Starting phenix.real_space_refine on Thu Feb 5 19:36:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v28_64720/02_2026/9v28_64720.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v28_64720/02_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_64720/02_2026/9v28_64720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v28_64720/02_2026/9v28_64720.map" model { file = "/net/cci-nas-00/data/ceres_data/9v28_64720/02_2026/9v28_64720.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v28_64720/02_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-2.0-5952/lib/python3.9/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: 4.18, per 1000 atoms: 0.21 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: 1.52 Conformation dependent library (CDL) restraints added in 553.4 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: 2.70 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: 4.43 Time building geometry restraints manager: 2.03 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: 0.740 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.110 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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= 0.273 Angle : 0.749 31.521 30608 Z= 0.431 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 covalent geometry : bond 0.00493 (20995) covalent geometry : angle 0.74884 (30606) SS BOND : bond 0.00490 ( 1) SS BOND : angle 1.21525 ( 2) hydrogen bonds : bond 0.21543 ( 691) hydrogen bonds : angle 7.33357 ( 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 : 0.504 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: 0.1339 time to fit residues: 40.7982 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 : 0.488 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: sg 22 ASN sg 151 GLN ** sq 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** sv 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.062823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.055097 restraints weight = 100544.420| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.95 r_work: 0.3251 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20996 Z= 0.175 Angle : 0.635 9.027 30608 Z= 0.328 Chirality : 0.039 0.236 3845 Planarity : 0.005 0.060 2084 Dihedral : 23.269 178.779 8587 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.48 % Favored : 93.35 % Rotamer: Outliers : 5.37 % Allowed : 27.12 % Favored : 67.51 % 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: -0.79 (0.24), residues: 1142 helix: 0.39 (0.24), residues: 452 sheet: 0.39 (0.42), residues: 157 loop : -1.64 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARGsA 76 TYR 0.016 0.001 TYRsq 114 PHE 0.013 0.001 PHEsd 25 TRP 0.006 0.001 TRPsl 65 HIS 0.006 0.001 HISsv 2 Details of bonding type rmsd covalent geometry : bond 0.00348 (20995) covalent geometry : angle 0.63539 (30606) SS BOND : bond 0.00292 ( 1) SS BOND : angle 0.86286 ( 2) hydrogen bonds : bond 0.05941 ( 691) hydrogen bonds : angle 4.33714 ( 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 185 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 0.406 Fit side-chains REVERT: sD 19 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8720 (mm) REVERT: sE 36 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9068 (mt) REVERT: sd 137 MET cc_start: 0.8321 (mmm) cc_final: 0.7345 (mmm) REVERT: sg 74 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8541 (tp) REVERT: sl 13 LYS cc_start: 0.9535 (ttmt) cc_final: 0.9117 (tmmt) REVERT: ss 110 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7916 (tttp) REVERT: st 14 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.7367 (ttp-110) REVERT: su 116 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8265 (mttp) REVERT: sv 68 ASN cc_start: 0.8023 (m-40) cc_final: 0.7794 (m-40) REVERT: sv 74 MET cc_start: 0.8517 (tpp) cc_final: 0.8303 (tpt) outliers start: 55 outliers final: 31 residues processed: 175 average time/residue: 0.1309 time to fit residues: 35.4703 Evaluate side-chains 148 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 112 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 19 LEU Chi-restraints excluded: chain sD residue 55 ILE Chi-restraints excluded: chain sD residue 59 LEU Chi-restraints excluded: chain sE residue 36 LEU 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 74 LEU 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 44 LEU Chi-restraints excluded: chain sl residue 45 MET Chi-restraints excluded: chain sq residue 50 LEU Chi-restraints excluded: chain sq residue 60 LEU Chi-restraints excluded: chain sq residue 100 SER Chi-restraints excluded: chain sq residue 111 LEU Chi-restraints excluded: chain ss residue 22 VAL Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 63 VAL Chi-restraints excluded: chain ss residue 110 LYS 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 43 CYS Chi-restraints excluded: chain sv residue 134 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: 0.4980 chunk 106 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 39 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 overall best weight: 6.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sl 59 ASN sq 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.061721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.053787 restraints weight = 103445.597| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.97 r_work: 0.3210 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20996 Z= 0.228 Angle : 0.669 8.724 30608 Z= 0.344 Chirality : 0.041 0.272 3845 Planarity : 0.005 0.060 2084 Dihedral : 23.294 178.299 8537 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.57 % Favored : 93.26 % Rotamer: Outliers : 7.22 % Allowed : 25.85 % Favored : 66.93 % 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: -0.54 (0.24), residues: 1142 helix: 0.73 (0.25), residues: 444 sheet: 0.35 (0.41), residues: 157 loop : -1.54 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGsd 192 TYR 0.016 0.002 TYRsg 154 PHE 0.024 0.002 PHEsg 21 TRP 0.005 0.001 TRPsl 65 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd covalent geometry : bond 0.00458 (20995) covalent geometry : angle 0.66852 (30606) SS BOND : bond 0.01349 ( 1) SS BOND : angle 1.33760 ( 2) hydrogen bonds : bond 0.06787 ( 691) hydrogen bonds : angle 4.12254 ( 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 205 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 131 time to evaluate : 0.544 Fit side-chains REVERT: sD 19 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8838 (mm) REVERT: sE 14 TYR cc_start: 0.7457 (m-10) cc_final: 0.7189 (m-10) REVERT: sE 36 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9272 (mt) REVERT: sd 42 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8770 (mt-10) REVERT: sg 23 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7347 (mtmm) REVERT: sg 74 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8784 (tp) REVERT: sg 177 ASP cc_start: 0.8355 (p0) cc_final: 0.8117 (p0) REVERT: sg 178 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8132 (tp30) REVERT: sl 13 LYS cc_start: 0.9584 (ttmt) cc_final: 0.9033 (pptt) REVERT: sl 24 HIS cc_start: 0.8090 (OUTLIER) cc_final: 0.7830 (m-70) REVERT: sq 29 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: sq 41 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7618 (ptp90) REVERT: sq 88 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6460 (ptt) REVERT: ss 110 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7677 (tttp) REVERT: ss 158 ARG cc_start: 0.4929 (OUTLIER) cc_final: 0.1823 (mtt180) REVERT: st 18 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7421 (mm-30) REVERT: sv 68 ASN cc_start: 0.8011 (m-40) cc_final: 0.7764 (m-40) REVERT: sv 131 MET cc_start: 0.8388 (mtt) cc_final: 0.8027 (mtt) REVERT: sv 137 GLN cc_start: 0.8773 (mp10) cc_final: 0.8444 (mp10) outliers start: 74 outliers final: 39 residues processed: 188 average time/residue: 0.1525 time to fit residues: 43.9438 Evaluate side-chains 175 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 124 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 42 GLU Chi-restraints excluded: chain sd residue 170 TYR Chi-restraints excluded: chain sd residue 198 ILE 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 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 24 HIS 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 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 22 VAL Chi-restraints excluded: chain ss residue 54 ILE Chi-restraints excluded: chain ss residue 61 ILE Chi-restraints excluded: chain ss residue 63 VAL Chi-restraints excluded: chain ss residue 110 LYS 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 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 39 LYS Chi-restraints excluded: chain sv residue 43 CYS Chi-restraints excluded: chain sv residue 134 ILE 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: 8.9990 chunk 141 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 116 optimal weight: 0.8980 chunk 152 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sD 14 GLN su 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.061215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.053765 restraints weight = 98645.990| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.95 r_work: 0.3226 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20996 Z= 0.218 Angle : 0.640 9.035 30608 Z= 0.331 Chirality : 0.040 0.271 3845 Planarity : 0.005 0.061 2084 Dihedral : 23.270 178.468 8537 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.65 % Favored : 93.17 % Rotamer: Outliers : 6.15 % Allowed : 28.39 % Favored : 65.46 % 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: 0.88 (0.24), residues: 444 sheet: 0.15 (0.41), residues: 157 loop : -1.63 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGsA 76 TYR 0.019 0.002 TYRsq 44 PHE 0.037 0.002 PHEss 111 TRP 0.005 0.001 TRPsg 24 HIS 0.005 0.001 HISsu 121 Details of bonding type rmsd covalent geometry : bond 0.00439 (20995) covalent geometry : angle 0.63993 (30606) SS BOND : bond 0.00359 ( 1) SS BOND : angle 1.08829 ( 2) hydrogen bonds : bond 0.06065 ( 691) hydrogen bonds : angle 3.90672 ( 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 195 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 132 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: sD 19 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8849 (mm) REVERT: sd 203 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7629 (tmm) REVERT: sg 74 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8757 (tp) REVERT: sg 177 ASP cc_start: 0.8281 (p0) cc_final: 0.7988 (p0) REVERT: sg 178 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8309 (tp30) REVERT: sl 24 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7647 (m-70) REVERT: sl 43 MET cc_start: 0.8307 (mmm) cc_final: 0.8091 (mmm) REVERT: sq 41 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7563 (ptp90) REVERT: sq 60 LEU cc_start: 0.9098 (mt) cc_final: 0.8798 (pp) REVERT: sq 88 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6062 (ptp) REVERT: ss 79 ASP cc_start: 0.7336 (m-30) cc_final: 0.7083 (m-30) REVERT: ss 158 ARG cc_start: 0.4914 (OUTLIER) cc_final: 0.1822 (mtt180) REVERT: st 18 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: sv 5 SER cc_start: 0.8621 (m) cc_final: 0.8362 (t) REVERT: sv 21 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7942 (pm20) REVERT: sv 55 TYR cc_start: 0.8768 (m-80) cc_final: 0.8283 (m-80) REVERT: sv 68 ASN cc_start: 0.7951 (m-40) cc_final: 0.7692 (m-40) REVERT: sv 78 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7612 (ptp-170) REVERT: sv 137 GLN cc_start: 0.8851 (mp10) cc_final: 0.8580 (mp10) outliers start: 63 outliers final: 40 residues processed: 178 average time/residue: 0.1496 time to fit residues: 41.2653 Evaluate side-chains 172 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 121 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 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 170 TYR Chi-restraints excluded: chain sd residue 198 ILE Chi-restraints excluded: chain sd residue 203 MET 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 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 24 HIS 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 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 22 VAL 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 105 ILE Chi-restraints excluded: chain ss residue 158 ARG Chi-restraints excluded: chain st residue 4 VAL Chi-restraints excluded: chain st residue 9 VAL Chi-restraints excluded: chain st residue 17 ILE Chi-restraints excluded: chain st residue 18 GLU Chi-restraints excluded: chain su residue 27 VAL Chi-restraints excluded: chain su residue 53 VAL Chi-restraints excluded: chain su residue 68 ILE 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 134 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 90 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 chunk 138 optimal weight: 0.9980 chunk 30 optimal weight: 20.0000 chunk 72 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.061597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.054156 restraints weight = 98129.830| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.93 r_work: 0.3234 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20996 Z= 0.194 Angle : 0.624 8.864 30608 Z= 0.323 Chirality : 0.039 0.269 3845 Planarity : 0.004 0.060 2084 Dihedral : 23.259 178.249 8536 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.65 % Favored : 93.17 % Rotamer: Outliers : 7.12 % Allowed : 27.51 % Favored : 65.37 % 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: -0.44 (0.24), residues: 1142 helix: 1.05 (0.24), residues: 442 sheet: 0.17 (0.41), residues: 157 loop : -1.62 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGst 14 TYR 0.014 0.002 TYRsE 14 PHE 0.038 0.002 PHEss 111 TRP 0.005 0.001 TRPsl 65 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd covalent geometry : bond 0.00391 (20995) covalent geometry : angle 0.62372 (30606) SS BOND : bond 0.00890 ( 1) SS BOND : angle 1.41533 ( 2) hydrogen bonds : bond 0.05982 ( 691) hydrogen bonds : angle 3.81842 ( 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 204 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 131 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sD 14 GLN cc_start: 0.7898 (mm110) cc_final: 0.7664 (mm110) REVERT: sD 19 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8904 (mm) REVERT: sd 203 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7648 (tmm) REVERT: sg 74 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8775 (tp) REVERT: sg 177 ASP cc_start: 0.8272 (p0) cc_final: 0.7957 (p0) REVERT: sg 178 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8262 (tp30) REVERT: sl 24 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7648 (m-70) REVERT: sq 41 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7541 (ptp90) REVERT: sq 60 LEU cc_start: 0.9104 (mt) cc_final: 0.8789 (pp) REVERT: sq 88 MET cc_start: 0.6928 (OUTLIER) cc_final: 0.6680 (ptp) REVERT: ss 20 LYS cc_start: 0.7264 (OUTLIER) cc_final: 0.6891 (ttpt) REVERT: ss 79 ASP cc_start: 0.7483 (m-30) cc_final: 0.7277 (m-30) REVERT: ss 110 LYS cc_start: 0.7957 (tptm) cc_final: 0.7744 (tptt) REVERT: ss 158 ARG cc_start: 0.4891 (OUTLIER) cc_final: 0.3561 (mtt-85) REVERT: st 18 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: sv 5 SER cc_start: 0.8599 (m) cc_final: 0.8346 (t) REVERT: sv 21 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: sv 55 TYR cc_start: 0.8796 (m-80) cc_final: 0.8342 (m-80) REVERT: sv 68 ASN cc_start: 0.7944 (m-40) cc_final: 0.7678 (m-40) REVERT: sv 78 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7602 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8744 (mtt90) outliers start: 73 outliers final: 44 residues processed: 186 average time/residue: 0.1498 time to fit residues: 43.7065 Evaluate side-chains 181 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 124 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 19 LEU 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 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 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 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 24 HIS 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 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 20 LYS Chi-restraints excluded: chain ss residue 22 VAL 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 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 9 VAL Chi-restraints excluded: chain st residue 17 ILE 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 53 VAL Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 82 VAL Chi-restraints excluded: chain su residue 116 LYS 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 sw residue 39 VAL Chi-restraints excluded: chain sw residue 54 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 93 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 89 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ss 47 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.060362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.053041 restraints weight = 98341.062| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.86 r_work: 0.3207 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20996 Z= 0.268 Angle : 0.689 9.320 30608 Z= 0.356 Chirality : 0.042 0.298 3845 Planarity : 0.005 0.062 2084 Dihedral : 23.319 177.690 8534 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.18 % Favored : 92.73 % Rotamer: Outliers : 7.80 % Allowed : 27.71 % 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: -0.68 (0.24), residues: 1142 helix: 0.84 (0.24), residues: 449 sheet: 0.06 (0.40), residues: 159 loop : -1.80 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGst 59 TYR 0.018 0.002 TYRsE 14 PHE 0.023 0.002 PHEss 111 TRP 0.005 0.001 TRPsl 65 HIS 0.007 0.001 HISsu 121 Details of bonding type rmsd covalent geometry : bond 0.00542 (20995) covalent geometry : angle 0.68931 (30606) SS BOND : bond 0.00855 ( 1) SS BOND : angle 1.50681 ( 2) hydrogen bonds : bond 0.06862 ( 691) hydrogen bonds : angle 3.93260 ( 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 209 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 129 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: sD 19 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.9028 (mm) REVERT: sg 74 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8816 (tp) REVERT: sg 177 ASP cc_start: 0.8184 (p0) cc_final: 0.7893 (p0) REVERT: sg 178 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: sl 24 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.6850 (m90) REVERT: sq 60 LEU cc_start: 0.9104 (mt) cc_final: 0.8822 (pp) REVERT: sq 88 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6153 (ptp) REVERT: ss 158 ARG cc_start: 0.4850 (OUTLIER) cc_final: 0.3594 (mtt-85) REVERT: st 18 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7839 (mt-10) REVERT: sv 5 SER cc_start: 0.8796 (m) cc_final: 0.8512 (t) REVERT: sv 21 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8002 (pm20) REVERT: sv 68 ASN cc_start: 0.7972 (m-40) cc_final: 0.7725 (m-40) REVERT: sv 78 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7757 (ptp-170) REVERT: sv 107 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8458 (mp10) REVERT: sv 121 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8710 (mtt90) REVERT: sv 137 GLN cc_start: 0.8838 (mp10) cc_final: 0.8634 (mp10) outliers start: 80 outliers final: 52 residues processed: 192 average time/residue: 0.1392 time to fit residues: 42.2577 Evaluate side-chains 187 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 124 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 110 THR Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 19 LEU Chi-restraints excluded: chain sD residue 31 VAL 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 28 ASP 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 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 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 24 HIS 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 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 22 VAL 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 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 9 VAL Chi-restraints excluded: chain st residue 17 ILE 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 32 THR Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 82 VAL Chi-restraints excluded: chain su residue 116 LYS 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 49 LEU Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 107 GLN Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 131 MET Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 65 THR Chi-restraints excluded: chain sw residue 82 MET Chi-restraints excluded: chain sw residue 107 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 chunk 86 optimal weight: 9.9990 chunk 134 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ss 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.061393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.053992 restraints weight = 98199.852| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.95 r_work: 0.3227 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20996 Z= 0.181 Angle : 0.624 8.935 30608 Z= 0.323 Chirality : 0.039 0.273 3845 Planarity : 0.004 0.061 2084 Dihedral : 23.297 178.077 8534 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.39 % Favored : 93.43 % Rotamer: Outliers : 6.15 % Allowed : 29.56 % Favored : 64.29 % 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: -0.50 (0.24), residues: 1142 helix: 1.06 (0.24), residues: 449 sheet: 0.06 (0.41), residues: 156 loop : -1.72 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGst 14 TYR 0.023 0.002 TYRsE 14 PHE 0.011 0.001 PHEst 53 TRP 0.005 0.001 TRPsu 83 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd covalent geometry : bond 0.00364 (20995) covalent geometry : angle 0.62405 (30606) SS BOND : bond 0.00426 ( 1) SS BOND : angle 1.28239 ( 2) hydrogen bonds : bond 0.05908 ( 691) hydrogen bonds : angle 3.82783 ( 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 193 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 130 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: sd 203 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7569 (tmm) REVERT: sg 177 ASP cc_start: 0.8215 (p0) cc_final: 0.7878 (p0) REVERT: sg 178 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: sl 24 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.6576 (m90) REVERT: sq 88 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6601 (ptp) REVERT: ss 158 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.3597 (mtt-85) REVERT: st 7 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7676 (ptpp) REVERT: st 18 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7833 (mt-10) REVERT: sv 5 SER cc_start: 0.8640 (m) cc_final: 0.8399 (t) REVERT: sv 21 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7994 (pm20) REVERT: sv 68 ASN cc_start: 0.7956 (m-40) cc_final: 0.7698 (m-40) REVERT: sv 78 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7519 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8746 (mtt90) outliers start: 63 outliers final: 45 residues processed: 175 average time/residue: 0.1343 time to fit residues: 37.4127 Evaluate side-chains 179 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 124 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 110 THR Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 31 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 28 ASP 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 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 24 HIS Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET 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 38 LYS 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 9 VAL 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 32 THR Chi-restraints excluded: chain su residue 53 VAL Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 82 VAL Chi-restraints excluded: chain su residue 97 SER 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 49 LEU Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 131 MET Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 82 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 150 optimal weight: 5.9990 chunk 152 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 26 optimal weight: 40.0000 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 137 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: sD 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.061555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.053732 restraints weight = 102514.724| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.96 r_work: 0.3209 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20996 Z= 0.208 Angle : 0.642 9.062 30608 Z= 0.332 Chirality : 0.040 0.282 3845 Planarity : 0.005 0.061 2084 Dihedral : 23.293 178.004 8534 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.91 % Rotamer: Outliers : 6.05 % Allowed : 29.76 % Favored : 64.20 % 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: -0.56 (0.24), residues: 1142 helix: 1.00 (0.24), residues: 457 sheet: 0.05 (0.41), residues: 156 loop : -1.79 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGst 59 TYR 0.026 0.002 TYRsE 14 PHE 0.038 0.002 PHEsq 32 TRP 0.005 0.001 TRPsl 65 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd covalent geometry : bond 0.00419 (20995) covalent geometry : angle 0.64198 (30606) SS BOND : bond 0.00518 ( 1) SS BOND : angle 1.31037 ( 2) hydrogen bonds : bond 0.06147 ( 691) hydrogen bonds : angle 3.82380 ( 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 184 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 122 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sd 203 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7559 (tmm) REVERT: sg 177 ASP cc_start: 0.8201 (p0) cc_final: 0.7871 (p0) REVERT: sg 178 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8280 (tp30) REVERT: sl 24 HIS cc_start: 0.8113 (OUTLIER) cc_final: 0.7731 (m-70) REVERT: sq 88 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6625 (ptp) REVERT: ss 158 ARG cc_start: 0.4858 (OUTLIER) cc_final: 0.3649 (mtt-85) REVERT: st 7 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7720 (ptpp) REVERT: su 60 MET cc_start: 0.8256 (tmm) cc_final: 0.7988 (tmm) REVERT: sv 5 SER cc_start: 0.8743 (m) cc_final: 0.8474 (t) REVERT: sv 21 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8027 (pm20) REVERT: sv 55 TYR cc_start: 0.8853 (m-80) cc_final: 0.8436 (m-80) REVERT: sv 68 ASN cc_start: 0.7955 (m-40) cc_final: 0.7701 (m-40) REVERT: sv 78 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7605 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8740 (mtt90) outliers start: 62 outliers final: 51 residues processed: 168 average time/residue: 0.1386 time to fit residues: 37.0518 Evaluate side-chains 177 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 117 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 110 THR Chi-restraints excluded: chain sD residue 11 ILE Chi-restraints excluded: chain sD residue 17 GLU Chi-restraints excluded: chain sD residue 31 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 28 ASP 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 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 24 HIS 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 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 20 LYS 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 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 9 VAL 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 32 THR Chi-restraints excluded: chain su residue 53 VAL Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 82 VAL Chi-restraints excluded: chain su residue 97 SER 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 49 LEU Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 131 MET Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 82 MET Chi-restraints excluded: chain sw residue 107 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 48 optimal weight: 20.0000 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.061697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.053885 restraints weight = 101776.238| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.93 r_work: 0.3213 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20996 Z= 0.207 Angle : 0.645 9.904 30608 Z= 0.333 Chirality : 0.040 0.283 3845 Planarity : 0.005 0.062 2084 Dihedral : 23.298 178.047 8534 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.74 % Favored : 93.17 % Rotamer: Outliers : 6.05 % Allowed : 29.85 % Favored : 64.10 % 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: -0.53 (0.24), residues: 1142 helix: 1.03 (0.24), residues: 457 sheet: 0.09 (0.41), residues: 156 loop : -1.80 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsA 76 TYR 0.025 0.002 TYRsE 14 PHE 0.042 0.002 PHEsq 32 TRP 0.005 0.001 TRPsl 65 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd covalent geometry : bond 0.00418 (20995) covalent geometry : angle 0.64520 (30606) SS BOND : bond 0.00486 ( 1) SS BOND : angle 1.31894 ( 2) hydrogen bonds : bond 0.06149 ( 691) hydrogen bonds : angle 3.81580 ( 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 182 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 120 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: sd 203 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7544 (tmm) REVERT: sg 177 ASP cc_start: 0.8195 (p0) cc_final: 0.7871 (p0) REVERT: sg 178 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8277 (tp30) REVERT: sl 24 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7734 (m-70) REVERT: sq 88 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6568 (ptp) REVERT: ss 158 ARG cc_start: 0.4852 (OUTLIER) cc_final: 0.3541 (mtt-85) REVERT: st 7 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.7748 (ptpp) REVERT: sv 5 SER cc_start: 0.8747 (m) cc_final: 0.8500 (t) REVERT: sv 21 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: sv 55 TYR cc_start: 0.8776 (m-80) cc_final: 0.8382 (m-80) REVERT: sv 68 ASN cc_start: 0.7950 (m-40) cc_final: 0.7695 (m-40) REVERT: sv 78 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7616 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9101 (OUTLIER) cc_final: 0.8750 (mtt90) REVERT: sw 51 LYS cc_start: 0.7067 (mmmm) cc_final: 0.6824 (mmtt) outliers start: 62 outliers final: 49 residues processed: 167 average time/residue: 0.1321 time to fit residues: 34.9600 Evaluate side-chains 176 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 118 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 110 THR 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 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 24 HIS 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 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 38 LYS 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 9 VAL 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 53 VAL Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 68 ILE Chi-restraints excluded: chain su residue 82 VAL Chi-restraints excluded: chain su residue 97 SER 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 49 LEU Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 131 MET Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 82 MET Chi-restraints excluded: chain sw residue 107 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 chunk 128 optimal weight: 0.1980 chunk 34 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 26 optimal weight: 40.0000 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 4.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.061845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.054490 restraints weight = 98221.009| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.94 r_work: 0.3246 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 20996 Z= 0.174 Angle : 0.622 10.116 30608 Z= 0.321 Chirality : 0.039 0.273 3845 Planarity : 0.004 0.061 2084 Dihedral : 23.293 178.373 8534 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.74 % Favored : 93.08 % Rotamer: Outliers : 5.56 % Allowed : 30.24 % Favored : 64.20 % 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: -0.44 (0.24), residues: 1142 helix: 1.11 (0.24), residues: 456 sheet: 0.16 (0.41), residues: 156 loop : -1.75 (0.25), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGst 14 TYR 0.022 0.001 TYRsE 14 PHE 0.044 0.002 PHEsq 32 TRP 0.005 0.001 TRPsu 83 HIS 0.005 0.001 HISsv 92 Details of bonding type rmsd covalent geometry : bond 0.00351 (20995) covalent geometry : angle 0.62217 (30606) SS BOND : bond 0.00411 ( 1) SS BOND : angle 1.12132 ( 2) hydrogen bonds : bond 0.05810 ( 691) hydrogen bonds : angle 3.78119 ( 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 180 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 123 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: sd 203 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7463 (tmm) REVERT: sg 177 ASP cc_start: 0.8213 (p0) cc_final: 0.7887 (p0) REVERT: sg 178 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: sl 24 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.6658 (m90) REVERT: sl 26 ASP cc_start: 0.7878 (t0) cc_final: 0.7638 (t0) REVERT: sq 88 MET cc_start: 0.6814 (OUTLIER) cc_final: 0.6571 (ptp) REVERT: ss 158 ARG cc_start: 0.5015 (OUTLIER) cc_final: 0.3553 (mtt-85) REVERT: st 7 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7755 (ptpp) REVERT: sv 5 SER cc_start: 0.8705 (m) cc_final: 0.8467 (t) REVERT: sv 21 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8016 (pm20) REVERT: sv 55 TYR cc_start: 0.8790 (m-80) cc_final: 0.8360 (m-80) REVERT: sv 68 ASN cc_start: 0.7923 (m-40) cc_final: 0.7652 (m-40) REVERT: sv 78 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7526 (ptp-170) REVERT: sv 121 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8768 (mtt90) outliers start: 57 outliers final: 45 residues processed: 164 average time/residue: 0.1442 time to fit residues: 37.4212 Evaluate side-chains 172 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 118 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain sA residue 49 LEU Chi-restraints excluded: chain sA residue 110 THR 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 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 24 HIS Chi-restraints excluded: chain sl residue 44 LEU Chi-restraints excluded: chain sl residue 45 MET 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 38 LYS 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 32 THR Chi-restraints excluded: chain su residue 53 VAL Chi-restraints excluded: chain su residue 61 THR Chi-restraints excluded: chain su residue 82 VAL Chi-restraints excluded: chain su residue 97 SER 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 49 LEU Chi-restraints excluded: chain sv residue 78 ARG Chi-restraints excluded: chain sv residue 121 ARG Chi-restraints excluded: chain sv residue 131 MET Chi-restraints excluded: chain sv residue 138 VAL Chi-restraints excluded: chain sw residue 54 VAL Chi-restraints excluded: chain sw residue 82 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 161 random chunks: chunk 111 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 62 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 129 optimal weight: 0.8980 overall best weight: 6.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.061619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.054268 restraints weight = 98782.399| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 1.95 r_work: 0.3238 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20996 Z= 0.208 Angle : 0.647 9.897 30608 Z= 0.333 Chirality : 0.040 0.284 3845 Planarity : 0.005 0.061 2084 Dihedral : 23.302 178.103 8532 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.27 % Favored : 92.64 % Rotamer: Outliers : 5.66 % Allowed : 30.73 % Favored : 63.61 % 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: -0.52 (0.24), residues: 1142 helix: 1.04 (0.24), residues: 458 sheet: 0.14 (0.41), residues: 155 loop : -1.81 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGsA 76 TYR 0.045 0.002 TYRsE 14 PHE 0.033 0.001 PHEsq 32 TRP 0.005 0.001 TRPsl 65 HIS 0.005 0.001 HISsu 121 Details of bonding type rmsd covalent geometry : bond 0.00420 (20995) covalent geometry : angle 0.64679 (30606) SS BOND : bond 0.00519 ( 1) SS BOND : angle 1.26384 ( 2) hydrogen bonds : bond 0.06162 ( 691) hydrogen bonds : angle 3.81757 ( 1561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.34 seconds wall clock time: 62 minutes 8.20 seconds (3728.20 seconds total)