Starting phenix.real_space_refine on Sat Dec 28 12:39:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pop_17794/12_2024/8pop_17794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pop_17794/12_2024/8pop_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_17794/12_2024/8pop_17794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pop_17794/12_2024/8pop_17794.map" model { file = "/net/cci-nas-00/data/ceres_data/8pop_17794/12_2024/8pop_17794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pop_17794/12_2024/8pop_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-5532/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: 5.65, per 1000 atoms: 0.63 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: 2.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 3.25 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: 2.51 Time building geometry restraints manager: 2.99 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: 0.120 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.560 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 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:12.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.900 ------------------------------------------------------------------------------- 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 : 1.026 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: 1.8071 time to fit residues: 556.5565 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 : 1.118 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 LYS cc_start: 0.8256 (mtpt) cc_final: 0.8036 (mtpt) REVERT: A 18 MET cc_start: 0.7727 (tpt) cc_final: 0.7384 (mmt) REVERT: A 37 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8443 (mmmt) REVERT: A 64 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8076 (mt-10) REVERT: A 77 LYS cc_start: 0.8009 (mttt) cc_final: 0.7604 (mptt) REVERT: A 96 LYS cc_start: 0.8139 (ttpt) cc_final: 0.7936 (ttpt) REVERT: A 115 ASP cc_start: 0.8695 (t70) cc_final: 0.8401 (t0) REVERT: B 47 ARG cc_start: 0.9064 (mtt90) cc_final: 0.8221 (mtp180) REVERT: B 100 LYS cc_start: 0.8213 (tptt) cc_final: 0.7877 (mmtm) REVERT: C 39 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7822 (tm-30) REVERT: C 64 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7993 (mm-30) REVERT: C 81 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7839 (mppt) REVERT: C 121 HIS cc_start: 0.8029 (t-90) cc_final: 0.7700 (t-90) REVERT: D 36 LYS cc_start: 0.8374 (tptt) cc_final: 0.7952 (ptpp) REVERT: D 81 LYS cc_start: 0.8017 (ttmt) cc_final: 0.7667 (ttmm) REVERT: D 82 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7925 (mp0) REVERT: D 100 LYS cc_start: 0.8362 (mttt) cc_final: 0.7794 (tptp) REVERT: E 64 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8584 (mm-30) REVERT: E 71 TYR cc_start: 0.9137 (t80) cc_final: 0.8900 (t80) REVERT: E 77 LYS cc_start: 0.8500 (tttt) cc_final: 0.8165 (tmtt) REVERT: E 81 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8030 (tttt) REVERT: E 96 LYS cc_start: 0.7974 (ttmt) cc_final: 0.7771 (tttp) REVERT: E 100 LYS cc_start: 0.7848 (mttt) cc_final: 0.7450 (tptp) REVERT: E 115 ASP cc_start: 0.8801 (t70) cc_final: 0.8529 (t0) REVERT: E 117 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8593 (mt0) REVERT: F 39 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8224 (tm-30) REVERT: F 52 ASP cc_start: 0.8131 (m-30) cc_final: 0.7863 (p0) REVERT: F 91 ASP cc_start: 0.7923 (t0) cc_final: 0.7402 (t0) REVERT: F 115 ASP cc_start: 0.8250 (t70) cc_final: 0.7986 (t0) REVERT: G 44 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8295 (t0) REVERT: G 78 ASP cc_start: 0.8022 (m-30) cc_final: 0.7817 (m-30) REVERT: G 82 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7795 (mp0) REVERT: G 85 ILE cc_start: 0.7833 (mt) cc_final: 0.7466 (mp) REVERT: H 81 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7727 (tmtm) REVERT: H 84 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7267 (mpp-170) REVERT: I 107 ARG cc_start: 0.8409 (mtt180) cc_final: 0.7554 (mtp85) outliers start: 24 outliers final: 5 residues processed: 239 average time/residue: 1.7995 time to fit residues: 448.8929 Evaluate side-chains 227 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 219 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 39 GLU Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 84 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 74 optimal weight: 0.0370 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9184 Z= 0.239 Angle : 0.585 6.513 12636 Z= 0.323 Chirality : 0.037 0.117 1415 Planarity : 0.005 0.050 1461 Dihedral : 21.927 148.039 1682 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 3.11 % Allowed : 17.56 % Favored : 79.33 % 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: 3.46 (0.26), residues: 935 helix: 2.72 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.21 (0.32), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 42 HIS 0.004 0.001 HIS F 31 PHE 0.009 0.001 PHE G 41 TYR 0.009 0.001 TYR D 71 ARG 0.008 0.001 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 250 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 1.080 Fit side-chains REVERT: A 4 LYS cc_start: 0.8267 (mtpt) cc_final: 0.8034 (mtpt) REVERT: A 18 MET cc_start: 0.7744 (tpt) cc_final: 0.7363 (mmt) REVERT: A 37 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8456 (mmmt) REVERT: A 64 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8014 (mt-10) REVERT: A 77 LYS cc_start: 0.8068 (mttt) cc_final: 0.7647 (mptt) REVERT: A 115 ASP cc_start: 0.8750 (t70) cc_final: 0.8539 (t0) REVERT: B 47 ARG cc_start: 0.9012 (mtt90) cc_final: 0.8161 (mtp-110) REVERT: B 145 ASN cc_start: 0.6398 (m-40) cc_final: 0.6195 (m-40) REVERT: C 82 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7848 (tp30) REVERT: C 121 HIS cc_start: 0.7941 (t-90) cc_final: 0.7547 (t-90) REVERT: D 24 ASP cc_start: 0.6221 (p0) cc_final: 0.5934 (p0) REVERT: D 36 LYS cc_start: 0.8386 (tptt) cc_final: 0.8170 (mmtt) REVERT: D 47 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8104 (mtt-85) REVERT: D 82 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7802 (mp0) REVERT: D 100 LYS cc_start: 0.8246 (mttt) cc_final: 0.7714 (tptp) REVERT: E 64 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8510 (mm-30) REVERT: E 77 LYS cc_start: 0.8540 (tttt) cc_final: 0.8248 (tmtt) REVERT: E 100 LYS cc_start: 0.7914 (mttt) cc_final: 0.7485 (tptp) REVERT: E 115 ASP cc_start: 0.8720 (t70) cc_final: 0.8464 (t0) REVERT: E 117 GLN cc_start: 0.9027 (mm-40) cc_final: 0.8725 (mt0) REVERT: F 39 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8214 (tm-30) REVERT: G 44 ASP cc_start: 0.8787 (m-30) cc_final: 0.8269 (t0) REVERT: G 82 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7689 (mp0) REVERT: G 85 ILE cc_start: 0.7653 (mt) cc_final: 0.7352 (mp) REVERT: H 81 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7529 (tmtm) REVERT: I 77 LYS cc_start: 0.7955 (tttt) cc_final: 0.7694 (tmtt) REVERT: I 107 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7358 (mtp85) outliers start: 26 outliers final: 11 residues processed: 230 average time/residue: 1.8842 time to fit residues: 452.5084 Evaluate side-chains 222 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 F 124 ASN I 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3714 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= 0.227 Angle : 0.569 7.135 12636 Z= 0.310 Chirality : 0.036 0.112 1415 Planarity : 0.004 0.030 1461 Dihedral : 21.894 146.979 1682 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 3.70 % Allowed : 18.76 % Favored : 77.54 % 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: 3.64 (0.26), residues: 935 helix: 2.86 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.23 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 42 HIS 0.004 0.001 HIS A 119 PHE 0.008 0.001 PHE G 41 TYR 0.007 0.001 TYR E 71 ARG 0.009 0.000 ARG F 86 *********************** 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 250 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 219 time to evaluate : 1.080 Fit side-chains REVERT: A 4 LYS cc_start: 0.8265 (mtpt) cc_final: 0.8037 (mtpt) REVERT: A 18 MET cc_start: 0.7822 (tpt) cc_final: 0.7453 (mmt) REVERT: A 27 ASP cc_start: 0.8692 (m-30) cc_final: 0.8462 (m-30) REVERT: A 37 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8463 (mmmt) REVERT: A 64 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7996 (mt-10) REVERT: A 77 LYS cc_start: 0.8064 (mttt) cc_final: 0.7637 (mptt) REVERT: A 115 ASP cc_start: 0.8739 (t70) cc_final: 0.8527 (t0) REVERT: B 47 ARG cc_start: 0.9004 (mtt90) cc_final: 0.8161 (mtp-110) REVERT: B 81 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7992 (ttmt) REVERT: C 39 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7608 (tm-30) REVERT: C 82 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8038 (tp30) REVERT: C 121 HIS cc_start: 0.7921 (t-90) cc_final: 0.7540 (t-90) REVERT: D 24 ASP cc_start: 0.6192 (p0) cc_final: 0.5830 (p0) REVERT: D 36 LYS cc_start: 0.8381 (tptt) cc_final: 0.8163 (mmtt) REVERT: D 47 ARG cc_start: 0.8748 (mtm110) cc_final: 0.8112 (mtt-85) REVERT: D 82 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7760 (mp0) REVERT: D 100 LYS cc_start: 0.8291 (mttt) cc_final: 0.7719 (tptp) REVERT: E 64 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8542 (mm-30) REVERT: E 77 LYS cc_start: 0.8555 (tttt) cc_final: 0.8202 (tmtt) REVERT: E 81 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8023 (tmtt) REVERT: E 100 LYS cc_start: 0.7950 (mttt) cc_final: 0.7487 (tptp) REVERT: E 115 ASP cc_start: 0.8490 (t70) cc_final: 0.8213 (t0) REVERT: E 117 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8760 (mt0) REVERT: F 39 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8209 (tm-30) REVERT: F 52 ASP cc_start: 0.8200 (p0) cc_final: 0.7964 (p0) REVERT: F 91 ASP cc_start: 0.7611 (t0) cc_final: 0.7333 (t0) REVERT: G 44 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8301 (t0) REVERT: G 85 ILE cc_start: 0.7574 (mt) cc_final: 0.7254 (mp) REVERT: H 80 ARG cc_start: 0.7723 (OUTLIER) cc_final: 0.6326 (mpp-170) REVERT: H 81 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7668 (tmtm) REVERT: I 77 LYS cc_start: 0.8028 (tttt) cc_final: 0.7722 (tmtt) REVERT: I 83 GLU cc_start: 0.7608 (tm-30) cc_final: 0.6532 (mt-10) REVERT: I 107 ARG cc_start: 0.8180 (mtt180) cc_final: 0.7460 (mtp180) outliers start: 31 outliers final: 12 residues processed: 227 average time/residue: 1.8174 time to fit residues: 431.7626 Evaluate side-chains 226 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 210 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 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 E residue 81 LYS Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 80 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 48 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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 H 124 ASN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3758 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= 0.293 Angle : 0.607 7.360 12636 Z= 0.330 Chirality : 0.038 0.120 1415 Planarity : 0.005 0.038 1461 Dihedral : 21.861 145.294 1682 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 4.18 % Allowed : 19.24 % Favored : 76.58 % 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: 3.39 (0.26), residues: 935 helix: 2.71 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.06 (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 0.002 TYR E 71 ARG 0.007 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 254 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 219 time to evaluate : 0.852 Fit side-chains REVERT: A 4 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7966 (mtpt) REVERT: A 18 MET cc_start: 0.7754 (tpt) cc_final: 0.7355 (mmt) REVERT: A 27 ASP cc_start: 0.8732 (m-30) cc_final: 0.8492 (m-30) REVERT: A 37 LYS cc_start: 0.8744 (mmtt) cc_final: 0.8472 (mmmt) REVERT: A 64 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8029 (mt-10) REVERT: A 77 LYS cc_start: 0.8092 (mttt) cc_final: 0.7668 (mptt) REVERT: A 115 ASP cc_start: 0.8782 (t70) cc_final: 0.8549 (t0) REVERT: B 47 ARG cc_start: 0.9017 (mtt90) cc_final: 0.8149 (mtp-110) REVERT: B 81 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7983 (ttmt) REVERT: C 39 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7639 (tm-30) REVERT: C 64 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7985 (mm-30) REVERT: C 80 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7867 (tpp-160) REVERT: C 82 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8034 (tp30) REVERT: C 121 HIS cc_start: 0.8027 (t-90) cc_final: 0.7608 (t-90) REVERT: D 36 LYS cc_start: 0.8398 (tptt) cc_final: 0.8166 (mmtt) REVERT: D 47 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8132 (mtt-85) REVERT: D 82 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7781 (mp0) REVERT: D 100 LYS cc_start: 0.8294 (mttt) cc_final: 0.7751 (tptp) REVERT: E 35 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: E 64 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8508 (mm-30) REVERT: E 77 LYS cc_start: 0.8552 (tttt) cc_final: 0.8192 (tmtt) REVERT: E 84 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7393 (mtp180) REVERT: E 100 LYS cc_start: 0.8022 (mttt) cc_final: 0.7450 (tptt) REVERT: E 115 ASP cc_start: 0.8539 (t70) cc_final: 0.8262 (t0) REVERT: E 117 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8747 (mt0) REVERT: F 39 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8234 (tm-30) REVERT: F 52 ASP cc_start: 0.8279 (p0) cc_final: 0.8073 (p0) REVERT: G 44 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8290 (t0) REVERT: G 82 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7441 (tp30) REVERT: G 86 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.5858 (ttm170) REVERT: H 80 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6315 (tpp-160) REVERT: H 81 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7629 (tmtm) REVERT: I 39 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8260 (pm20) REVERT: I 77 LYS cc_start: 0.8048 (tttt) cc_final: 0.7726 (tmtt) REVERT: I 104 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7112 (tp30) outliers start: 35 outliers final: 17 residues processed: 231 average time/residue: 1.7605 time to fit residues: 424.9739 Evaluate side-chains 238 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 214 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 80 ARG Chi-restraints excluded: chain C residue 105 LEU 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 36 LYS Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP 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 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3969 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= 0.229 Angle : 0.569 7.843 12636 Z= 0.311 Chirality : 0.036 0.118 1415 Planarity : 0.004 0.032 1461 Dihedral : 21.718 145.276 1682 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.11 % Allowed : 20.43 % Favored : 76.46 % 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 (0.26), residues: 935 helix: 2.85 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.13 (0.33), residues: 254 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 0.008 0.001 PHE G 41 TYR 0.007 0.001 TYR E 71 ARG 0.006 0.000 ARG F 86 *********************** 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 243 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 217 time to evaluate : 0.973 Fit side-chains REVERT: A 4 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7971 (mtpt) REVERT: A 18 MET cc_start: 0.7752 (tpt) cc_final: 0.7366 (mmt) REVERT: A 19 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7879 (ttpp) REVERT: A 27 ASP cc_start: 0.8677 (m-30) cc_final: 0.8450 (m-30) REVERT: A 37 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8431 (mmmt) REVERT: A 64 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7989 (mt-10) REVERT: A 77 LYS cc_start: 0.8083 (mttt) cc_final: 0.7654 (mptt) REVERT: B 47 ARG cc_start: 0.8985 (mtt90) cc_final: 0.8137 (mtp-110) REVERT: B 81 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7990 (ttmt) REVERT: C 39 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7674 (tm-30) REVERT: C 82 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8013 (tp30) REVERT: C 121 HIS cc_start: 0.7926 (t-90) cc_final: 0.7517 (t-90) REVERT: D 36 LYS cc_start: 0.8386 (tptt) cc_final: 0.8156 (mmtt) REVERT: D 47 ARG cc_start: 0.8743 (mtm110) cc_final: 0.8146 (mtt-85) REVERT: D 78 ASP cc_start: 0.8307 (m-30) cc_final: 0.8028 (m-30) REVERT: D 82 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7716 (mp0) REVERT: D 100 LYS cc_start: 0.8245 (mttt) cc_final: 0.7700 (tptp) REVERT: E 35 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: E 64 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8548 (mm-30) REVERT: E 77 LYS cc_start: 0.8568 (tttt) cc_final: 0.8222 (tmtt) REVERT: E 81 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7952 (tmtt) REVERT: E 100 LYS cc_start: 0.8030 (mttt) cc_final: 0.7504 (tptp) REVERT: E 115 ASP cc_start: 0.8489 (t70) cc_final: 0.8221 (t0) REVERT: E 117 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8780 (mt0) REVERT: F 39 GLU cc_start: 0.8862 (mt-10) cc_final: 0.8217 (tm-30) REVERT: F 52 ASP cc_start: 0.8286 (p0) cc_final: 0.8064 (p0) REVERT: F 83 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7733 (mt-10) REVERT: G 44 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8270 (t0) REVERT: G 82 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7408 (tp30) REVERT: H 81 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7646 (tmtm) REVERT: I 77 LYS cc_start: 0.8096 (tttt) cc_final: 0.7764 (tmtt) REVERT: I 104 GLU cc_start: 0.7398 (mm-30) cc_final: 0.7109 (tp30) outliers start: 26 outliers final: 15 residues processed: 227 average time/residue: 1.6924 time to fit residues: 402.2460 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 : 1.056 ------------------------------------------------------------------------------- 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 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 36 LYS Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 SER Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9184 Z= 0.231 Angle : 0.570 8.589 12636 Z= 0.312 Chirality : 0.036 0.120 1415 Planarity : 0.004 0.033 1461 Dihedral : 21.655 143.923 1682 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 3.46 % Allowed : 21.03 % 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: 3.67 (0.26), residues: 935 helix: 2.90 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.17 (0.33), residues: 254 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 0.008 0.001 PHE G 41 TYR 0.008 0.001 TYR E 71 ARG 0.006 0.000 ARG F 86 *********************** 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 243 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.043 Fit side-chains REVERT: A 4 LYS cc_start: 0.8206 (mtpt) cc_final: 0.7980 (mtpt) REVERT: A 18 MET cc_start: 0.7789 (tpt) cc_final: 0.7408 (mmt) REVERT: A 27 ASP cc_start: 0.8685 (m-30) cc_final: 0.8470 (m-30) REVERT: A 37 LYS cc_start: 0.8634 (mmtt) cc_final: 0.8337 (mmmt) REVERT: A 64 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7985 (mt-10) REVERT: A 77 LYS cc_start: 0.8020 (mttt) cc_final: 0.7574 (mptt) REVERT: A 80 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7622 (mpt180) REVERT: B 47 ARG cc_start: 0.8987 (mtt90) cc_final: 0.8138 (mtp-110) REVERT: B 81 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.7975 (ttmt) REVERT: C 39 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7682 (tm-30) REVERT: C 82 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8008 (tp30) REVERT: C 121 HIS cc_start: 0.8014 (t-90) cc_final: 0.7575 (t-90) REVERT: D 36 LYS cc_start: 0.8409 (tptt) cc_final: 0.8200 (mmtt) REVERT: D 47 ARG cc_start: 0.8750 (mtm110) cc_final: 0.8149 (mtt-85) REVERT: D 78 ASP cc_start: 0.8318 (m-30) cc_final: 0.8042 (m-30) REVERT: D 82 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7640 (mp0) REVERT: D 100 LYS cc_start: 0.8344 (mttt) cc_final: 0.7842 (tptp) REVERT: E 35 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: E 64 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8535 (mm-30) REVERT: E 77 LYS cc_start: 0.8593 (tttt) cc_final: 0.8251 (tmtt) REVERT: E 81 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7940 (tmtt) REVERT: E 100 LYS cc_start: 0.7934 (mttt) cc_final: 0.7413 (tptp) REVERT: E 115 ASP cc_start: 0.8460 (t70) cc_final: 0.8190 (t0) REVERT: E 117 GLN cc_start: 0.9050 (mm-40) cc_final: 0.8774 (mt0) REVERT: F 39 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8233 (tm-30) REVERT: F 52 ASP cc_start: 0.8321 (p0) cc_final: 0.8120 (p0) REVERT: G 44 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8273 (t0) REVERT: G 82 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7399 (tp30) REVERT: G 85 ILE cc_start: 0.7105 (mt) cc_final: 0.6872 (mp) REVERT: G 115 ASP cc_start: 0.9214 (t70) cc_final: 0.8901 (t70) REVERT: H 80 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.6343 (tpp-160) REVERT: H 81 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7643 (tmtm) REVERT: I 77 LYS cc_start: 0.8132 (tttt) cc_final: 0.7814 (tmtt) REVERT: I 104 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7081 (tp30) REVERT: I 107 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7470 (mtp180) outliers start: 29 outliers final: 19 residues processed: 226 average time/residue: 1.7103 time to fit residues: 404.8167 Evaluate side-chains 235 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 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 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 72 ILE 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 81 LYS Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP 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 48 SER Chi-restraints excluded: chain H residue 80 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 0.0010 chunk 8 optimal weight: 10.0000 chunk 74 optimal weight: 0.2980 chunk 85 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 overall best weight: 3.8592 ------------------------------------------------------------------------------- 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 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9184 Z= 0.269 Angle : 0.599 9.200 12636 Z= 0.327 Chirality : 0.037 0.129 1415 Planarity : 0.005 0.039 1461 Dihedral : 21.654 142.575 1682 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 3.82 % Allowed : 21.03 % Favored : 75.15 % 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: 3.52 (0.26), residues: 935 helix: 2.80 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.10 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 42 HIS 0.004 0.001 HIS F 119 PHE 0.009 0.002 PHE G 41 TYR 0.012 0.001 TYR E 71 ARG 0.011 0.000 ARG F 86 *********************** 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 248 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.961 Fit side-chains REVERT: A 4 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7986 (mtpt) REVERT: A 18 MET cc_start: 0.7808 (tpt) cc_final: 0.7415 (mmt) REVERT: A 27 ASP cc_start: 0.8701 (m-30) cc_final: 0.8486 (m-30) REVERT: A 37 LYS cc_start: 0.8633 (mmtt) cc_final: 0.8336 (mmmt) REVERT: A 64 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8003 (mt-10) REVERT: A 77 LYS cc_start: 0.8125 (mttt) cc_final: 0.7677 (mptt) REVERT: B 47 ARG cc_start: 0.8984 (mtt90) cc_final: 0.8127 (mtp-110) REVERT: B 81 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7967 (ttmt) REVERT: C 39 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7645 (tm-30) REVERT: C 82 GLU cc_start: 0.8313 (mm-30) cc_final: 0.8073 (tp30) REVERT: C 86 ARG cc_start: 0.6505 (mtt-85) cc_final: 0.6218 (mtt-85) REVERT: C 121 HIS cc_start: 0.8017 (t-90) cc_final: 0.7571 (t-90) REVERT: D 36 LYS cc_start: 0.8439 (tptt) cc_final: 0.8189 (mmtt) REVERT: D 47 ARG cc_start: 0.8747 (mtm110) cc_final: 0.8146 (mtt-85) REVERT: D 78 ASP cc_start: 0.8310 (m-30) cc_final: 0.8025 (m-30) REVERT: D 82 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7756 (mp0) REVERT: D 100 LYS cc_start: 0.8269 (mttt) cc_final: 0.7757 (tptp) REVERT: E 35 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: E 64 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8552 (mm-30) REVERT: E 77 LYS cc_start: 0.8586 (tttt) cc_final: 0.8238 (tmtt) REVERT: E 81 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.8007 (tmtt) REVERT: E 84 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7460 (mtp180) REVERT: E 100 LYS cc_start: 0.7954 (mttt) cc_final: 0.7428 (tptp) REVERT: E 115 ASP cc_start: 0.8494 (t70) cc_final: 0.8226 (t0) REVERT: E 117 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8760 (mt0) REVERT: F 39 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8247 (tm-30) REVERT: G 44 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8308 (t0) REVERT: G 82 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7393 (tp30) REVERT: G 85 ILE cc_start: 0.7097 (mt) cc_final: 0.6859 (mp) REVERT: G 115 ASP cc_start: 0.9234 (t70) cc_final: 0.8920 (t70) REVERT: H 80 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6364 (tpp-160) REVERT: H 81 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7661 (tmtm) REVERT: I 77 LYS cc_start: 0.8158 (tttt) cc_final: 0.7835 (tmtt) REVERT: I 96 LYS cc_start: 0.7634 (ptpt) cc_final: 0.7348 (ptmm) REVERT: I 104 GLU cc_start: 0.7361 (mm-30) cc_final: 0.7054 (tp30) REVERT: I 107 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7496 (mtp180) outliers start: 32 outliers final: 19 residues processed: 230 average time/residue: 1.7905 time to fit residues: 430.3288 Evaluate side-chains 237 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 212 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 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 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 72 ILE 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 81 LYS Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP 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 H residue 120 SER Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 124 ASN D 101 GLN H 124 ASN I 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9184 Z= 0.274 Angle : 0.599 9.490 12636 Z= 0.327 Chirality : 0.037 0.123 1415 Planarity : 0.005 0.034 1461 Dihedral : 21.599 142.221 1682 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 3.23 % Allowed : 21.98 % Favored : 74.79 % 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 (0.26), residues: 935 helix: 2.76 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.10 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 42 HIS 0.004 0.001 HIS B 43 PHE 0.009 0.002 PHE G 41 TYR 0.011 0.001 TYR E 71 ARG 0.005 0.000 ARG F 86 *********************** 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 243 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.900 Fit side-chains REVERT: A 4 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7988 (mtpt) REVERT: A 18 MET cc_start: 0.7802 (tpt) cc_final: 0.7414 (mmt) REVERT: A 27 ASP cc_start: 0.8714 (m-30) cc_final: 0.8494 (m-30) REVERT: A 37 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8329 (mmmt) REVERT: A 64 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8000 (mt-10) REVERT: A 77 LYS cc_start: 0.8068 (mttt) cc_final: 0.7604 (mptt) REVERT: A 80 ARG cc_start: 0.8065 (tpp80) cc_final: 0.7861 (mpt180) REVERT: B 47 ARG cc_start: 0.8977 (mtt90) cc_final: 0.8124 (mtp-110) REVERT: B 81 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7948 (ttmt) REVERT: C 27 ASP cc_start: 0.8294 (m-30) cc_final: 0.7987 (m-30) REVERT: C 82 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8075 (tp30) REVERT: C 86 ARG cc_start: 0.6522 (mtt-85) cc_final: 0.6223 (mtt-85) REVERT: C 121 HIS cc_start: 0.8030 (t-90) cc_final: 0.7707 (t-90) REVERT: D 36 LYS cc_start: 0.8438 (tptt) cc_final: 0.8214 (mmtt) REVERT: D 47 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8145 (mtt-85) REVERT: D 78 ASP cc_start: 0.8319 (m-30) cc_final: 0.8087 (m-30) REVERT: D 82 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7722 (mp0) REVERT: D 100 LYS cc_start: 0.8316 (mttt) cc_final: 0.7842 (tptp) REVERT: E 35 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: E 64 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8553 (mm-30) REVERT: E 77 LYS cc_start: 0.8586 (tttt) cc_final: 0.8237 (tmtt) REVERT: E 81 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7928 (tmtt) REVERT: E 84 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.7458 (mtp180) REVERT: E 100 LYS cc_start: 0.7954 (mttt) cc_final: 0.7412 (tptp) REVERT: E 115 ASP cc_start: 0.8505 (t70) cc_final: 0.8232 (t0) REVERT: E 117 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8755 (mt0) REVERT: F 39 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8236 (tm-30) REVERT: G 44 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8306 (t0) REVERT: G 82 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7389 (tp30) REVERT: G 85 ILE cc_start: 0.7104 (mt) cc_final: 0.6865 (mp) REVERT: G 115 ASP cc_start: 0.9238 (t70) cc_final: 0.8927 (t70) REVERT: H 80 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6365 (tpp-160) REVERT: H 81 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7663 (tmtm) REVERT: I 77 LYS cc_start: 0.8158 (tttt) cc_final: 0.7840 (tmtt) REVERT: I 96 LYS cc_start: 0.7623 (ptpt) cc_final: 0.7337 (ptmm) REVERT: I 104 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7142 (tp30) REVERT: I 107 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7494 (mtp180) outliers start: 27 outliers final: 18 residues processed: 226 average time/residue: 1.8287 time to fit residues: 431.9376 Evaluate side-chains 235 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 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 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 72 ILE 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 81 LYS Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 72 ILE Chi-restraints excluded: chain G residue 44 ASP 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 120 SER Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.0570 chunk 64 optimal weight: 0.3980 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.2100 ------------------------------------------------------------------------------- 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 69 GLN ** I 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 0.068 9184 Z= 0.203 Angle : 0.563 9.692 12636 Z= 0.308 Chirality : 0.034 0.116 1415 Planarity : 0.004 0.033 1461 Dihedral : 21.483 142.360 1682 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.39 % Allowed : 23.06 % 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 (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: 3.90 (0.26), residues: 935 helix: 3.04 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.39 (0.34), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 54 HIS 0.004 0.001 HIS B 43 PHE 0.005 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: 20 poor density : 211 time to evaluate : 0.991 Fit side-chains REVERT: A 4 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7994 (mtpt) REVERT: A 18 MET cc_start: 0.7788 (tpt) cc_final: 0.7440 (mmt) REVERT: A 27 ASP cc_start: 0.8689 (m-30) cc_final: 0.8469 (m-30) REVERT: A 37 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8375 (mmmt) REVERT: A 64 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7965 (mt-10) REVERT: A 77 LYS cc_start: 0.8053 (mttt) cc_final: 0.7655 (mptt) REVERT: A 80 ARG cc_start: 0.8028 (tpp80) cc_final: 0.7768 (mpt180) REVERT: B 47 ARG cc_start: 0.8946 (mtt90) cc_final: 0.8108 (mtp-110) REVERT: B 81 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7875 (tppt) REVERT: C 27 ASP cc_start: 0.8288 (m-30) cc_final: 0.8057 (m-30) REVERT: C 39 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7707 (tm-30) REVERT: C 82 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7925 (tp30) REVERT: C 86 ARG cc_start: 0.6414 (mtt-85) cc_final: 0.6192 (mtt-85) REVERT: C 121 HIS cc_start: 0.7987 (t-90) cc_final: 0.7564 (t-90) REVERT: D 36 LYS cc_start: 0.8459 (tptt) cc_final: 0.8228 (mmtt) REVERT: D 47 ARG cc_start: 0.8741 (mtm110) cc_final: 0.8132 (mtt-85) REVERT: D 100 LYS cc_start: 0.8319 (mttt) cc_final: 0.7827 (tptp) REVERT: E 64 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8480 (mm-30) REVERT: E 77 LYS cc_start: 0.8647 (tttt) cc_final: 0.8285 (tmtt) REVERT: E 81 LYS cc_start: 0.8101 (ttmt) cc_final: 0.7681 (tptt) REVERT: E 84 ARG cc_start: 0.7611 (ttp-170) cc_final: 0.7356 (mtm110) REVERT: E 100 LYS cc_start: 0.7857 (mttt) cc_final: 0.7395 (mmmt) REVERT: E 115 ASP cc_start: 0.8395 (t70) cc_final: 0.8147 (t0) REVERT: E 117 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8757 (mt0) REVERT: F 35 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7741 (mm-30) REVERT: F 64 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7776 (mt-10) REVERT: F 81 LYS cc_start: 0.7691 (ttmm) cc_final: 0.7075 (ttpt) REVERT: G 36 LYS cc_start: 0.7733 (tmtm) cc_final: 0.7277 (mmtm) REVERT: G 44 ASP cc_start: 0.8760 (m-30) cc_final: 0.8371 (t0) REVERT: G 82 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7338 (tp30) REVERT: G 85 ILE cc_start: 0.7063 (mt) cc_final: 0.6834 (mp) REVERT: G 115 ASP cc_start: 0.9190 (t70) cc_final: 0.8856 (t70) REVERT: H 77 LYS cc_start: 0.7678 (mmmt) cc_final: 0.7348 (mppt) REVERT: H 81 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7561 (tmtm) REVERT: H 86 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7631 (mmt90) REVERT: I 77 LYS cc_start: 0.8080 (tttt) cc_final: 0.7773 (tmtt) REVERT: I 86 ARG cc_start: 0.7269 (mtt-85) cc_final: 0.6930 (mmt180) REVERT: I 96 LYS cc_start: 0.7432 (ptpt) cc_final: 0.7177 (ptmm) REVERT: I 104 GLU cc_start: 0.7407 (mm-30) cc_final: 0.7193 (tm-30) REVERT: I 107 ARG cc_start: 0.8048 (mtt180) cc_final: 0.7457 (mtp180) outliers start: 20 outliers final: 12 residues processed: 221 average time/residue: 1.7090 time to fit residues: 395.0275 Evaluate side-chains 216 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 204 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain B residue 52 ASP Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 30 SER Chi-restraints excluded: chain D residue 30 SER Chi-restraints excluded: chain D residue 39 GLU Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain I residue 84 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.127097 restraints weight = 11101.586| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.36 r_work: 0.3391 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9184 Z= 0.203 Angle : 0.559 9.554 12636 Z= 0.306 Chirality : 0.034 0.126 1415 Planarity : 0.004 0.031 1461 Dihedral : 21.445 140.890 1682 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Rotamer: Outliers : 2.03 % Allowed : 23.30 % 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: 3.98 (0.26), residues: 935 helix: 3.07 (0.19), residues: 681 sheet: None (None), residues: 0 loop : 1.49 (0.35), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 42 HIS 0.004 0.001 HIS B 43 PHE 0.006 0.001 PHE G 41 TYR 0.008 0.001 TYR E 71 ARG 0.008 0.000 ARG F 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5577.25 seconds wall clock time: 99 minutes 26.90 seconds (5966.90 seconds total)