628 (mt0) REVERT: F 86 ARG cc_start: 0.6797 (mmt180) cc_final: 0.6531 (mmt90) REVERT: F 114 ARG cc_start: 0.7700 (ttp80) cc_final: 0.7287 (ttm110) REVERT: G 85 ILE cc_start: 0.7944 (mt) cc_final: 0.7619 (mp) REVERT: H 84 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7433 (mpp-170) REVERT: H 121 HIS cc_start: 0.8416 (t-90) cc_final: 0.8151 (t70) REVERT: I 107 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7607 (mtp85) outliers start: 27 outliers final: 10 residues processed: 234 average time/residue: 0.9378 time to fit residues: 228.4806 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 : 0.356 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 84 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: 4.9990 chunk 91 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 58 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 64 optimal weight: 0.0870 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN B 135 GLN C 43 HIS F 124 ASN G 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 = 0.3756 r_free = 0.3756 target = 0.148074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.127050 restraints weight = 11492.541| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.47 r_work: 0.3381 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9184 Z= 0.131 Angle : 0.524 8.388 12636 Z= 0.286 Chirality : 0.034 0.125 1415 Planarity : 0.004 0.028 1461 Dihedral : 21.779 147.114 1682 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.27 % Allowed : 20.79 % Favored : 76.94 % 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 aren not related in a simple way. whole: 4.11 (0.26), residues: 935 helix: 3.12 (0.20), residues: 681 sheet: None (None), residues: 0 loop : 1.67 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 47 TYR 0.004 0.001 TYR G 71 PHE 0.004 0.001 PHE G 41 TRP 0.004 0.001 TRP A 54 HIS 0.004 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9184) covalent geometry : angle 0.52355 (12636) hydrogen bonds : bond 0.05451 ( 589) hydrogen bonds : angle 3.10002 ( 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 235 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 216 time to evaluate : 0.346 Fit side-chains REVERT: A 37 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8467 (mmmt) REVERT: A 77 LYS cc_start: 0.8327 (mttt) cc_final: 0.7998 (mptt) REVERT: B 47 ARG cc_start: 0.8685 (mtt90) cc_final: 0.8078 (mtp-110) REVERT: B 81 LYS cc_start: 0.8169 (mtmt) cc_final: 0.7946 (ttmt) REVERT: C 39 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7540 (tm-30) REVERT: C 82 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7739 (tp30) REVERT: C 100 LYS cc_start: 0.8343 (ttmm) cc_final: 0.8077 (mtpt) REVERT: D 81 LYS cc_start: 0.7656 (ttmt) cc_final: 0.7410 (tptp) REVERT: D 82 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7280 (mp0) REVERT: E 84 ARG cc_start: 0.7502 (mtp180) cc_final: 0.7271 (ttp-170) REVERT: E 97 ASP cc_start: 0.7620 (t0) cc_final: 0.7231 (t0) REVERT: E 117 GLN cc_start: 0.8859 (mm-40) cc_final: 0.8616 (mt0) REVERT: F 86 ARG cc_start: 0.6862 (mmt180) cc_final: 0.6567 (mmt90) REVERT: F 96 LYS cc_start: 0.8280 (ttpt) cc_final: 0.7826 (ttpp) REVERT: G 82 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7138 (tp30) REVERT: G 85 ILE cc_start: 0.7665 (mt) cc_final: 0.7354 (mp) REVERT: G 97 ASP cc_start: 0.7945 (m-30) cc_final: 0.7710 (m-30) REVERT: H 77 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7470 (mppt) REVERT: H 115 ASP cc_start: 0.8762 (t0) cc_final: 0.8536 (t70) REVERT: H 121 HIS cc_start: 0.8483 (t-90) cc_final: 0.8221 (t70) REVERT: I 101 GLN cc_start: 0.8514 (mt0) cc_final: 0.8235 (mt0) REVERT: I 104 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6814 (tp30) REVERT: I 107 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7612 (mtp180) outliers start: 19 outliers final: 8 residues processed: 223 average time/residue: 0.8751 time to fit residues: 203.8765 Evaluate side-chains 208 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 200 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 100 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 142 ASN C 43 HIS F 124 ASN G 69 GLN H 124 ASN I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116488 restraints weight = 11531.057| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.48 r_work: 0.3231 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9184 Z= 0.238 Angle : 0.648 7.293 12636 Z= 0.350 Chirality : 0.039 0.128 1415 Planarity : 0.005 0.043 1461 Dihedral : 21.841 144.166 1682 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 4.18 % Allowed : 20.43 % Favored : 75.39 % 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 aren not related in a simple way. whole: 3.49 (0.26), residues: 935 helix: 2.74 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.24 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 114 TYR 0.014 0.002 TYR E 71 PHE 0.012 0.002 PHE G 41 TRP 0.011 0.001 TRP F 42 HIS 0.006 0.002 HIS F 119 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 9184) covalent geometry : angle 0.64808 (12636) hydrogen bonds : bond 0.08653 ( 589) hydrogen bonds : angle 3.56178 ( 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 255 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.356 Fit side-chains REVERT: A 37 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8531 (mmmt) REVERT: A 77 LYS cc_start: 0.8368 (mttt) cc_final: 0.8064 (mptt) REVERT: B 81 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8187 (ttmt) REVERT: C 82 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7979 (tp30) REVERT: C 100 LYS cc_start: 0.8498 (ttmm) cc_final: 0.8216 (mtpt) REVERT: D 27 ASP cc_start: 0.8749 (m-30) cc_final: 0.8529 (m-30) REVERT: D 82 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7598 (mp0) REVERT: E 35 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: E 84 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7453 (ttp-170) REVERT: E 101 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8241 (mm-40) REVERT: E 117 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8765 (mt0) REVERT: F 81 LYS cc_start: 0.8360 (ttmm) cc_final: 0.7910 (ttmm) REVERT: F 86 ARG cc_start: 0.7235 (mmt180) cc_final: 0.6851 (mmt90) REVERT: G 82 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7366 (tp30) REVERT: G 96 LYS cc_start: 0.8479 (mtpp) cc_final: 0.8253 (mtpt) REVERT: G 97 ASP cc_start: 0.7976 (m-30) cc_final: 0.7709 (m-30) REVERT: H 80 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.6332 (tpp-160) REVERT: H 86 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7639 (mtp85) REVERT: H 121 HIS cc_start: 0.8434 (t-90) cc_final: 0.8159 (t70) REVERT: I 83 GLU cc_start: 0.7721 (tm-30) cc_final: 0.6660 (mt-10) REVERT: I 101 GLN cc_start: 0.8744 (mt0) cc_final: 0.8442 (mt0) REVERT: I 104 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6947 (tp30) REVERT: I 107 ARG cc_start: 0.8184 (mtt180) cc_final: 0.7724 (mtp85) outliers start: 35 outliers final: 17 residues processed: 232 average time/residue: 0.8917 time to fit residues: 215.9784 Evaluate side-chains 234 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.361 ------------------------------------------------------------------------------- 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 B residue 81 LYS 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 53 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 79 LEU 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: 2.9990 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 0.0000 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 142 ASN C 43 HIS I 106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120016 restraints weight = 11468.956| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.46 r_work: 0.3283 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9184 Z= 0.165 Angle : 0.570 7.551 12636 Z= 0.311 Chirality : 0.035 0.156 1415 Planarity : 0.004 0.038 1461 Dihedral : 21.675 145.318 1682 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 3.94 % Allowed : 21.51 % 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 aren not related in a simple way. whole: 3.67 (0.26), residues: 935 helix: 2.86 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.33 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 47 TYR 0.006 0.001 TYR E 71 PHE 0.007 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 covalent geometry : bond 0.00357 ( 9184) covalent geometry : angle 0.56956 (12636) hydrogen bonds : bond 0.07094 ( 589) hydrogen bonds : angle 3.36191 ( 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 253 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.351 Fit side-chains REVERT: A 4 LYS cc_start: 0.7873 (mtpt) cc_final: 0.7647 (tttt) REVERT: A 37 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8455 (mmmt) REVERT: A 77 LYS cc_start: 0.8353 (mttt) cc_final: 0.8042 (mptt) REVERT: B 47 ARG cc_start: 0.8792 (mtt90) cc_final: 0.8107 (mtp-110) REVERT: C 37 LYS cc_start: 0.8881 (mttp) cc_final: 0.8585 (mttm) REVERT: C 69 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: C 77 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7502 (mttp) REVERT: C 82 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7891 (tp30) REVERT: C 100 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8160 (mtpt) REVERT: D 78 ASP cc_start: 0.7989 (m-30) cc_final: 0.7649 (m-30) REVERT: D 82 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7416 (mp0) REVERT: E 84 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7315 (ttp-170) REVERT: E 97 ASP cc_start: 0.7795 (t0) cc_final: 0.7469 (t0) REVERT: E 101 GLN cc_start: 0.8612 (mm-40) cc_final: 0.8333 (mm-40) REVERT: E 117 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8737 (mt0) REVERT: F 81 LYS cc_start: 0.8073 (ttmm) cc_final: 0.7610 (ttmm) REVERT: F 86 ARG cc_start: 0.7189 (mmt180) cc_final: 0.6835 (mmt90) REVERT: F 96 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8065 (ttpp) REVERT: G 82 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7290 (tp30) REVERT: G 97 ASP cc_start: 0.8002 (m-30) cc_final: 0.7741 (m-30) REVERT: H 35 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6971 (mp0) REVERT: H 80 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6414 (tpp-160) REVERT: H 86 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7570 (mtp85) REVERT: H 121 HIS cc_start: 0.8446 (t-90) cc_final: 0.8189 (t70) REVERT: I 39 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8131 (pm20) REVERT: I 101 GLN cc_start: 0.8634 (mt0) cc_final: 0.8351 (mt0) REVERT: I 104 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6900 (tp30) REVERT: I 107 ARG cc_start: 0.8112 (mtt180) cc_final: 0.7784 (mtp180) outliers start: 33 outliers final: 15 residues processed: 234 average time/residue: 0.8699 time to fit residues: 212.4599 Evaluate side-chains 234 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 213 time to evaluate : 0.336 ------------------------------------------------------------------------------- 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 100 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 77 LYS 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 D residue 103 VAL Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 39 GLU 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: 10.0000 chunk 71 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 142 ASN C 124 ASN H 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 = 0.3691 r_free = 0.3691 target = 0.142582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.121626 restraints weight = 11493.535| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.47 r_work: 0.3305 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9184 Z= 0.158 Angle : 0.568 7.858 12636 Z= 0.308 Chirality : 0.035 0.146 1415 Planarity : 0.004 0.033 1461 Dihedral : 21.613 144.021 1682 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 4.06 % Allowed : 22.22 % 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 aren not related in a simple way. whole: 3.84 (0.26), residues: 935 helix: 2.98 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.40 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 76 TYR 0.006 0.001 TYR E 71 PHE 0.007 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 covalent geometry : bond 0.00342 ( 9184) covalent geometry : angle 0.56754 (12636) hydrogen bonds : bond 0.06514 ( 589) hydrogen bonds : angle 3.27269 ( 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 250 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.362 Fit side-chains REVERT: A 4 LYS cc_start: 0.7940 (mtpt) cc_final: 0.7703 (tttp) REVERT: A 37 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8418 (mmmt) REVERT: A 77 LYS cc_start: 0.8380 (mttt) cc_final: 0.8040 (mptt) REVERT: A 80 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7461 (mpt180) REVERT: B 47 ARG cc_start: 0.8787 (mtt90) cc_final: 0.8098 (mtp-110) REVERT: C 69 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: C 82 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7872 (tp30) REVERT: C 100 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8160 (mtpt) REVERT: D 78 ASP cc_start: 0.7981 (m-30) cc_final: 0.7662 (m-30) REVERT: D 82 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7374 (mp0) REVERT: E 35 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7597 (mt-10) REVERT: E 97 ASP cc_start: 0.7818 (t0) cc_final: 0.7470 (t0) REVERT: E 101 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8302 (mm-40) REVERT: E 117 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8745 (mt0) REVERT: F 81 LYS cc_start: 0.7990 (ttmm) cc_final: 0.7565 (ttmm) REVERT: F 86 ARG cc_start: 0.7179 (mmt180) cc_final: 0.6831 (mmt90) REVERT: F 96 LYS cc_start: 0.8390 (ttpt) cc_final: 0.8069 (ttpp) REVERT: G 82 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7277 (tp30) REVERT: G 85 ILE cc_start: 0.7526 (mt) cc_final: 0.7276 (mp) REVERT: G 97 ASP cc_start: 0.8119 (m-30) cc_final: 0.7837 (m-30) REVERT: H 35 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7062 (mp0) REVERT: H 77 LYS cc_start: 0.7777 (mmmt) cc_final: 0.7340 (mppt) REVERT: H 80 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.6305 (tpp-160) REVERT: H 86 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7568 (mtp85) REVERT: H 121 HIS cc_start: 0.8428 (t-90) cc_final: 0.8140 (t70) REVERT: I 39 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: I 83 GLU cc_start: 0.7818 (tm-30) cc_final: 0.6680 (mt-10) REVERT: I 101 GLN cc_start: 0.8611 (mt0) cc_final: 0.8336 (mt0) REVERT: I 104 GLU cc_start: 0.7088 (mm-30) cc_final: 0.6864 (tp30) REVERT: I 107 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7732 (mtp180) outliers start: 34 outliers final: 18 residues processed: 230 average time/residue: 0.8593 time to fit residues: 206.4848 Evaluate side-chains 240 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 217 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 100 LYS 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 53 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 100 LYS Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 48 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain I residue 79 LEU 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: 1.9990 chunk 64 optimal weight: 0.0070 chunk 18 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 142 ASN C 124 ASN H 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 = 0.3723 r_free = 0.3723 target = 0.145362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124487 restraints weight = 11394.144| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.45 r_work: 0.3344 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4568 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= 0.143 Angle : 0.545 7.651 12636 Z= 0.300 Chirality : 0.034 0.146 1415 Planarity : 0.004 0.038 1461 Dihedral : 21.525 142.741 1682 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.99 % Allowed : 23.06 % 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 aren not related in a simple way. whole: 4.08 (0.26), residues: 935 helix: 3.15 (0.19), residues: 679 sheet: None (None), residues: 0 loop : 1.56 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 114 TYR 0.006 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 covalent geometry : bond 0.00306 ( 9184) covalent geometry : angle 0.54509 (12636) hydrogen bonds : bond 0.05663 ( 589) hydrogen bonds : angle 3.17746 ( 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 238 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.356 Fit side-chains REVERT: A 37 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8407 (mmmt) REVERT: A 77 LYS cc_start: 0.8390 (mttt) cc_final: 0.8116 (mptt) REVERT: A 80 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7717 (mpt180) REVERT: B 47 ARG cc_start: 0.8763 (mtt90) cc_final: 0.8088 (mtp-110) REVERT: B 100 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8111 (mmtm) REVERT: C 27 ASP cc_start: 0.7520 (m-30) cc_final: 0.7137 (m-30) REVERT: C 69 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: C 77 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7517 (mttp) REVERT: C 82 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7817 (tp30) REVERT: C 100 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8196 (mtpt) REVERT: D 78 ASP cc_start: 0.7931 (m-30) cc_final: 0.7722 (m-30) REVERT: E 81 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8091 (tptt) REVERT: E 97 ASP cc_start: 0.7812 (t0) cc_final: 0.7495 (t0) REVERT: E 101 GLN cc_start: 0.8534 (mm-40) cc_final: 0.8260 (mm-40) REVERT: E 117 GLN cc_start: 0.8940 (mm-40) cc_final: 0.8728 (mt0) REVERT: F 81 LYS cc_start: 0.7817 (ttmm) cc_final: 0.7367 (ttmm) REVERT: F 86 ARG cc_start: 0.7188 (mmt180) cc_final: 0.6801 (mmt90) REVERT: G 82 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7194 (tp30) REVERT: G 85 ILE cc_start: 0.7378 (mt) cc_final: 0.7133 (mp) REVERT: G 97 ASP cc_start: 0.8055 (m-30) cc_final: 0.7704 (m-30) REVERT: H 35 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7224 (mp0) REVERT: H 76 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8198 (ttm110) REVERT: H 77 LYS cc_start: 0.7708 (mmmt) cc_final: 0.7313 (mppt) REVERT: H 80 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.6305 (tpp-160) REVERT: H 86 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7476 (mtp85) REVERT: H 115 ASP cc_start: 0.8841 (t0) cc_final: 0.8595 (t70) REVERT: H 121 HIS cc_start: 0.8410 (t-90) cc_final: 0.8138 (t70) REVERT: I 39 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: I 83 GLU cc_start: 0.7787 (tm-30) cc_final: 0.6778 (mt-10) REVERT: I 96 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7782 (ptmm) REVERT: I 101 GLN cc_start: 0.8585 (mt0) cc_final: 0.8311 (mt0) REVERT: I 104 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6834 (tp30) REVERT: I 107 ARG cc_start: 0.8063 (mtt180) cc_final: 0.7704 (mtp180) outliers start: 25 outliers final: 12 residues processed: 224 average time/residue: 0.7852 time to fit residues: 183.8495 Evaluate side-chains 223 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 100 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 77 LYS 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 48 SER Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain I residue 39 GLU 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: 0.9980 chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 18 optimal weight: 0.6980 chunk 59 optimal weight: 8.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 142 ASN C 124 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 = 0.3749 r_free = 0.3749 target = 0.147535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126600 restraints weight = 11268.203| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.46 r_work: 0.3375 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9184 Z= 0.138 Angle : 0.548 7.919 12636 Z= 0.299 Chirality : 0.033 0.145 1415 Planarity : 0.004 0.037 1461 Dihedral : 21.423 141.330 1682 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.87 % Allowed : 23.54 % Favored : 73.60 % 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 aren not related in a simple way. whole: 4.20 (0.26), residues: 935 helix: 3.19 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.71 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 114 TYR 0.005 0.001 TYR E 71 PHE 0.005 0.001 PHE G 41 TRP 0.004 0.001 TRP C 42 HIS 0.003 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9184) covalent geometry : angle 0.54846 (12636) hydrogen bonds : bond 0.05199 ( 589) hydrogen bonds : angle 3.11089 ( 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 227 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.331 Fit side-chains REVERT: A 4 LYS cc_start: 0.7612 (tttp) cc_final: 0.7349 (tttt) REVERT: A 37 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8392 (mmmt) REVERT: A 77 LYS cc_start: 0.8358 (mttt) cc_final: 0.8090 (mptt) REVERT: A 80 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7673 (mpt180) REVERT: B 47 ARG cc_start: 0.8724 (mtt90) cc_final: 0.8058 (mtp-110) REVERT: B 100 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8030 (mmtm) REVERT: C 27 ASP cc_start: 0.7524 (m-30) cc_final: 0.7237 (m-30) REVERT: C 69 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8037 (mt0) REVERT: C 77 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7444 (mttp) REVERT: C 82 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7855 (tp30) REVERT: C 100 LYS cc_start: 0.8365 (ttmm) cc_final: 0.8159 (mtpt) REVERT: E 81 LYS cc_start: 0.8545 (tmtt) cc_final: 0.7960 (tptt) REVERT: E 101 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8330 (mm-40) REVERT: F 81 LYS cc_start: 0.7786 (ttmm) cc_final: 0.7332 (ttmm) REVERT: F 114 ARG cc_start: 0.7646 (ttp80) cc_final: 0.7264 (ttp80) REVERT: G 82 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7204 (tp30) REVERT: G 85 ILE cc_start: 0.7191 (mt) cc_final: 0.6932 (mp) REVERT: G 97 ASP cc_start: 0.7983 (m-30) cc_final: 0.7600 (m-30) REVERT: H 35 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7174 (mp0) REVERT: H 77 LYS cc_start: 0.7912 (mmmt) cc_final: 0.7512 (mppt) REVERT: H 80 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6309 (tpp-160) REVERT: H 115 ASP cc_start: 0.8835 (t0) cc_final: 0.8579 (t70) REVERT: H 121 HIS cc_start: 0.8325 (t-90) cc_final: 0.8050 (t70) REVERT: I 39 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8087 (pm20) REVERT: I 83 GLU cc_start: 0.7507 (tm-30) cc_final: 0.6809 (mt-10) REVERT: I 96 LYS cc_start: 0.7981 (ptpt) cc_final: 0.7721 (ptmm) REVERT: I 101 GLN cc_start: 0.8471 (mt0) cc_final: 0.8181 (mt0) REVERT: I 107 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7533 (mtp180) outliers start: 24 outliers final: 12 residues processed: 215 average time/residue: 0.7854 time to fit residues: 176.4273 Evaluate side-chains 214 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 B residue 100 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 77 LYS 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 F residue 72 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 39 GLU 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: 2.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 64 optimal weight: 0.0010 chunk 18 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 142 ASN C 124 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 = 0.3777 r_free = 0.3777 target = 0.148541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128851 restraints weight = 11114.303| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.36 r_work: 0.3423 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 9184 Z= 0.144 Angle : 0.559 8.357 12636 Z= 0.306 Chirality : 0.034 0.145 1415 Planarity : 0.004 0.037 1461 Dihedral : 21.346 139.849 1682 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.15 % Allowed : 24.49 % Favored : 73.36 % 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 aren not related in a simple way. whole: 4.19 (0.26), residues: 935 helix: 3.19 (0.19), residues: 679 sheet: None (None), residues: 0 loop : 1.69 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 114 TYR 0.009 0.001 TYR E 71 PHE 0.006 0.001 PHE G 41 TRP 0.005 0.001 TRP C 42 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9184) covalent geometry : angle 0.55924 (12636) hydrogen bonds : bond 0.05466 ( 589) hydrogen bonds : angle 3.15127 ( 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 220 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.297 Fit side-chains REVERT: A 37 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8416 (mmmt) REVERT: A 77 LYS cc_start: 0.8372 (mttt) cc_final: 0.8156 (mptt) REVERT: A 80 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7692 (mpt180) REVERT: B 47 ARG cc_start: 0.8709 (mtt90) cc_final: 0.8074 (mtp-110) REVERT: B 100 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8117 (mmtm) REVERT: C 27 ASP cc_start: 0.7366 (m-30) cc_final: 0.7154 (m-30) REVERT: C 69 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8082 (mt0) REVERT: C 77 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7529 (mttp) REVERT: C 82 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7822 (tp30) REVERT: E 81 LYS cc_start: 0.8568 (tmtt) cc_final: 0.8045 (tptt) REVERT: E 101 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8268 (mm-40) REVERT: F 81 LYS cc_start: 0.7801 (ttmm) cc_final: 0.7193 (ttpt) REVERT: F 114 ARG cc_start: 0.7574 (ttp80) cc_final: 0.7235 (ttp80) REVERT: G 82 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7240 (tp30) REVERT: G 85 ILE cc_start: 0.7377 (mt) cc_final: 0.7157 (mp) REVERT: G 97 ASP cc_start: 0.7992 (m-30) cc_final: 0.7665 (m-30) REVERT: H 35 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7190 (mp0) REVERT: H 77 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7566 (mppt) REVERT: H 80 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6302 (tpp-160) REVERT: H 115 ASP cc_start: 0.8690 (t0) cc_final: 0.8420 (t70) REVERT: H 121 HIS cc_start: 0.8293 (t-90) cc_final: 0.8008 (t70) REVERT: I 39 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8137 (pm20) REVERT: I 81 LYS cc_start: 0.7760 (tppt) cc_final: 0.6989 (ttpt) REVERT: I 83 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6850 (mt-10) REVERT: I 96 LYS cc_start: 0.8007 (ptpt) cc_final: 0.7797 (ptmm) REVERT: I 101 GLN cc_start: 0.8553 (mt0) cc_final: 0.8292 (mt0) REVERT: I 107 ARG cc_start: 0.7917 (mtt180) cc_final: 0.7614 (mtp180) outliers start: 18 outliers final: 11 residues processed: 211 average time/residue: 0.7367 time to fit residues: 162.4940 Evaluate side-chains 213 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 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 100 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 77 LYS 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 F residue 72 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 39 GLU 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 79 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 142 ASN C 124 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 = 0.3818 r_free = 0.3818 target = 0.152184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.132416 restraints weight = 11176.399| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.39 r_work: 0.3467 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9184 Z= 0.136 Angle : 0.551 8.748 12636 Z= 0.302 Chirality : 0.033 0.144 1415 Planarity : 0.004 0.035 1461 Dihedral : 21.275 139.785 1682 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.79 % Allowed : 25.09 % 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 aren not related in a simple way. whole: 4.28 (0.26), residues: 935 helix: 3.23 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.81 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 114 TYR 0.005 0.001 TYR E 71 PHE 0.004 0.001 PHE G 41 TRP 0.004 0.000 TRP F 42 HIS 0.004 0.001 HIS B 43 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 9184) covalent geometry : angle 0.55055 (12636) hydrogen bonds : bond 0.04748 ( 589) hydrogen bonds : angle 3.07541 ( 1634) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4097.87 seconds wall clock time: 70 minutes 17.06 seconds (4217.06 seconds total)