Starting phenix.real_space_refine on Thu Feb 13 00:25:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pop_17794/02_2025/8pop_17794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pop_17794/02_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_17794/02_2025/8pop_17794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pop_17794/02_2025/8pop_17794.map" model { file = "/net/cci-nas-00/data/ceres_data/8pop_17794/02_2025/8pop_17794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pop_17794/02_2025/8pop_17794.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.36, per 1000 atoms: 0.60 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: 2.50 Conformation dependent library (CDL) restraints added in 926.6 milliseconds 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 0 sheets defined 81.8% alpha, 0.0% beta 28 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 3.14 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: 2.53 Time building geometry restraints manager: 2.80 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: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.400 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:16.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.820 ------------------------------------------------------------------------------- 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= 0.543 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (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 TRP 0.028 0.007 TRP A 42 HIS 0.024 0.005 HIS A 31 PHE 0.039 0.009 PHE H 41 TYR 0.024 0.008 TYR G 71 ARG 0.028 0.003 ARG H 114 *********************** 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 : 0.963 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: 1.7725 time to fit residues: 545.3170 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 : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 88 optimal weight: 0.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 = 0.3699 r_free = 0.3699 target = 0.141943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121810 restraints weight = 11092.060| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 1.45 r_work: 0.3317 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2722 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= 0.253 Angle : 0.641 6.291 12636 Z= 0.357 Chirality : 0.039 0.129 1415 Planarity : 0.005 0.030 1461 Dihedral : 21.839 148.404 1682 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.87 % Allowed : 13.14 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.26), residues: 935 helix: 2.27 (0.19), residues: 686 sheet: None (None), residues: 0 loop : 1.02 (0.33), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 42 HIS 0.005 0.001 HIS A 119 PHE 0.008 0.001 PHE C 41 TYR 0.008 0.001 TYR D 71 ARG 0.005 0.001 ARG D 107 *********************** 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 257 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7635 (t0) cc_final: 0.7416 (t70) REVERT: A 37 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8479 (mmmt) REVERT: A 64 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8183 (mt-10) REVERT: A 77 LYS cc_start: 0.8382 (mttt) cc_final: 0.8088 (mptt) REVERT: B 47 ARG cc_start: 0.8797 (mtt90) cc_final: 0.8182 (mtp180) REVERT: B 100 LYS cc_start: 0.8659 (tptt) cc_final: 0.8278 (mmtm) REVERT: C 64 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7771 (mm-30) REVERT: C 81 LYS cc_start: 0.8219 (mtmt) cc_final: 0.7974 (mppt) REVERT: C 100 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8247 (mtpt) REVERT: D 81 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7591 (ttmm) REVERT: D 82 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7805 (mp0) REVERT: D 100 LYS cc_start: 0.8631 (mttt) cc_final: 0.8418 (tptp) REVERT: E 71 TYR cc_start: 0.9231 (t80) cc_final: 0.8981 (t80) REVERT: E 77 LYS cc_start: 0.8713 (tttt) cc_final: 0.8502 (tmtt) REVERT: E 96 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7853 (tttp) REVERT: E 117 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8436 (mt0) REVERT: F 91 ASP cc_start: 0.8236 (t0) cc_final: 0.7743 (t0) REVERT: F 115 ASP cc_start: 0.7825 (t70) cc_final: 0.7608 (t0) REVERT: G 82 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7873 (mp0) REVERT: G 85 ILE cc_start: 0.8333 (mt) cc_final: 0.7997 (mp) REVERT: H 81 LYS cc_start: 0.8468 (ttmt) cc_final: 0.8211 (tmtm) REVERT: H 84 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7200 (mpp-170) REVERT: H 121 HIS cc_start: 0.8479 (t-90) cc_final: 0.8236 (t70) REVERT: I 107 ARG cc_start: 0.8308 (mtt180) cc_final: 0.7895 (mtp85) REVERT: I 114 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.8199 (ttt180) outliers start: 24 outliers final: 5 residues processed: 239 average time/residue: 1.8040 time to fit residues: 450.3463 Evaluate side-chains 226 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 219 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 15 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN B 101 GLN B 135 GLN D 101 GLN F 124 ASN I 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121076 restraints weight = 11447.376| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.43 r_work: 0.3299 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9184 Z= 0.217 Angle : 0.574 7.372 12636 Z= 0.318 Chirality : 0.036 0.127 1415 Planarity : 0.004 0.055 1461 Dihedral : 21.919 148.250 1682 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.99 % Allowed : 18.52 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.26), residues: 935 helix: 2.77 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.33 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 54 HIS 0.004 0.001 HIS A 119 PHE 0.008 0.001 PHE G 41 TYR 0.008 0.001 TYR D 71 ARG 0.009 0.000 ARG H 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1870 Ramachandran restraints generated. 935 Oldfield, 0 Emsley, 935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 1.019 Fit side-chains REVERT: A 37 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8499 (mmmt) REVERT: A 77 LYS cc_start: 0.8351 (mttt) cc_final: 0.8062 (mptt) REVERT: B 47 ARG cc_start: 0.8745 (mtt90) cc_final: 0.8130 (mtp-110) REVERT: B 145 ASN cc_start: 0.7340 (m-40) cc_final: 0.7138 (m-40) REVERT: C 82 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7622 (tp30) REVERT: C 100 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8223 (mtpt) REVERT: D 82 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7657 (mp0) REVERT: E 84 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: E 117 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8608 (mt0) REVERT: F 64 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7729 (mm-30) REVERT: F 86 ARG cc_start: 0.6863 (mmt180) cc_final: 0.6600 (mmt90) REVERT: F 114 ARG cc_start: 0.7812 (ttp80) cc_final: 0.7439 (ttm110) REVERT: G 85 ILE cc_start: 0.8052 (mt) cc_final: 0.7747 (mp) REVERT: H 81 LYS cc_start: 0.8408 (ttmt) cc_final: 0.8013 (tmtm) REVERT: H 84 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7516 (mpp-170) REVERT: H 121 HIS cc_start: 0.8417 (t-90) cc_final: 0.8145 (t70) REVERT: I 101 GLN cc_start: 0.8578 (mt0) cc_final: 0.8290 (mt0) REVERT: I 107 ARG cc_start: 0.8104 (mtt180) cc_final: 0.7637 (mtp85) outliers start: 25 outliers final: 10 residues processed: 233 average time/residue: 1.8478 time to fit residues: 449.7733 Evaluate side-chains 224 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 48 SER Chi-restraints excluded: chain E residue 84 ARG 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 84 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 I 69 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.117455 restraints weight = 11315.061| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.44 r_work: 0.3247 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9184 Z= 0.289 Angle : 0.618 8.663 12636 Z= 0.333 Chirality : 0.038 0.123 1415 Planarity : 0.005 0.032 1461 Dihedral : 21.946 146.242 1682 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 3.94 % Allowed : 19.12 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.26), residues: 935 helix: 2.68 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.18 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 42 HIS 0.005 0.001 HIS F 119 PHE 0.010 0.002 PHE G 41 TYR 0.010 0.001 TYR E 71 ARG 0.006 0.001 ARG H 76 *********************** 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 257 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 1.013 Fit side-chains REVERT: A 37 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8526 (mmmt) REVERT: A 77 LYS cc_start: 0.8384 (mttt) cc_final: 0.8072 (mptt) REVERT: B 47 ARG cc_start: 0.8818 (mtt90) cc_final: 0.8154 (mtp-110) REVERT: B 81 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8171 (ttmt) REVERT: C 39 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7537 (tm-30) REVERT: C 80 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7655 (tpp-160) REVERT: C 82 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7780 (tp30) REVERT: C 100 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8233 (mtpt) REVERT: D 82 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7659 (mp0) REVERT: E 84 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7505 (ttp-170) REVERT: E 117 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8718 (mt0) REVERT: F 86 ARG cc_start: 0.7161 (mmt180) cc_final: 0.6830 (mmt90) REVERT: G 82 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7359 (tp30) REVERT: G 97 ASP cc_start: 0.7940 (m-30) cc_final: 0.7727 (m-30) REVERT: H 80 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6384 (tpp-160) REVERT: H 81 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8041 (tmtm) REVERT: H 121 HIS cc_start: 0.8408 (t-90) cc_final: 0.8157 (t70) REVERT: I 83 GLU cc_start: 0.7668 (tm-30) cc_final: 0.6718 (mt-10) REVERT: I 101 GLN cc_start: 0.8768 (mt0) cc_final: 0.8453 (mt0) REVERT: I 104 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6900 (tp30) REVERT: I 107 ARG cc_start: 0.8158 (mtt180) cc_final: 0.7679 (mtp85) outliers start: 33 outliers final: 15 residues processed: 234 average time/residue: 1.7458 time to fit residues: 426.8111 Evaluate side-chains 233 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 214 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 80 ARG 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 D residue 103 VAL Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 96 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 86 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 overall best weight: 4.7986 ------------------------------------------------------------------------------- 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 B 142 ASN C 124 ASN H 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.138055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117108 restraints weight = 11278.251| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.44 r_work: 0.3243 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9184 Z= 0.306 Angle : 0.616 7.991 12636 Z= 0.334 Chirality : 0.038 0.159 1415 Planarity : 0.005 0.043 1461 Dihedral : 21.897 145.706 1682 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 4.54 % Allowed : 19.95 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.25), residues: 935 helix: 2.73 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 0.99 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 42 HIS 0.005 0.001 HIS F 119 PHE 0.010 0.002 PHE G 41 TYR 0.009 0.001 TYR E 71 ARG 0.008 0.001 ARG I 86 *********************** 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 259 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 1.062 Fit side-chains REVERT: A 37 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8505 (mmmt) REVERT: A 77 LYS cc_start: 0.8382 (mttt) cc_final: 0.8081 (mptt) REVERT: B 47 ARG cc_start: 0.8807 (mtt90) cc_final: 0.8136 (mtp-110) REVERT: B 81 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (ttmt) REVERT: C 39 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7707 (tm-30) REVERT: C 64 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7785 (mm-30) REVERT: C 80 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7647 (tpp-160) REVERT: C 82 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7841 (tp30) REVERT: C 100 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8135 (mtpt) REVERT: D 27 ASP cc_start: 0.8778 (m-30) cc_final: 0.8565 (m-30) REVERT: D 78 ASP cc_start: 0.8035 (m-30) cc_final: 0.7655 (m-30) REVERT: D 82 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7598 (mp0) REVERT: E 35 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7749 (mt-10) REVERT: E 84 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7495 (ttp-170) REVERT: E 117 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8705 (mt0) REVERT: F 81 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7848 (ttmm) REVERT: F 86 ARG cc_start: 0.7296 (mmt180) cc_final: 0.6926 (mmt90) REVERT: G 82 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7342 (tp30) REVERT: G 86 ARG cc_start: 0.6929 (OUTLIER) cc_final: 0.5202 (ttm170) REVERT: G 97 ASP cc_start: 0.7928 (m-30) cc_final: 0.7678 (m-30) REVERT: H 80 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6340 (tpp-160) REVERT: H 81 LYS cc_start: 0.8442 (ttmt) cc_final: 0.8098 (tmtm) REVERT: H 84 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.7395 (mpp-170) REVERT: H 121 HIS cc_start: 0.8438 (t-90) cc_final: 0.8196 (t70) REVERT: I 39 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8033 (pm20) REVERT: I 101 GLN cc_start: 0.8763 (mt0) cc_final: 0.8473 (mt0) REVERT: I 104 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6858 (tp30) outliers start: 38 outliers final: 19 residues processed: 233 average time/residue: 1.7760 time to fit residues: 433.4788 Evaluate side-chains 241 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 213 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 100 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 80 ARG 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 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 36 LYS Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 44 ASP Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 86 ARG Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 39 GLU Chi-restraints excluded: chain I residue 96 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 95 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.0570 chunk 45 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 overall best weight: 2.7104 ------------------------------------------------------------------------------- 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 B 142 ASN C 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.120118 restraints weight = 11251.372| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 1.43 r_work: 0.3284 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4184 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= 0.219 Angle : 0.575 7.717 12636 Z= 0.313 Chirality : 0.035 0.147 1415 Planarity : 0.004 0.036 1461 Dihedral : 21.731 145.446 1682 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 3.46 % Allowed : 21.86 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.25), residues: 935 helix: 2.92 (0.19), residues: 656 sheet: None (None), residues: 0 loop : 1.11 (0.32), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 42 HIS 0.004 0.001 HIS A 119 PHE 0.007 0.001 PHE G 41 TYR 0.006 0.001 TYR E 71 ARG 0.007 0.000 ARG D 47 *********************** 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 249 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 220 time to evaluate : 0.940 Fit side-chains REVERT: A 19 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8013 (ttpp) REVERT: A 37 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8440 (mmmt) REVERT: A 77 LYS cc_start: 0.8344 (mttt) cc_final: 0.8041 (mptt) REVERT: B 47 ARG cc_start: 0.8784 (mtt90) cc_final: 0.8103 (mtp-110) REVERT: C 82 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7856 (tp30) REVERT: C 100 LYS cc_start: 0.8430 (ttmm) cc_final: 0.8134 (mtpt) REVERT: D 78 ASP cc_start: 0.7945 (m-30) cc_final: 0.7568 (m-30) REVERT: D 82 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7439 (mp0) REVERT: E 35 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7672 (mt-10) REVERT: E 84 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7318 (ttp-170) REVERT: E 101 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8366 (mm-40) REVERT: E 117 GLN cc_start: 0.8989 (mm-40) cc_final: 0.8742 (mt0) REVERT: F 81 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7605 (ttmm) REVERT: F 83 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7414 (mt-10) REVERT: F 86 ARG cc_start: 0.7261 (mmt180) cc_final: 0.7018 (mmt90) REVERT: G 82 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7279 (tp30) REVERT: G 85 ILE cc_start: 0.7645 (mt) cc_final: 0.7424 (mp) REVERT: G 97 ASP cc_start: 0.8089 (m-30) cc_final: 0.7842 (m-30) REVERT: H 81 LYS cc_start: 0.8377 (ttmt) cc_final: 0.8045 (tmtm) REVERT: H 121 HIS cc_start: 0.8446 (t-90) cc_final: 0.8162 (t70) REVERT: I 39 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: I 101 GLN cc_start: 0.8651 (mt0) cc_final: 0.8372 (mt0) outliers start: 29 outliers final: 13 residues processed: 230 average time/residue: 1.6743 time to fit residues: 402.9039 Evaluate side-chains 229 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 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 E residue 35 GLU Chi-restraints excluded: chain E residue 84 ARG 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 I residue 39 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 91 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 B 142 ASN C 124 ASN H 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.139112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.118105 restraints weight = 11435.399| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.46 r_work: 0.3260 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9184 Z= 0.273 Angle : 0.606 8.556 12636 Z= 0.330 Chirality : 0.037 0.149 1415 Planarity : 0.005 0.036 1461 Dihedral : 21.717 143.451 1682 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.58 % Allowed : 22.10 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.25), residues: 935 helix: 2.84 (0.19), residues: 654 sheet: None (None), residues: 0 loop : 1.06 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 42 HIS 0.004 0.001 HIS F 119 PHE 0.009 0.001 PHE G 41 TYR 0.011 0.001 TYR E 71 ARG 0.007 0.001 ARG D 47 *********************** 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 247 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 0.936 Fit side-chains REVERT: A 37 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8435 (mmmt) REVERT: A 77 LYS cc_start: 0.8375 (mttt) cc_final: 0.8072 (mptt) REVERT: B 47 ARG cc_start: 0.8801 (mtt90) cc_final: 0.8108 (mtp-110) REVERT: C 77 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7527 (mttp) REVERT: C 82 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7905 (tp30) REVERT: C 86 ARG cc_start: 0.6623 (mtt-85) cc_final: 0.6376 (mtt-85) REVERT: C 100 LYS cc_start: 0.8480 (ttmm) cc_final: 0.8212 (mtpt) REVERT: D 78 ASP cc_start: 0.7959 (m-30) cc_final: 0.7581 (m-30) REVERT: D 82 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7538 (mp0) REVERT: E 35 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7743 (mt-10) REVERT: E 84 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7326 (ttp-170) REVERT: E 101 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8417 (mm-40) REVERT: E 117 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8712 (mt0) REVERT: F 81 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7684 (ttmm) REVERT: F 83 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7398 (mt-10) REVERT: F 86 ARG cc_start: 0.7319 (mmt180) cc_final: 0.7072 (mmt90) REVERT: G 82 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7306 (tp30) REVERT: G 85 ILE cc_start: 0.7555 (mt) cc_final: 0.7331 (mp) REVERT: G 97 ASP cc_start: 0.8121 (m-30) cc_final: 0.7833 (m-30) REVERT: H 80 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6244 (tpp-160) REVERT: H 81 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8039 (tmtm) REVERT: H 121 HIS cc_start: 0.8464 (t-90) cc_final: 0.8168 (t70) REVERT: I 39 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: I 101 GLN cc_start: 0.8779 (mt0) cc_final: 0.8516 (mt0) outliers start: 30 outliers final: 13 residues processed: 230 average time/residue: 1.7361 time to fit residues: 417.7065 Evaluate side-chains 231 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER 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 D residue 100 LYS Chi-restraints excluded: chain E residue 35 GLU 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 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 39 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 B 142 ASN C 124 ASN H 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124454 restraints weight = 11416.742| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.41 r_work: 0.3356 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9184 Z= 0.221 Angle : 0.577 8.896 12636 Z= 0.315 Chirality : 0.035 0.147 1415 Planarity : 0.004 0.035 1461 Dihedral : 21.617 143.270 1682 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.99 % Allowed : 22.82 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.72 (0.26), residues: 935 helix: 2.91 (0.19), residues: 679 sheet: None (None), residues: 0 loop : 1.33 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 42 HIS 0.003 0.001 HIS A 119 PHE 0.007 0.001 PHE G 41 TYR 0.006 0.001 TYR E 71 ARG 0.008 0.000 ARG D 47 *********************** 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 241 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 1.015 Fit side-chains REVERT: A 4 LYS cc_start: 0.7608 (tttp) cc_final: 0.7216 (tttt) REVERT: A 37 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8375 (mmmt) REVERT: A 77 LYS cc_start: 0.8405 (mttt) cc_final: 0.8128 (mptt) REVERT: A 80 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7841 (mpt180) REVERT: B 47 ARG cc_start: 0.8731 (mtt90) cc_final: 0.8083 (mtp-110) REVERT: B 100 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8202 (mmtm) REVERT: C 77 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7493 (mttp) REVERT: C 82 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7739 (tp30) REVERT: C 100 LYS cc_start: 0.8418 (ttmm) cc_final: 0.8083 (mtpt) REVERT: D 78 ASP cc_start: 0.7927 (m-30) cc_final: 0.7587 (m-30) REVERT: D 82 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7381 (mp0) REVERT: E 35 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: E 81 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8172 (ttmm) REVERT: F 81 LYS cc_start: 0.7956 (ttmm) cc_final: 0.7551 (ttmm) REVERT: F 83 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7263 (mt-10) REVERT: F 86 ARG cc_start: 0.7246 (mmt180) cc_final: 0.7013 (mmt90) REVERT: G 82 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7318 (tp30) REVERT: G 97 ASP cc_start: 0.8077 (m-30) cc_final: 0.7782 (m-30) REVERT: H 121 HIS cc_start: 0.8397 (t-90) cc_final: 0.8125 (t70) REVERT: I 39 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: I 101 GLN cc_start: 0.8623 (mt0) cc_final: 0.8362 (mt0) outliers start: 25 outliers final: 11 residues processed: 225 average time/residue: 1.7068 time to fit residues: 402.0440 Evaluate side-chains 222 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 207 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER 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 D residue 100 LYS Chi-restraints excluded: chain E residue 35 GLU 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 I residue 39 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 1 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 B 142 ASN C 124 ASN H 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118782 restraints weight = 11201.287| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.36 r_work: 0.3281 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 9184 Z= 0.392 Angle : 0.689 9.363 12636 Z= 0.371 Chirality : 0.041 0.150 1415 Planarity : 0.005 0.035 1461 Dihedral : 21.672 140.505 1682 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 3.23 % Allowed : 22.70 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.25), residues: 935 helix: 2.68 (0.19), residues: 654 sheet: None (None), residues: 0 loop : 0.90 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 42 HIS 0.006 0.002 HIS F 119 PHE 0.012 0.002 PHE G 41 TYR 0.018 0.002 TYR E 71 ARG 0.007 0.001 ARG I 90 *********************** 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 242 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.934 Fit side-chains REVERT: A 4 LYS cc_start: 0.7643 (tttp) cc_final: 0.7388 (tttt) REVERT: A 37 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8466 (mmmt) REVERT: A 77 LYS cc_start: 0.8396 (mttt) cc_final: 0.8143 (mptt) REVERT: B 47 ARG cc_start: 0.8800 (mtt90) cc_final: 0.8127 (mtp-110) REVERT: B 81 LYS cc_start: 0.8617 (tppt) cc_final: 0.8393 (ttmt) REVERT: C 64 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7884 (mm-30) REVERT: C 77 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7564 (mttp) REVERT: C 82 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7900 (tp30) REVERT: D 78 ASP cc_start: 0.7989 (m-30) cc_final: 0.7715 (m-30) REVERT: D 82 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7598 (mp0) REVERT: E 35 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7786 (mt-10) REVERT: E 77 LYS cc_start: 0.8891 (ttmt) cc_final: 0.8601 (tmtt) REVERT: F 81 LYS cc_start: 0.8262 (ttmm) cc_final: 0.7949 (ttmm) REVERT: F 83 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7404 (mt-10) REVERT: F 86 ARG cc_start: 0.7333 (mmt180) cc_final: 0.7067 (mmt90) REVERT: F 91 ASP cc_start: 0.8220 (t0) cc_final: 0.8020 (t0) REVERT: G 82 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7419 (tp30) REVERT: G 97 ASP cc_start: 0.8126 (m-30) cc_final: 0.7863 (m-30) REVERT: H 80 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.6333 (tpp-160) REVERT: H 121 HIS cc_start: 0.8365 (t-90) cc_final: 0.8112 (t70) REVERT: I 39 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8133 (pm20) REVERT: I 101 GLN cc_start: 0.8744 (mt0) cc_final: 0.8501 (mt0) outliers start: 27 outliers final: 17 residues processed: 226 average time/residue: 1.7539 time to fit residues: 414.1957 Evaluate side-chains 231 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 B residue 103 VAL Chi-restraints excluded: chain C residue 30 SER 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 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 36 LYS Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain I residue 39 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 69 GLN I 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122947 restraints weight = 11151.885| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.34 r_work: 0.3341 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9184 Z= 0.240 Angle : 0.617 9.800 12636 Z= 0.337 Chirality : 0.036 0.144 1415 Planarity : 0.004 0.033 1461 Dihedral : 21.565 141.946 1682 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 2.27 % Allowed : 23.66 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.53 (0.26), residues: 935 helix: 2.89 (0.19), residues: 654 sheet: None (None), residues: 0 loop : 1.06 (0.32), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 42 HIS 0.004 0.001 HIS B 43 PHE 0.007 0.001 PHE G 41 TYR 0.006 0.001 TYR E 71 ARG 0.006 0.000 ARG A 80 ********************** 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 231 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 212 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 37 LYS cc_start: 0.8787 (mmtt) cc_final: 0.8376 (mmmt) REVERT: A 77 LYS cc_start: 0.8418 (mttt) cc_final: 0.8157 (mptt) REVERT: A 80 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7725 (mpt180) REVERT: B 47 ARG cc_start: 0.8737 (mtt90) cc_final: 0.8092 (mtp-110) REVERT: C 64 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7604 (mm-30) REVERT: C 77 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7529 (mttp) REVERT: C 82 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7756 (tp30) REVERT: C 100 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8188 (mtpt) REVERT: D 78 ASP cc_start: 0.7969 (m-30) cc_final: 0.7684 (m-30) REVERT: D 82 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7534 (mp0) REVERT: E 35 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: E 77 LYS cc_start: 0.8894 (ttmt) cc_final: 0.8605 (tmtt) REVERT: F 81 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7645 (ttmm) REVERT: F 86 ARG cc_start: 0.7280 (mmt180) cc_final: 0.7035 (mmt90) REVERT: G 37 LYS cc_start: 0.7809 (mmpt) cc_final: 0.7607 (mmmt) REVERT: G 82 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7320 (tp30) REVERT: G 85 ILE cc_start: 0.8130 (mp) cc_final: 0.7785 (mt) REVERT: G 97 ASP cc_start: 0.8111 (m-30) cc_final: 0.7829 (m-30) REVERT: H 86 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7432 (mmt90) REVERT: H 121 HIS cc_start: 0.8293 (t-90) cc_final: 0.8049 (t70) REVERT: I 39 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8132 (pm20) REVERT: I 101 GLN cc_start: 0.8629 (mt0) cc_final: 0.8385 (mt0) outliers start: 19 outliers final: 12 residues processed: 219 average time/residue: 1.7260 time to fit residues: 395.3079 Evaluate side-chains 224 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 C residue 30 SER 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 E residue 35 GLU Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain I residue 39 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 10.0000 chunk 2 optimal weight: 0.0470 chunk 25 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.8086 ------------------------------------------------------------------------------- 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 B 142 ASN C 124 ASN I 69 GLN I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.141530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.121618 restraints weight = 11385.881| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.39 r_work: 0.3320 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9184 Z= 0.276 Angle : 0.615 9.712 12636 Z= 0.337 Chirality : 0.037 0.148 1415 Planarity : 0.005 0.033 1461 Dihedral : 21.533 140.921 1682 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.39 % Allowed : 23.78 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.26), residues: 935 helix: 2.70 (0.19), residues: 679 sheet: None (None), residues: 0 loop : 1.15 (0.34), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 42 HIS 0.004 0.001 HIS B 43 PHE 0.009 0.001 PHE G 41 TYR 0.013 0.001 TYR E 71 ARG 0.005 0.001 ARG A 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7926.99 seconds wall clock time: 140 minutes 0.60 seconds (8400.60 seconds total)