Starting phenix.real_space_refine on Sat Jul 4 09:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v28_64720/07_2026/9v28_64720.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v28_64720/07_2026/9v28_64720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v28_64720/07_2026/9v28_64720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v28_64720/07_2026/9v28_64720.map" model { file = "/net/cci-nas-00/data/ceres_data/9v28_64720/07_2026/9v28_64720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v28_64720/07_2026/9v28_64720.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 475 5.49 5 S 64 5.16 5 C 10574 2.51 5 N 3597 2.21 5 O 4939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19649 Number of models: 1 Model: "" Number of chains: 13 Chain: "sA" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 325 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 2 Chain: "sD" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "sE" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 442 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "sa" Number of atoms: 10153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 10153 Classifications: {'RNA': 475} Modifications used: {'rna2p_pur': 44, 'rna2p_pyr': 36, 'rna3p_pur': 225, 'rna3p_pyr': 170} Link IDs: {'rna2p': 80, 'rna3p': 394} Chain breaks: 3 Chain: "sd" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1385 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 5, 'TRANS': 177} Chain breaks: 4 Chain: "sg" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1391 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain breaks: 2 Chain: "sl" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain breaks: 2 Chain: "sq" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 723 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain breaks: 1 Chain: "ss" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 891 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 2 Chain: "st" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 565 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "su" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1107 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "sv" Number of atoms: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1123 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 1 Chain: "sw" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 563 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain breaks: 2 Time building chain proxies: 3.90, per 1000 atoms: 0.20 Number of scatterers: 19649 At special positions: 0 Unit cell: (110.21, 131.61, 141.24, 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 64 16.00 P 475 15.00 O 4939 8.00 N 3597 7.00 C 10574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSsE 24 " - pdb=" SG CYSsE 42 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 509.0 milliseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2228 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 8 sheets defined 43.7% alpha, 11.8% beta 127 base pairs and 229 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'sA' and resid 71 through 76 removed outlier: 3.510A pdb=" N ARGsA 76 " --> pdb=" O VALsA 72 " (cutoff:3.500A) Processing helix chain 'sA' and resid 80 through 90 removed outlier: 3.790A pdb=" N ILEsA 86 " --> pdb=" O SERsA 82 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEUsA 88 " --> pdb=" O ALAsA 84 " (cutoff:3.500A) Processing helix chain 'sE' and resid 32 through 36 Processing helix chain 'sE' and resid 42 through 51 removed outlier: 3.622A pdb=" N LYSsE 46 " --> pdb=" O CYSsE 42 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VALsE 48 " --> pdb=" O ARGsE 44 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N GLUsE 49 " --> pdb=" O GLUsE 45 " (cutoff:3.500A) Processing helix chain 'sd' and resid 20 through 43 removed outlier: 3.556A pdb=" N PHEsd 25 " --> pdb=" O ARGsd 21 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VALsd 26 " --> pdb=" O LYSsd 22 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARGsd 41 " --> pdb=" O GLUsd 37 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLUsd 42 " --> pdb=" O LEUsd 38 " (cutoff:3.500A) Processing helix chain 'sd' and resid 44 through 46 No H-bonds generated for 'chain 'sd' and resid 44 through 46' Processing helix chain 'sd' and resid 84 through 92 Processing helix chain 'sd' and resid 111 through 125 Processing helix chain 'sd' and resid 128 through 142 Processing helix chain 'sd' and resid 176 through 180 Processing helix chain 'sg' and resid 64 through 68 Processing helix chain 'sg' and resid 69 through 77 removed outlier: 3.695A pdb=" N CYSsg 77 " --> pdb=" O ARGsg 73 " (cutoff:3.500A) Processing helix chain 'sg' and resid 87 through 107 removed outlier: 3.544A pdb=" N ALAsg 91 " --> pdb=" O LYSsg 87 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VALsg 94 " --> pdb=" O LEUsg 90 " (cutoff:3.500A) Processing helix chain 'sg' and resid 109 through 121 Processing helix chain 'sg' and resid 144 through 165 Processing helix chain 'sg' and resid 170 through 184 removed outlier: 3.972A pdb=" N LYSsg 184 " --> pdb=" O VALsg 180 " (cutoff:3.500A) Processing helix chain 'sg' and resid 189 through 206 Processing helix chain 'sl' and resid 4 through 15 removed outlier: 3.766A pdb=" N ILEsl 9 " --> pdb=" O THRsl 5 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALAsl 10 " --> pdb=" O LYSsl 6 " (cutoff:3.500A) Processing helix chain 'sl' and resid 37 through 51 removed outlier: 3.741A pdb=" N VALsl 41 " --> pdb=" O PROsl 37 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLYsl 47 " --> pdb=" O METsl 43 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEUsl 48 " --> pdb=" O LEUsl 44 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N THRsl 50 " --> pdb=" O LYSsl 46 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYSsl 51 " --> pdb=" O GLYsl 47 " (cutoff:3.500A) Processing helix chain 'sq' and resid 31 through 36 Processing helix chain 'sq' and resid 37 through 46 Processing helix chain 'sq' and resid 49 through 62 removed outlier: 3.763A pdb=" N LYSsq 58 " --> pdb=" O ARGsq 54 " (cutoff:3.500A) Processing helix chain 'sq' and resid 85 through 89 Processing helix chain 'sq' and resid 114 through 119 removed outlier: 3.851A pdb=" N PHEsq 118 " --> pdb=" O LEUsq 115 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SERsq 119 " --> pdb=" O GLYsq 116 " (cutoff:3.500A) Processing helix chain 'ss' and resid 52 through 54 No H-bonds generated for 'chain 'ss' and resid 52 through 54' Processing helix chain 'ss' and resid 56 through 58 No H-bonds generated for 'chain 'ss' and resid 56 through 58' Processing helix chain 'ss' and resid 59 through 64 Processing helix chain 'ss' and resid 90 through 111 removed outlier: 3.658A pdb=" N ILEss 105 " --> pdb=" O ALAss 101 " (cutoff:3.500A) Processing helix chain 'ss' and resid 128 through 132 Processing helix chain 'st' and resid 6 through 20 removed outlier: 3.862A pdb=" N ALAst 12 " --> pdb=" O THRst 8 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYSst 19 " --> pdb=" O ASNst 15 " (cutoff:3.500A) Processing helix chain 'st' and resid 27 through 39 removed outlier: 3.549A pdb=" N ASNst 31 " --> pdb=" O ASPst 27 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARGst 33 " --> pdb=" O HISst 29 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLUst 37 " --> pdb=" O ARGst 33 " (cutoff:3.500A) Processing helix chain 'st' and resid 43 through 64 removed outlier: 3.626A pdb=" N ARGst 59 " --> pdb=" O THRst 55 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARGst 60 " --> pdb=" O HISst 56 " (cutoff:3.500A) Processing helix chain 'su' and resid 26 through 31 Processing helix chain 'su' and resid 32 through 34 No H-bonds generated for 'chain 'su' and resid 32 through 34' Processing helix chain 'su' and resid 39 through 50 Processing helix chain 'su' and resid 61 through 74 removed outlier: 3.624A pdb=" N ILEsu 65 " --> pdb=" O THRsu 61 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYSsu 67 " --> pdb=" O ALAsu 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASPsu 70 " --> pdb=" O GLUsu 66 " (cutoff:3.500A) Processing helix chain 'su' and resid 75 through 79 removed outlier: 3.953A pdb=" N LYSsu 79 " --> pdb=" O LEUsu 76 " (cutoff:3.500A) Processing helix chain 'su' and resid 81 through 85 Processing helix chain 'su' and resid 102 through 118 removed outlier: 4.283A pdb=" N THRsu 106 " --> pdb=" O ASNsu 102 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILEsu 112 " --> pdb=" O LEUsu 108 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N METsu 118 " --> pdb=" O ALAsu 114 " (cutoff:3.500A) Processing helix chain 'su' and resid 120 through 128 Processing helix chain 'sv' and resid 6 through 10 Processing helix chain 'sv' and resid 11 through 19 Processing helix chain 'sv' and resid 52 through 68 removed outlier: 3.568A pdb=" N ALAsv 60 " --> pdb=" O ILEsv 56 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEUsv 67 " --> pdb=" O ARGsv 63 " (cutoff:3.500A) Processing helix chain 'sv' and resid 72 through 80 Processing helix chain 'sv' and resid 98 through 112 Processing helix chain 'sv' and resid 124 through 144 removed outlier: 3.817A pdb=" N GLNsv 137 " --> pdb=" O LYSsv 133 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VALsv 138 " --> pdb=" O ILEsv 134 " (cutoff:3.500A) Processing helix chain 'sw' and resid 28 through 40 removed outlier: 3.593A pdb=" N VALsw 32 " --> pdb=" O LYSsw 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'sD' and resid 55 through 58 removed outlier: 6.885A pdb=" N ARGsD 32 " --> pdb=" O THRsD 16 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILEsD 18 " --> pdb=" O GLNsD 30 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLNsD 30 " --> pdb=" O ILEsD 18 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARGsD 40 " --> pdb=" O ILEsD 35 " (cutoff:3.500A) removed outlier: 12.096A pdb=" N ALAsg 140 " --> pdb=" O LEUsD 43 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASNsD 45 " --> pdb=" O ALAsg 140 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASPsg 142 " --> pdb=" O ASNsD 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'sd' and resid 162 through 169 removed outlier: 3.813A pdb=" N GLYsd 147 " --> pdb=" O METsd 203 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'sl' and resid 21 through 24 removed outlier: 3.595A pdb=" N THRsl 57 " --> pdb=" O TYRsl 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THRsl 66 " --> pdb=" O LYSsl 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'sq' and resid 75 through 77 removed outlier: 6.224A pdb=" N VALsq 75 " --> pdb=" O GLYsq 94 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N TYRsq 96 " --> pdb=" O VALsq 75 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THRsq 77 " --> pdb=" O TYRsq 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'ss' and resid 21 through 27 removed outlier: 3.520A pdb=" N LEUss 36 " --> pdb=" O LYSss 81 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARGss 45 " --> pdb=" O ILEss 82 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VALss 84 " --> pdb=" O ARGss 45 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'su' and resid 13 through 16 removed outlier: 3.727A pdb=" N LEUsu 14 " --> pdb=" O LEUsu 21 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'sv' and resid 83 through 84 Processing sheet with id=AA8, first strand: chain 'sw' and resid 54 through 66 removed outlier: 5.815A pdb=" N ARGsw 55 " --> pdb=" O VALsw 88 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VALsw 88 " --> pdb=" O ARGsw 55 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYSsw 86 " --> pdb=" O PROsw 57 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THRsw 21 " --> pdb=" O ALAsw 115 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 299 hydrogen bonds 466 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 229 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2728 1.33 - 1.45: 7925 1.45 - 1.57: 9313 1.57 - 1.69: 932 1.69 - 1.81: 97 Bond restraints: 20995 Sorted by residual: bond pdb=" O3' Csa1791 " pdb=" P Usa1792 " ideal model delta sigma weight residual 1.607 1.504 0.103 1.50e-02 4.44e+03 4.74e+01 bond pdb=" C1' Asa1597 " pdb=" N9 Asa1597 " ideal model delta sigma weight residual 1.465 1.378 0.087 1.50e-02 4.44e+03 3.37e+01 bond pdb=" O3' Gsa1668 " pdb=" P Asa1669 " ideal model delta sigma weight residual 1.607 1.525 0.082 1.50e-02 4.44e+03 2.99e+01 bond pdb=" O3' Gsa1788 " pdb=" P Csa1789 " ideal model delta sigma weight residual 1.607 1.526 0.081 1.50e-02 4.44e+03 2.91e+01 bond pdb=" C1' Asa1587 " pdb=" N9 Asa1587 " ideal model delta sigma weight residual 1.475 1.394 0.081 1.50e-02 4.44e+03 2.91e+01 ... (remaining 20990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.30: 30572 6.30 - 12.61: 30 12.61 - 18.91: 1 18.91 - 25.22: 2 25.22 - 31.52: 1 Bond angle restraints: 30606 Sorted by residual: angle pdb=" O2' Gsa1788 " pdb=" C2' Gsa1788 " pdb=" C1' Gsa1788 " ideal model delta sigma weight residual 108.40 76.88 31.52 1.50e+00 4.44e-01 4.42e+02 angle pdb=" O2' Csa1791 " pdb=" C2' Csa1791 " pdb=" C1' Csa1791 " ideal model delta sigma weight residual 108.40 87.21 21.19 1.50e+00 4.44e-01 2.00e+02 angle pdb=" O2' Csa1790 " pdb=" C2' Csa1790 " pdb=" C1' Csa1790 " ideal model delta sigma weight residual 108.40 87.24 21.16 1.50e+00 4.44e-01 1.99e+02 angle pdb=" O2' Usa1427 " pdb=" C2' Usa1427 " pdb=" C1' Usa1427 " ideal model delta sigma weight residual 111.80 96.12 15.68 1.50e+00 4.44e-01 1.09e+02 angle pdb=" C3' Usa1596 " pdb=" O3' Usa1596 " pdb=" P Asa1597 " ideal model delta sigma weight residual 120.20 108.13 12.07 1.50e+00 4.44e-01 6.48e+01 ... (remaining 30601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 11864 35.93 - 71.85: 1152 71.85 - 107.78: 109 107.78 - 143.71: 7 143.71 - 179.63: 20 Dihedral angle restraints: 13152 sinusoidal: 9714 harmonic: 3438 Sorted by residual: dihedral pdb=" O4' Usa1271 " pdb=" C1' Usa1271 " pdb=" N1 Usa1271 " pdb=" C2 Usa1271 " ideal model delta sinusoidal sigma weight residual -160.00 16.18 -176.18 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' Csa1383 " pdb=" C1' Csa1383 " pdb=" N1 Csa1383 " pdb=" C2 Csa1383 " ideal model delta sinusoidal sigma weight residual 200.00 24.96 175.04 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' Csa1563 " pdb=" C1' Csa1563 " pdb=" N1 Csa1563 " pdb=" C2 Csa1563 " ideal model delta sinusoidal sigma weight residual 200.00 48.29 151.71 1 1.50e+01 4.44e-03 8.02e+01 ... (remaining 13149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3474 0.064 - 0.128: 310 0.128 - 0.192: 44 0.192 - 0.256: 12 0.256 - 0.319: 5 Chirality restraints: 3845 Sorted by residual: chirality pdb=" P Csa1660 " pdb=" OP1 Csa1660 " pdb=" OP2 Csa1660 " pdb=" O5' Csa1660 " both_signs ideal model delta sigma weight residual True 2.41 -2.73 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" P Usa1792 " pdb=" OP1 Usa1792 " pdb=" OP2 Usa1792 " pdb=" O5' Usa1792 " both_signs ideal model delta sigma weight residual True 2.41 -2.11 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C3' Gsa1668 " pdb=" C4' Gsa1668 " pdb=" O3' Gsa1668 " pdb=" C2' Gsa1668 " both_signs ideal model delta sigma weight residual False -2.48 -2.78 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3842 not shown) Planarity restraints: 2084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' Asa1669 " 0.062 2.00e-02 2.50e+03 2.80e-02 2.15e+01 pdb=" N9 Asa1669 " -0.063 2.00e-02 2.50e+03 pdb=" C8 Asa1669 " -0.000 2.00e-02 2.50e+03 pdb=" N7 Asa1669 " -0.008 2.00e-02 2.50e+03 pdb=" C5 Asa1669 " -0.004 2.00e-02 2.50e+03 pdb=" C6 Asa1669 " 0.010 2.00e-02 2.50e+03 pdb=" N6 Asa1669 " 0.019 2.00e-02 2.50e+03 pdb=" N1 Asa1669 " 0.006 2.00e-02 2.50e+03 pdb=" C2 Asa1669 " -0.007 2.00e-02 2.50e+03 pdb=" N3 Asa1669 " -0.012 2.00e-02 2.50e+03 pdb=" C4 Asa1669 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' Asa1395 " -0.046 2.00e-02 2.50e+03 2.24e-02 1.38e+01 pdb=" N9 Asa1395 " 0.039 2.00e-02 2.50e+03 pdb=" C8 Asa1395 " 0.013 2.00e-02 2.50e+03 pdb=" N7 Asa1395 " 0.003 2.00e-02 2.50e+03 pdb=" C5 Asa1395 " -0.027 2.00e-02 2.50e+03 pdb=" C6 Asa1395 " -0.015 2.00e-02 2.50e+03 pdb=" N6 Asa1395 " 0.002 2.00e-02 2.50e+03 pdb=" N1 Asa1395 " -0.011 2.00e-02 2.50e+03 pdb=" C2 Asa1395 " 0.016 2.00e-02 2.50e+03 pdb=" N3 Asa1395 " 0.007 2.00e-02 2.50e+03 pdb=" C4 Asa1395 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' Asa1396 " 0.018 2.00e-02 2.50e+03 2.16e-02 1.28e+01 pdb=" N9 Asa1396 " 0.005 2.00e-02 2.50e+03 pdb=" C8 Asa1396 " 0.015 2.00e-02 2.50e+03 pdb=" N7 Asa1396 " 0.003 2.00e-02 2.50e+03 pdb=" C5 Asa1396 " -0.023 2.00e-02 2.50e+03 pdb=" C6 Asa1396 " 0.008 2.00e-02 2.50e+03 pdb=" N6 Asa1396 " 0.007 2.00e-02 2.50e+03 pdb=" N1 Asa1396 " 0.012 2.00e-02 2.50e+03 pdb=" C2 Asa1396 " 0.010 2.00e-02 2.50e+03 pdb=" N3 Asa1396 " 0.006 2.00e-02 2.50e+03 pdb=" C4 Asa1396 " -0.060 2.00e-02 2.50e+03 ... (remaining 2081 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 483 2.63 - 3.19: 16878 3.19 - 3.76: 35885 3.76 - 4.33: 48022 4.33 - 4.90: 69843 Nonbonded interactions: 171111 Sorted by model distance: nonbonded pdb=" OP1 Asa1722 " pdb=" OH TYRsq 114 " model vdw 2.058 3.040 nonbonded pdb=" OG1 THRsw 68 " pdb=" O CYSsw 70 " model vdw 2.074 3.040 nonbonded pdb=" O2' Csa1441 " pdb=" O5' Asa1442 " model vdw 2.074 3.040 nonbonded pdb=" OG1 THRsD 16 " pdb=" OE1 GLUsD 17 " model vdw 2.151 3.040 nonbonded pdb=" N2 Gsa1750 " pdb=" O2' Gsa1776 " model vdw 2.158 3.120 ... (remaining 171106 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.780 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.940 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 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 : 0.005 0.103 20996 Z= 0.378 Angle : 0.749 31.521 30608 Z= 0.569 Chirality : 0.042 0.319 3845 Planarity : 0.004 0.060 2084 Dihedral : 23.213 179.633 10921 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.83 % Favored : 93.08 % Rotamer: Outliers : 6.15 % Allowed : 29.37 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.24), residues: 1142 helix: 0.08 (0.25), residues: 428 sheet: 0.48 (0.43), residues: 156 loop : -1.68 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsA 76 TYR 0.036 0.002 TYRst 21 PHE 0.027 0.002 PHEsq 32 TRP 0.006 0.001 TRPsl 65 HIS 0.005 0.001 HISsu 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.38 (20995) covalent geometry : angle 0.74892 / 0.57 (30606) SS BOND : bond 0.00490 / 0.26 ( 1) SS BOND : angle 1.21525 / 0.69 ( 2) hydrogen bonds : bond 0.21543 / 14.50 ( 691) hydrogen bonds : angle 7.33357 / 4.99 ( 1561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 147 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: sA 76 ARG cc_start: 0.7487 (ptp90) cc_final: 0.7274 (ptp90) REVERT: sd 52 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7445 (mt-10) REVERT: sd 156 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7804 (mt) REVERT: sg 92 MET cc_start: 0.8210 (ttp) cc_final: 0.7965 (ttm) REVERT: sq 88 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6262 (ptt) REVERT: st 14 ARG cc_start: 0.7424 (mtm-85) cc_final: 0.7194 (ttp-110) REVERT: su 109 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.5541 (ttp-170) outliers start: 63 outliers final: 38 residues processed: 197 average time/residue: 0.1345 time to fit residues: 41.2174 Evaluate side-chains 155 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 113 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 13 ASN Chi-restraints excluded: chain sE residue 18 SER Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 52 GLU Chi-restraints excluded: chain sd residue 156 LEU Chi-restraints excluded: chain sd residue 170 TYR Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 116 ASP Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 168 SER Chi-restraints excluded: chain sl residue 20 CYS Chi-restraints excluded: chain sl residue 36 ILE Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 57 THR Chi-restraints excluded: chain sq residue 29 GLU Chi-restraints excluded: chain sq residue 85 LEU Chi-restraints excluded: chain sq residue 88 MET Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 38 LYS Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 25 THR Chi-restraints excluded: chain st residue 34 VAL Chi-restraints excluded: chain su residue 53 VAL Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 104 VAL Chi-restraints excluded: chain su residue 109 ARG Chi-restraints excluded: chain sv residue 68 ASN Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 20 ILE Chi-restraints excluded: chain sw residue 23 THR Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 63 ILE Chi-restraints excluded: chain sw residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.0050 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sg 22 ASN sg 112 GLN sq 78 HIS sq 87 ASN sv 89 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.063131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.055281 restraints weight = 101842.313| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.95 r_work: 0.3252 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20996 Z= 0.173 Angle : 0.597 9.398 30608 Z= 0.347 Chirality : 0.041 0.257 3845 Planarity : 0.005 0.059 2084 Dihedral : 23.385 178.440 8587 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.74 % Favored : 93.08 % Rotamer: Outliers : 5.76 % Allowed : 27.22 % Favored : 67.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.24), residues: 1142 helix: 0.37 (0.24), residues: 444 sheet: 0.38 (0.41), residues: 158 loop : -1.53 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGsA 76 TYR 0.020 0.002 TYRsq 114 PHE 0.017 0.002 PHEst 53 TRP 0.005 0.001 TRPsl 65 HIS 0.009 0.001 HISsv 2 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (20995) covalent geometry : angle 0.59653 / 0.35 (30606) SS BOND : bond 0.00256 / 0.13 ( 1) SS BOND : angle 0.94239 / 0.51 ( 2) hydrogen bonds : bond 0.07840 / 5.31 ( 691) hydrogen bonds : angle 4.72319 / 3.20 ( 1561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 125 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: sE 27 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7991 (mtt-85) REVERT: sE 36 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9001 (mt) REVERT: sl 13 LYS cc_start: 0.9522 (ttmt) cc_final: 0.9052 (pptt) REVERT: ss 38 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7836 (ttpp) REVERT: st 14 ARG cc_start: 0.7511 (mtm-85) cc_final: 0.6952 (mtm110) REVERT: st 63 LYS cc_start: 0.8919 (ttpt) cc_final: 0.8708 (mmtt) REVERT: su 116 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8280 (mttp) REVERT: sv 74 MET cc_start: 0.8504 (tpp) cc_final: 0.8286 (tpt) outliers start: 59 outliers final: 35 residues processed: 171 average time/residue: 0.1344 time to fit residues: 35.2608 Evaluate side-chains 154 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 115 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 87 LEU Chi-restraints excluded: chain sD residue 52 VAL Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 27 ARG Chi-restraints excluded: chain sE residue 36 LEU Chi-restraints excluded: chain sE residue 42 CYS Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sg residue 22 ASN Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 92 MET Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 8 ILE Chi-restraints excluded: chain sl residue 9 ILE Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sl residue 46 LYS Chi-restraints excluded: chain sl residue 66 THR Chi-restraints excluded: chain sq residue 60 LEU Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 38 LYS Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 63 VAL Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 116 LYS Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 20 ILE Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 65 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 136 optimal weight: 9.9990 chunk 106 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 45 optimal weight: 30.0000 chunk 39 optimal weight: 40.0000 chunk 63 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 142 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 overall best weight: 10.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sv 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.060777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.053128 restraints weight = 101888.478| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.20 r_work: 0.3168 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 20996 Z= 0.287 Angle : 0.670 9.347 30608 Z= 0.386 Chirality : 0.046 0.297 3845 Planarity : 0.006 0.062 2084 Dihedral : 23.371 177.767 8544 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.09 % Favored : 92.73 % Rotamer: Outliers : 7.71 % Allowed : 27.22 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.24), residues: 1142 helix: 0.45 (0.24), residues: 446 sheet: -0.04 (0.40), residues: 160 loop : -1.69 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGst 59 TYR 0.018 0.002 TYRsv 66 PHE 0.023 0.002 PHEss 111 TRP 0.006 0.001 TRPsg 24 HIS 0.007 0.002 HISsu 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.29 (20995) covalent geometry : angle 0.67035 / 0.39 (30606) SS BOND : bond 0.00723 / 0.38 ( 1) SS BOND : angle 1.72503 / 0.97 ( 2) hydrogen bonds : bond 0.08427 / 5.53 ( 691) hydrogen bonds : angle 4.47784 / 3.04 ( 1561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 131 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sD 19 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8794 (mm) REVERT: sE 36 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9232 (mt) REVERT: sd 42 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.8766 (mt-10) REVERT: sd 137 MET cc_start: 0.8578 (mmm) cc_final: 0.7626 (mmm) REVERT: sd 203 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7771 (tmm) REVERT: sg 74 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8769 (tp) REVERT: sg 177 ASP cc_start: 0.8477 (p0) cc_final: 0.8274 (p0) REVERT: sg 178 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: sl 13 LYS cc_start: 0.9569 (ttmt) cc_final: 0.9066 (pptt) REVERT: sq 37 ASP cc_start: 0.7366 (t0) cc_final: 0.7107 (t0) REVERT: sq 41 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7375 (ptp90) REVERT: ss 158 ARG cc_start: 0.5177 (OUTLIER) cc_final: 0.1824 (mtt180) REVERT: st 18 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7308 (mm-30) REVERT: st 59 ARG cc_start: 0.6599 (mtt180) cc_final: 0.6256 (mtt180) REVERT: sv 78 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7844 (ptp-170) outliers start: 79 outliers final: 51 residues processed: 194 average time/residue: 0.1425 time to fit residues: 42.1649 Evaluate side-chains 180 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 120 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 87 LEU Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 19 LEU Chi-restraints excluded: chain sD residue 42 ILE Chi-restraints excluded: chain sD residue 52 VAL Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 6 ILE Chi-restraints excluded: chain sE residue 36 LEU Chi-restraints excluded: chain sE residue 40 ARG Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 17 THR Chi-restraints excluded: chain sd residue 35 LEU Chi-restraints excluded: chain sd residue 42 GLU Chi-restraints excluded: chain sd residue 165 VAL Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET Chi-restraints excluded: chain sg residue 29 THR Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 74 LEU Chi-restraints excluded: chain sg residue 92 MET Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 178 GLU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 8 ILE Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 29 GLU Chi-restraints excluded: chain sq residue 41 ARG Chi-restraints excluded: chain sq residue 60 LEU Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain sq residue 126 THR Chi-restraints excluded: chain ss residue 22 VAL Chi-restraints excluded: chain ss residue 35 CYS Chi-restraints excluded: chain ss residue 38 LYS Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 43 THR Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 32 THR Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 82 VAL Chi-restraints excluded: chain sv residue 37 THR Chi-restraints excluded: chain sv residue 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 65 THR Chi-restraints excluded: chain sw residue 82 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 0 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 116 optimal weight: 0.0470 chunk 152 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 160 optimal weight: 7.9990 chunk 40 optimal weight: 40.0000 overall best weight: 6.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sg 22 ASN sl 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.061568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.053774 restraints weight = 101961.265| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.95 r_work: 0.3212 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20996 Z= 0.185 Angle : 0.566 9.365 30608 Z= 0.333 Chirality : 0.042 0.276 3845 Planarity : 0.005 0.060 2084 Dihedral : 23.396 178.340 8542 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.57 % Favored : 93.26 % Rotamer: Outliers : 7.22 % Allowed : 28.49 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.24), residues: 1142 helix: 0.58 (0.24), residues: 449 sheet: -0.03 (0.40), residues: 157 loop : -1.69 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGst 59 TYR 0.016 0.002 TYRsq 114 PHE 0.031 0.002 PHEss 111 TRP 0.010 0.001 TRPsg 24 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.18 (20995) covalent geometry : angle 0.56619 / 0.33 (30606) SS BOND : bond 0.00394 / 0.21 ( 1) SS BOND : angle 0.81161 / 0.44 ( 2) hydrogen bonds : bond 0.07156 / 4.68 ( 691) hydrogen bonds : angle 4.18016 / 2.83 ( 1561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 125 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sD 19 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8786 (mm) REVERT: sE 36 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9227 (mt) REVERT: sd 28 ASP cc_start: 0.8472 (t0) cc_final: 0.8237 (t0) REVERT: sd 137 MET cc_start: 0.8432 (mmm) cc_final: 0.7536 (mmm) REVERT: sd 203 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7655 (tmm) REVERT: sg 178 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: sq 37 ASP cc_start: 0.7577 (t0) cc_final: 0.7357 (t0) REVERT: sq 41 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7379 (ptp90) REVERT: ss 158 ARG cc_start: 0.4973 (OUTLIER) cc_final: 0.1906 (mtt180) REVERT: st 18 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7360 (mm-30) REVERT: sv 21 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: sv 78 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7629 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8711 (mtt90) outliers start: 74 outliers final: 45 residues processed: 180 average time/residue: 0.1398 time to fit residues: 38.9985 Evaluate side-chains 175 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 120 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 87 LEU Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 19 LEU Chi-restraints excluded: chain sD residue 52 VAL Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 6 ILE Chi-restraints excluded: chain sE residue 36 LEU Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 35 LEU Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET Chi-restraints excluded: chain sg residue 22 ASN Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 92 MET Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 178 GLU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 8 ILE Chi-restraints excluded: chain sl residue 20 CYS Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 29 GLU Chi-restraints excluded: chain sq residue 41 ARG Chi-restraints excluded: chain sq residue 60 LEU Chi-restraints excluded: chain sq residue 85 LEU Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 21 SER Chi-restraints excluded: chain ss residue 38 LYS Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 18 GLU Chi-restraints excluded: chain st residue 37 GLU Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain sv residue 1 MET Chi-restraints excluded: chain sv residue 21 GLU Chi-restraints excluded: chain sv residue 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 23 THR Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 65 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 90 optimal weight: 30.0000 chunk 127 optimal weight: 8.9990 chunk 156 optimal weight: 20.0000 chunk 32 optimal weight: 40.0000 chunk 99 optimal weight: 9.9990 chunk 36 optimal weight: 50.0000 chunk 35 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 72 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 overall best weight: 12.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sD 14 GLN ** sl 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.059235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.051773 restraints weight = 98464.809| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.03 r_work: 0.3162 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 20996 Z= 0.350 Angle : 0.708 9.639 30608 Z= 0.403 Chirality : 0.049 0.320 3845 Planarity : 0.006 0.063 2084 Dihedral : 23.416 177.857 8542 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.36 % Favored : 92.56 % Rotamer: Outliers : 9.27 % Allowed : 26.44 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.24), residues: 1142 helix: 0.42 (0.24), residues: 449 sheet: -0.33 (0.40), residues: 161 loop : -1.91 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGst 14 TYR 0.020 0.003 TYRsq 44 PHE 0.039 0.003 PHEss 111 TRP 0.012 0.002 TRPsg 24 HIS 0.008 0.002 HISsu 121 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.35 (20995) covalent geometry : angle 0.70797 / 0.40 (30606) SS BOND : bond 0.01032 / 0.54 ( 1) SS BOND : angle 1.52728 / 0.87 ( 2) hydrogen bonds : bond 0.08654 / 5.67 ( 691) hydrogen bonds : angle 4.35085 / 2.94 ( 1561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 126 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sD 19 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8867 (mm) REVERT: sE 14 TYR cc_start: 0.7614 (m-10) cc_final: 0.7399 (m-10) REVERT: sE 36 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9273 (mt) REVERT: sd 137 MET cc_start: 0.8512 (mmm) cc_final: 0.8049 (mmt) REVERT: sd 203 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7691 (tmm) REVERT: sg 74 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8772 (tp) REVERT: sg 178 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: ss 158 ARG cc_start: 0.5024 (OUTLIER) cc_final: 0.1776 (mtt180) REVERT: st 27 ASP cc_start: 0.8314 (t0) cc_final: 0.7976 (t0) REVERT: sv 5 SER cc_start: 0.8700 (m) cc_final: 0.8416 (t) REVERT: sv 21 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7933 (pm20) REVERT: sv 78 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7685 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8914 (mtt90) outliers start: 95 outliers final: 66 residues processed: 200 average time/residue: 0.1424 time to fit residues: 44.5012 Evaluate side-chains 199 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 124 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 76 ARG Chi-restraints excluded: chain sA residue 87 LEU Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 19 LEU Chi-restraints excluded: chain sD residue 52 VAL Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 6 ILE Chi-restraints excluded: chain sE residue 36 LEU Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 35 LEU Chi-restraints excluded: chain sd residue 156 LEU Chi-restraints excluded: chain sd residue 165 VAL Chi-restraints excluded: chain sd residue 188 CYS Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET Chi-restraints excluded: chain sg residue 29 THR Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 74 LEU Chi-restraints excluded: chain sg residue 92 MET Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 178 GLU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 8 ILE Chi-restraints excluded: chain sl residue 20 CYS Chi-restraints excluded: chain sl residue 29 CYS Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 41 ARG Chi-restraints excluded: chain sq residue 60 LEU Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 21 SER Chi-restraints excluded: chain ss residue 35 CYS Chi-restraints excluded: chain ss residue 38 LYS Chi-restraints excluded: chain ss residue 49 VAL Chi-restraints excluded: chain ss residue 52 ASP Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 85 THR Chi-restraints excluded: chain ss residue 105 ILE Chi-restraints excluded: chain ss residue 133 VAL Chi-restraints excluded: chain ss residue 156 SER Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 9 VAL Chi-restraints excluded: chain st residue 17 ILE Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 32 THR Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 82 VAL Chi-restraints excluded: chain su residue 104 VAL Chi-restraints excluded: chain su residue 106 THR Chi-restraints excluded: chain su residue 116 LYS Chi-restraints excluded: chain su residue 125 ARG Chi-restraints excluded: chain sv residue 1 MET Chi-restraints excluded: chain sv residue 21 GLU Chi-restraints excluded: chain sv residue 37 THR Chi-restraints excluded: chain sv residue 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 134 ILE Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 23 THR Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 65 THR Chi-restraints excluded: chain sw residue 82 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 93 optimal weight: 6.9990 chunk 27 optimal weight: 40.0000 chunk 116 optimal weight: 6.9990 chunk 57 optimal weight: 30.0000 chunk 147 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 89 optimal weight: 8.9990 chunk 148 optimal weight: 5.9990 chunk 51 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sg 22 ASN sl 24 HIS ** sv 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.060504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.053020 restraints weight = 97220.381| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.93 r_work: 0.3206 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20996 Z= 0.185 Angle : 0.577 9.701 30608 Z= 0.339 Chirality : 0.042 0.290 3845 Planarity : 0.005 0.062 2084 Dihedral : 23.427 177.816 8542 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.83 % Favored : 92.99 % Rotamer: Outliers : 6.73 % Allowed : 28.20 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.24), residues: 1142 helix: 0.66 (0.24), residues: 452 sheet: -0.22 (0.41), residues: 157 loop : -1.88 (0.24), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsu 15 TYR 0.016 0.002 TYRsq 44 PHE 0.017 0.002 PHEss 111 TRP 0.009 0.001 TRPsg 24 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.19 (20995) covalent geometry : angle 0.57731 / 0.34 (30606) SS BOND : bond 0.00677 / 0.36 ( 1) SS BOND : angle 0.92284 / 0.53 ( 2) hydrogen bonds : bond 0.07261 / 4.72 ( 691) hydrogen bonds : angle 4.10229 / 2.78 ( 1561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 135 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sD 19 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8852 (mm) REVERT: sd 137 MET cc_start: 0.8409 (mmm) cc_final: 0.7844 (mmt) REVERT: sd 203 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7631 (tmm) REVERT: sg 178 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8430 (tp30) REVERT: sl 43 MET cc_start: 0.8209 (mmm) cc_final: 0.7964 (mmm) REVERT: sq 41 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7320 (ptp90) REVERT: ss 20 LYS cc_start: 0.6808 (ptmt) cc_final: 0.6545 (ttmt) REVERT: ss 158 ARG cc_start: 0.4888 (OUTLIER) cc_final: 0.1911 (mtt180) REVERT: st 27 ASP cc_start: 0.8227 (t0) cc_final: 0.7836 (t0) REVERT: sv 5 SER cc_start: 0.8566 (m) cc_final: 0.8333 (t) REVERT: sv 21 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: sv 78 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7496 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8750 (mtt90) outliers start: 69 outliers final: 46 residues processed: 187 average time/residue: 0.1447 time to fit residues: 42.0856 Evaluate side-chains 181 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 127 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 87 LEU Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 19 LEU Chi-restraints excluded: chain sD residue 52 VAL Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 6 ILE Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 35 LEU Chi-restraints excluded: chain sd residue 156 LEU Chi-restraints excluded: chain sd residue 165 VAL Chi-restraints excluded: chain sd residue 170 TYR Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET Chi-restraints excluded: chain sg residue 22 ASN Chi-restraints excluded: chain sg residue 29 THR Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 178 GLU Chi-restraints excluded: chain sg residue 184 LYS Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 8 ILE Chi-restraints excluded: chain sl residue 20 CYS Chi-restraints excluded: chain sl residue 36 ILE Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 41 ARG Chi-restraints excluded: chain sq residue 60 LEU Chi-restraints excluded: chain sq residue 85 LEU Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 17 ILE Chi-restraints excluded: chain st residue 37 GLU Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain sv residue 1 MET Chi-restraints excluded: chain sv residue 21 GLU Chi-restraints excluded: chain sv residue 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 23 THR Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 65 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 104 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 86 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 114 optimal weight: 0.4980 chunk 150 optimal weight: 7.9990 chunk 62 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 19 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sD 14 GLN sl 24 HIS ss 92 GLN su 98 GLN ** sv 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.061748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.054329 restraints weight = 98172.598| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.94 r_work: 0.3236 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20996 Z= 0.135 Angle : 0.544 9.262 30608 Z= 0.319 Chirality : 0.040 0.268 3845 Planarity : 0.004 0.060 2084 Dihedral : 23.411 178.352 8535 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.92 % Favored : 92.91 % Rotamer: Outliers : 6.24 % Allowed : 30.24 % Favored : 63.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1142 helix: 0.84 (0.24), residues: 448 sheet: -0.14 (0.41), residues: 157 loop : -1.83 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsA 76 TYR 0.023 0.002 TYRsE 14 PHE 0.017 0.001 PHEss 111 TRP 0.011 0.001 TRPsg 24 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (20995) covalent geometry : angle 0.54360 / 0.32 (30606) SS BOND : bond 0.00138 / 0.07 ( 1) SS BOND : angle 0.97714 / 0.55 ( 2) hydrogen bonds : bond 0.06681 / 4.31 ( 691) hydrogen bonds : angle 3.95411 / 2.68 ( 1561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 132 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sD 14 GLN cc_start: 0.8002 (mm110) cc_final: 0.7726 (mm110) REVERT: sd 137 MET cc_start: 0.8348 (mmm) cc_final: 0.7669 (mmt) REVERT: sd 203 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7763 (tmm) REVERT: sg 23 LYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7659 (mtmm) REVERT: sg 178 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8183 (tp30) REVERT: sq 41 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7597 (ptp90) REVERT: sq 88 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6498 (ptp) REVERT: ss 79 ASP cc_start: 0.7456 (m-30) cc_final: 0.7210 (m-30) REVERT: ss 158 ARG cc_start: 0.4827 (OUTLIER) cc_final: 0.1746 (mtt180) REVERT: st 7 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7683 (ptpp) REVERT: sv 5 SER cc_start: 0.8545 (m) cc_final: 0.8323 (t) REVERT: sv 21 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: sv 55 TYR cc_start: 0.8731 (m-80) cc_final: 0.8287 (m-80) REVERT: sv 74 MET cc_start: 0.8509 (tpp) cc_final: 0.7951 (tpt) REVERT: sv 121 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8705 (mtt90) outliers start: 64 outliers final: 43 residues processed: 180 average time/residue: 0.1405 time to fit residues: 39.5784 Evaluate side-chains 179 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 127 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 87 LEU Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 6 ILE Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 35 LEU Chi-restraints excluded: chain sd residue 170 TYR Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET Chi-restraints excluded: chain sg residue 23 LYS Chi-restraints excluded: chain sg residue 29 THR Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 178 GLU Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 20 CYS Chi-restraints excluded: chain sl residue 29 CYS Chi-restraints excluded: chain sl residue 36 ILE Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 41 ARG Chi-restraints excluded: chain sq residue 85 LEU Chi-restraints excluded: chain sq residue 88 MET Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 105 ILE Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 7 LYS Chi-restraints excluded: chain st residue 37 GLU Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 53 VAL Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 116 LYS Chi-restraints excluded: chain sv residue 1 MET Chi-restraints excluded: chain sv residue 21 GLU Chi-restraints excluded: chain sv residue 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 23 THR Chi-restraints excluded: chain sw residue 54 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 150 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 26 optimal weight: 50.0000 chunk 82 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 37 optimal weight: 40.0000 chunk 21 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 30 optimal weight: 40.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sl 24 HIS ss 92 GLN ** sv 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.061308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.053970 restraints weight = 98606.111| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.86 r_work: 0.3209 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20996 Z= 0.206 Angle : 0.586 9.296 30608 Z= 0.340 Chirality : 0.042 0.289 3845 Planarity : 0.005 0.062 2084 Dihedral : 23.347 178.032 8535 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.83 % Favored : 92.99 % Rotamer: Outliers : 6.44 % Allowed : 30.24 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.24), residues: 1142 helix: 0.81 (0.24), residues: 449 sheet: -0.17 (0.41), residues: 157 loop : -1.87 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsA 76 TYR 0.020 0.002 TYRsE 14 PHE 0.017 0.002 PHEst 53 TRP 0.009 0.001 TRPsg 24 HIS 0.006 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.21 (20995) covalent geometry : angle 0.58559 / 0.34 (30606) SS BOND : bond 0.00608 / 0.32 ( 1) SS BOND : angle 1.35556 / 0.78 ( 2) hydrogen bonds : bond 0.07180 / 4.66 ( 691) hydrogen bonds : angle 3.99746 / 2.72 ( 1561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 134 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sA 103 ASP cc_start: 0.8206 (t0) cc_final: 0.8000 (t0) REVERT: sd 137 MET cc_start: 0.8416 (mmm) cc_final: 0.7713 (mmt) REVERT: sd 203 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7731 (tmm) REVERT: sg 178 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8068 (tp30) REVERT: sq 41 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7500 (ptp90) REVERT: ss 20 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6738 (ttmt) REVERT: ss 158 ARG cc_start: 0.4953 (OUTLIER) cc_final: 0.3585 (mtt-85) REVERT: st 7 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7723 (ptpp) REVERT: sv 5 SER cc_start: 0.8660 (m) cc_final: 0.8420 (t) REVERT: sv 21 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: sv 78 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7583 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8749 (mtt90) outliers start: 66 outliers final: 50 residues processed: 181 average time/residue: 0.1361 time to fit residues: 38.7931 Evaluate side-chains 187 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 128 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 76 ARG Chi-restraints excluded: chain sA residue 87 LEU Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 6 ILE Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 35 LEU Chi-restraints excluded: chain sd residue 165 VAL Chi-restraints excluded: chain sd residue 170 TYR Chi-restraints excluded: chain sd residue 188 CYS Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET Chi-restraints excluded: chain sg residue 29 THR Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 178 GLU Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 8 ILE Chi-restraints excluded: chain sl residue 20 CYS Chi-restraints excluded: chain sl residue 29 CYS Chi-restraints excluded: chain sl residue 36 ILE Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 41 ARG Chi-restraints excluded: chain sq residue 85 LEU Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 20 LYS Chi-restraints excluded: chain ss residue 30 THR Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 105 ILE Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 7 LYS Chi-restraints excluded: chain st residue 17 ILE Chi-restraints excluded: chain st residue 37 GLU Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 32 THR Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain sv residue 1 MET Chi-restraints excluded: chain sv residue 21 GLU Chi-restraints excluded: chain sv residue 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 23 THR Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 82 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 48 optimal weight: 30.0000 chunk 82 optimal weight: 7.9990 chunk 95 optimal weight: 0.0770 chunk 9 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ss 92 GLN ** sv 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.062824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.055251 restraints weight = 100268.383| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.84 r_work: 0.3323 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20996 Z= 0.149 Angle : 0.547 9.231 30608 Z= 0.320 Chirality : 0.040 0.275 3845 Planarity : 0.004 0.060 2084 Dihedral : 23.390 177.997 8535 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.48 % Favored : 93.35 % Rotamer: Outliers : 5.85 % Allowed : 30.93 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.24), residues: 1142 helix: 0.97 (0.24), residues: 449 sheet: -0.10 (0.40), residues: 157 loop : -1.80 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGsA 76 TYR 0.023 0.002 TYRsv 103 PHE 0.021 0.001 PHEst 71 TRP 0.006 0.001 TRPsu 83 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (20995) covalent geometry : angle 0.54653 / 0.32 (30606) SS BOND : bond 0.00162 / 0.09 ( 1) SS BOND : angle 1.15597 / 0.67 ( 2) hydrogen bonds : bond 0.06667 / 4.26 ( 691) hydrogen bonds : angle 3.88743 / 2.64 ( 1561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 131 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sd 137 MET cc_start: 0.8694 (mmm) cc_final: 0.7985 (mmt) REVERT: sd 203 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8024 (tmm) REVERT: sg 23 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7796 (mtmm) REVERT: sg 74 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8894 (tp) REVERT: sg 178 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: sq 41 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7967 (ptp90) REVERT: ss 158 ARG cc_start: 0.5247 (OUTLIER) cc_final: 0.3767 (mtt-85) REVERT: st 7 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7877 (ptpp) REVERT: sv 5 SER cc_start: 0.8738 (m) cc_final: 0.8532 (t) REVERT: sv 21 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8117 (pm20) REVERT: sv 74 MET cc_start: 0.8578 (tpp) cc_final: 0.8128 (tpt) REVERT: sv 78 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7714 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8677 (mtt90) outliers start: 60 outliers final: 45 residues processed: 176 average time/residue: 0.1364 time to fit residues: 37.7746 Evaluate side-chains 181 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 126 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 76 ARG Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 6 ILE Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 28 ASP Chi-restraints excluded: chain sd residue 35 LEU Chi-restraints excluded: chain sd residue 156 LEU Chi-restraints excluded: chain sd residue 170 TYR Chi-restraints excluded: chain sd residue 188 CYS Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET Chi-restraints excluded: chain sg residue 23 LYS Chi-restraints excluded: chain sg residue 29 THR Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 74 LEU Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 178 GLU Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 20 CYS Chi-restraints excluded: chain sl residue 29 CYS Chi-restraints excluded: chain sl residue 36 ILE Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 41 ARG Chi-restraints excluded: chain sq residue 85 LEU Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain sq residue 125 VAL Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 105 ILE Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 7 LYS Chi-restraints excluded: chain st residue 37 GLU Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 116 LYS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain sv residue 1 MET Chi-restraints excluded: chain sv residue 21 GLU Chi-restraints excluded: chain sv residue 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 23 THR Chi-restraints excluded: chain sw residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 149 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 34 optimal weight: 30.0000 chunk 127 optimal weight: 6.9990 chunk 26 optimal weight: 50.0000 chunk 73 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 79 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sg 151 GLN ** sv 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.063303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.056188 restraints weight = 100986.344| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.71 r_work: 0.3357 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20996 Z= 0.123 Angle : 0.532 8.920 30608 Z= 0.310 Chirality : 0.038 0.257 3845 Planarity : 0.004 0.061 2084 Dihedral : 23.365 179.048 8535 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.48 % Favored : 93.35 % Rotamer: Outliers : 4.98 % Allowed : 31.90 % Favored : 63.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.24), residues: 1142 helix: 1.09 (0.24), residues: 449 sheet: -0.06 (0.40), residues: 157 loop : -1.79 (0.25), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGsA 76 TYR 0.019 0.001 TYRsE 14 PHE 0.018 0.001 PHEst 71 TRP 0.007 0.001 TRPsu 83 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (20995) covalent geometry : angle 0.53209 / 0.31 (30606) SS BOND : bond 0.00266 / 0.14 ( 1) SS BOND : angle 1.16600 / 0.66 ( 2) hydrogen bonds : bond 0.06241 / 4.05 ( 691) hydrogen bonds : angle 3.80409 / 2.57 ( 1561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 127 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sd 137 MET cc_start: 0.8654 (mmm) cc_final: 0.7942 (mmt) REVERT: sd 203 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8006 (tmm) REVERT: sg 178 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: sq 41 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.7863 (ptp90) REVERT: ss 158 ARG cc_start: 0.5081 (OUTLIER) cc_final: 0.3503 (mtt-85) REVERT: st 7 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7890 (ptpp) REVERT: sv 21 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: sv 78 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7749 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8623 (mtt90) outliers start: 51 outliers final: 42 residues processed: 167 average time/residue: 0.1423 time to fit residues: 37.6855 Evaluate side-chains 170 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 120 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 6 ILE Chi-restraints excluded: chain sd residue 1 MET Chi-restraints excluded: chain sd residue 7 THR Chi-restraints excluded: chain sd residue 35 LEU Chi-restraints excluded: chain sd residue 156 LEU Chi-restraints excluded: chain sd residue 170 TYR Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET Chi-restraints excluded: chain sg residue 29 THR Chi-restraints excluded: chain sg residue 39 LEU Chi-restraints excluded: chain sg residue 43 SER Chi-restraints excluded: chain sg residue 160 CYS Chi-restraints excluded: chain sg residue 178 GLU Chi-restraints excluded: chain sl residue 5 THR Chi-restraints excluded: chain sl residue 20 CYS Chi-restraints excluded: chain sl residue 29 CYS Chi-restraints excluded: chain sl residue 36 ILE Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 41 ARG Chi-restraints excluded: chain sq residue 85 LEU Chi-restraints excluded: chain sq residue 91 SER Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain ss residue 30 THR Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 6 THR Chi-restraints excluded: chain st residue 7 LYS Chi-restraints excluded: chain st residue 37 GLU Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 116 LYS Chi-restraints excluded: chain su residue 137 THR Chi-restraints excluded: chain sv residue 1 MET Chi-restraints excluded: chain sv residue 21 GLU Chi-restraints excluded: chain sv residue 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 23 THR Chi-restraints excluded: chain sw residue 54 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 111 optimal weight: 5.9990 chunk 95 optimal weight: 30.0000 chunk 91 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 chunk 141 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 40.0000 chunk 46 optimal weight: 30.0000 chunk 37 optimal weight: 40.0000 chunk 129 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... sD 14 GLN ss 92 GLN ** sv 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.062346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.054768 restraints weight = 101838.518| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.85 r_work: 0.3300 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20996 Z= 0.226 Angle : 0.597 8.992 30608 Z= 0.343 Chirality : 0.042 0.291 3845 Planarity : 0.005 0.061 2084 Dihedral : 23.305 178.054 8532 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.91 % Rotamer: Outliers : 5.56 % Allowed : 31.61 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.24), residues: 1142 helix: 1.05 (0.24), residues: 450 sheet: -0.07 (0.40), residues: 158 loop : -1.83 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGst 59 TYR 0.021 0.002 TYRsv 103 PHE 0.017 0.002 PHEst 53 TRP 0.005 0.001 TRPsl 65 HIS 0.006 0.001 HISsv 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.23 (20995) covalent geometry : angle 0.59648 / 0.34 (30606) SS BOND : bond 0.00830 / 0.44 ( 1) SS BOND : angle 1.68796 / 0.99 ( 2) hydrogen bonds : bond 0.07019 / 4.54 ( 691) hydrogen bonds : angle 3.94456 / 2.67 ( 1561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3923.84 seconds wall clock time: 68 minutes 31.01 seconds (4111.01 seconds total)