Starting phenix.real_space_refine on Mon Oct 26 10:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36pg_77736/10_2026/36pg_77736.cif Found real_map, /net/cci-nas-00/data/ceres_data/36pg_77736/10_2026/36pg_77736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/36pg_77736/10_2026/36pg_77736.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36pg_77736/10_2026/36pg_77736.map" model { file = "/net/cci-nas-00/data/ceres_data/36pg_77736/10_2026/36pg_77736.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36pg_77736/10_2026/36pg_77736.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 147 5.49 5 S 143 5.16 5 C 12232 2.51 5 N 3427 2.21 5 O 4154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20103 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1924 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 23, 'rna2p_pyr': 16, 'rna3p_pur': 31, 'rna3p_pyr': 19} Link IDs: {'rna2p': 38, 'rna3p': 50} Chain: "B" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 670 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "C" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 525 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "D" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "E" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "F" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "G" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "H" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "I" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "J" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "K" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "L" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "M" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Chain: "N" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1544 Classifications: {'peptide': 195} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 186} Time building chain proxies: 4.39, per 1000 atoms: 0.22 Number of scatterers: 20103 At special positions: 0 Unit cell: (108.3, 100.32, 202.92, 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 143 16.00 P 147 15.00 O 4154 8.00 N 3427 7.00 C 12232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.30 Conformation dependent library (CDL) restraints added in 784.8 milliseconds 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4026 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 33 sheets defined 42.1% alpha, 34.5% beta 25 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 2.35 Creating SS restraints... Processing helix chain 'D' and resid 19 through 23 Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 42 through 58 removed outlier: 3.639A pdb=" N CYS D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 removed outlier: 3.690A pdb=" N LYS D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.765A pdb=" N ARG D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 158 through 173 Processing helix chain 'E' and resid 18 through 23 removed outlier: 4.561A pdb=" N LEU E 21 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP E 23 " --> pdb=" O THR E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 37 Processing helix chain 'E' and resid 42 through 57 Processing helix chain 'E' and resid 70 through 82 removed outlier: 3.723A pdb=" N CYS E 76 " --> pdb=" O MET E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 89 through 94 removed outlier: 3.549A pdb=" N ILE E 94 " --> pdb=" O ILE E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 116 Processing helix chain 'E' and resid 117 through 120 removed outlier: 6.700A pdb=" N ASP E 120 " --> pdb=" O LYS E 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 117 through 120' Processing helix chain 'E' and resid 158 through 173 removed outlier: 3.636A pdb=" N ASN E 171 " --> pdb=" O GLU E 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 23 removed outlier: 3.803A pdb=" N ASP F 23 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 37 removed outlier: 3.876A pdb=" N SER F 34 " --> pdb=" O LYS F 30 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU F 35 " --> pdb=" O TYR F 31 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER F 36 " --> pdb=" O HIS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 57 Processing helix chain 'F' and resid 70 through 82 Processing helix chain 'F' and resid 83 through 85 No H-bonds generated for 'chain 'F' and resid 83 through 85' Processing helix chain 'F' and resid 86 through 93 Processing helix chain 'F' and resid 111 through 116 Processing helix chain 'F' and resid 118 through 120 No H-bonds generated for 'chain 'F' and resid 118 through 120' Processing helix chain 'F' and resid 158 through 173 removed outlier: 3.634A pdb=" N MET F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 removed outlier: 3.571A pdb=" N ASP G 23 " --> pdb=" O THR G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 42 through 57 Processing helix chain 'G' and resid 70 through 82 Processing helix chain 'G' and resid 83 through 85 No H-bonds generated for 'chain 'G' and resid 83 through 85' Processing helix chain 'G' and resid 86 through 93 removed outlier: 3.667A pdb=" N ARG G 92 " --> pdb=" O LYS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 Processing helix chain 'G' and resid 117 through 120 removed outlier: 6.577A pdb=" N ASP G 120 " --> pdb=" O LYS G 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.651A pdb=" N ASP H 23 " --> pdb=" O THR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 37 removed outlier: 3.589A pdb=" N SER H 34 " --> pdb=" O LYS H 30 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU H 35 " --> pdb=" O TYR H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 57 Processing helix chain 'H' and resid 70 through 82 Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 86 through 93 removed outlier: 3.675A pdb=" N ASP H 91 " --> pdb=" O GLY H 87 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 Processing helix chain 'H' and resid 117 through 120 removed outlier: 6.375A pdb=" N ASP H 120 " --> pdb=" O LYS H 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 117 through 120' Processing helix chain 'H' and resid 158 through 173 removed outlier: 3.572A pdb=" N MET H 164 " --> pdb=" O GLU H 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 23 Processing helix chain 'I' and resid 26 through 37 Processing helix chain 'I' and resid 42 through 57 Processing helix chain 'I' and resid 70 through 82 Processing helix chain 'I' and resid 83 through 85 No H-bonds generated for 'chain 'I' and resid 83 through 85' Processing helix chain 'I' and resid 86 through 94 removed outlier: 3.595A pdb=" N ARG I 92 " --> pdb=" O LYS I 88 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE I 94 " --> pdb=" O ILE I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'I' and resid 117 through 120 removed outlier: 6.513A pdb=" N ASP I 120 " --> pdb=" O LYS I 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 117 through 120' Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'J' and resid 19 through 23 removed outlier: 3.583A pdb=" N ASP J 23 " --> pdb=" O THR J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 37 Processing helix chain 'J' and resid 42 through 57 removed outlier: 3.759A pdb=" N ALA J 50 " --> pdb=" O TYR J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 82 Processing helix chain 'J' and resid 83 through 85 No H-bonds generated for 'chain 'J' and resid 83 through 85' Processing helix chain 'J' and resid 86 through 94 removed outlier: 3.566A pdb=" N ASP J 91 " --> pdb=" O GLY J 87 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 116 Processing helix chain 'J' and resid 117 through 120 removed outlier: 6.448A pdb=" N ASP J 120 " --> pdb=" O LYS J 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 117 through 120' Processing helix chain 'J' and resid 158 through 173 removed outlier: 3.777A pdb=" N MET J 164 " --> pdb=" O GLU J 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 26 through 37 Processing helix chain 'K' and resid 42 through 57 Processing helix chain 'K' and resid 70 through 82 Processing helix chain 'K' and resid 83 through 85 No H-bonds generated for 'chain 'K' and resid 83 through 85' Processing helix chain 'K' and resid 86 through 93 removed outlier: 3.672A pdb=" N ARG K 92 " --> pdb=" O LYS K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 116 Processing helix chain 'K' and resid 117 through 120 removed outlier: 6.069A pdb=" N ASP K 120 " --> pdb=" O LYS K 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 117 through 120' Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'L' and resid 19 through 23 removed outlier: 3.649A pdb=" N ASP L 23 " --> pdb=" O THR L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 Processing helix chain 'L' and resid 42 through 57 Processing helix chain 'L' and resid 70 through 82 Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'L' and resid 86 through 93 removed outlier: 4.103A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 117 through 120 removed outlier: 6.473A pdb=" N ASP L 120 " --> pdb=" O LYS L 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 117 through 120' Processing helix chain 'L' and resid 158 through 173 Processing helix chain 'M' and resid 19 through 23 removed outlier: 3.751A pdb=" N ASP M 23 " --> pdb=" O THR M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 42 through 57 removed outlier: 3.659A pdb=" N TYR M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA M 47 " --> pdb=" O ASP M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 83 through 85 No H-bonds generated for 'chain 'M' and resid 83 through 85' Processing helix chain 'M' and resid 86 through 93 removed outlier: 4.109A pdb=" N ARG M 92 " --> pdb=" O LYS M 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 116 Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'N' and resid 19 through 23 removed outlier: 4.284A pdb=" N ASP N 23 " --> pdb=" O THR N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 42 through 57 Processing helix chain 'N' and resid 70 through 81 Processing helix chain 'N' and resid 86 through 93 removed outlier: 4.237A pdb=" N ARG N 92 " --> pdb=" O LYS N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 116 Processing helix chain 'N' and resid 118 through 120 No H-bonds generated for 'chain 'N' and resid 118 through 120' Processing helix chain 'N' and resid 158 through 173 Processing sheet with id=AA1, first strand: chain 'D' and resid 60 through 61 removed outlier: 4.474A pdb=" N PHE D 66 " --> pdb=" O MET D 103 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N VAL D 100 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N GLY D 149 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 94 through 96 removed outlier: 5.018A pdb=" N TRP D 144 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 3 " --> pdb=" O GLU D 192 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU D 192 " --> pdb=" O LEU D 3 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN D 5 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 15 Processing sheet with id=AA4, first strand: chain 'E' and resid 67 through 69 removed outlier: 9.509A pdb=" N VAL E 100 " --> pdb=" O GLY E 149 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N GLY E 149 " --> pdb=" O VAL E 100 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 147 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP E 144 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU E 3 " --> pdb=" O GLU E 192 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLU E 192 " --> pdb=" O LEU E 3 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN E 5 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AA6, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.284A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 60 through 61 removed outlier: 5.284A pdb=" N PHE F 66 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N VAL F 100 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY F 149 " --> pdb=" O VAL F 100 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU F 147 " --> pdb=" O PRO F 102 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N TRP F 144 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU F 3 " --> pdb=" O GLU F 192 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLU F 192 " --> pdb=" O LEU F 3 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN F 5 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AA9, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.736A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 60 through 61 removed outlier: 5.736A pdb=" N PHE G 66 " --> pdb=" O MET G 103 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N VAL G 100 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N GLY G 149 " --> pdb=" O VAL G 100 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU G 147 " --> pdb=" O PRO G 102 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N TRP G 144 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU G 3 " --> pdb=" O GLU G 192 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU G 192 " --> pdb=" O LEU G 3 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN G 5 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 14 through 15 Processing sheet with id=AB3, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.343A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 5.343A pdb=" N PHE H 66 " --> pdb=" O MET H 103 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N VAL H 100 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N GLY H 149 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU H 147 " --> pdb=" O PRO H 102 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N TRP H 144 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN H 5 " --> pdb=" O MET H 190 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 14 through 15 Processing sheet with id=AB6, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.334A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 60 through 61 removed outlier: 5.334A pdb=" N PHE I 66 " --> pdb=" O MET I 103 " (cutoff:3.500A) removed outlier: 9.682A pdb=" N VAL I 100 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N GLY I 149 " --> pdb=" O VAL I 100 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU I 147 " --> pdb=" O PRO I 102 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP I 144 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU I 3 " --> pdb=" O GLU I 192 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLU I 192 " --> pdb=" O LEU I 3 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN I 5 " --> pdb=" O MET I 190 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 14 through 15 Processing sheet with id=AB9, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.339A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 60 through 61 removed outlier: 5.339A pdb=" N PHE J 66 " --> pdb=" O MET J 103 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N VAL J 100 " --> pdb=" O GLY J 149 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY J 149 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU J 147 " --> pdb=" O PRO J 102 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N TRP J 144 " --> pdb=" O GLY J 10 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU J 3 " --> pdb=" O GLU J 192 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLU J 192 " --> pdb=" O LEU J 3 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ASN J 5 " --> pdb=" O MET J 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 14 through 15 removed outlier: 3.514A pdb=" N SER J 136 " --> pdb=" O LYS J 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.424A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 60 through 61 removed outlier: 5.424A pdb=" N PHE K 66 " --> pdb=" O MET K 103 " (cutoff:3.500A) removed outlier: 9.434A pdb=" N VAL K 100 " --> pdb=" O GLY K 149 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY K 149 " --> pdb=" O VAL K 100 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLU K 147 " --> pdb=" O PRO K 102 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TRP K 144 " --> pdb=" O GLY K 10 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU K 3 " --> pdb=" O GLU K 192 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU K 192 " --> pdb=" O LEU K 3 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN K 5 " --> pdb=" O MET K 190 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 14 through 15 Processing sheet with id=AC6, first strand: chain 'L' and resid 60 through 61 removed outlier: 5.566A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 60 through 61 removed outlier: 5.566A pdb=" N PHE L 66 " --> pdb=" O MET L 103 " (cutoff:3.500A) removed outlier: 9.566A pdb=" N VAL L 100 " --> pdb=" O GLY L 149 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY L 149 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLU L 147 " --> pdb=" O PRO L 102 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TRP L 144 " --> pdb=" O GLY L 10 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU L 3 " --> pdb=" O GLU L 192 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLU L 192 " --> pdb=" O LEU L 3 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN L 5 " --> pdb=" O MET L 190 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 14 through 15 Processing sheet with id=AC9, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AD1, first strand: chain 'M' and resid 94 through 96 removed outlier: 5.192A pdb=" N TRP M 144 " --> pdb=" O GLY M 10 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU M 3 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU M 192 " --> pdb=" O LEU M 3 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN M 5 " --> pdb=" O MET M 190 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 14 through 15 Processing sheet with id=AD3, first strand: chain 'M' and resid 60 through 61 Processing sheet with id=AD4, first strand: chain 'N' and resid 60 through 61 removed outlier: 4.876A pdb=" N PHE N 66 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N VAL N 100 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLY N 149 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU N 147 " --> pdb=" O PRO N 102 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 60 through 61 removed outlier: 4.876A pdb=" N PHE N 66 " --> pdb=" O MET N 103 " (cutoff:3.500A) removed outlier: 9.187A pdb=" N VAL N 100 " --> pdb=" O GLY N 149 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLY N 149 " --> pdb=" O VAL N 100 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU N 147 " --> pdb=" O PRO N 102 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N TRP N 144 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU N 3 " --> pdb=" O GLU N 192 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU N 192 " --> pdb=" O LEU N 3 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASN N 5 " --> pdb=" O MET N 190 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 14 through 15 removed outlier: 3.521A pdb=" N ALA N 132 " --> pdb=" O ILE N 129 " (cutoff:3.500A) 920 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 63 hydrogen bonds 122 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5229 1.34 - 1.45: 4159 1.45 - 1.57: 10867 1.57 - 1.69: 291 1.69 - 1.81: 242 Bond restraints: 20788 Sorted by residual: bond pdb=" C1' DC B 44 " pdb=" N1 DC B 44 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" C3' DT B 29 " pdb=" C2' DT B 29 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.18e+01 bond pdb=" C3' DA C 18 " pdb=" C2' DA C 18 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DA B 22 " pdb=" C2' DA B 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT C 21 " pdb=" C2' DT C 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 ... (remaining 20783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 27753 1.49 - 2.98: 846 2.98 - 4.47: 101 4.47 - 5.95: 13 5.95 - 7.44: 4 Bond angle restraints: 28717 Sorted by residual: angle pdb=" C3' G A 78 " pdb=" O3' G A 78 " pdb=" P U A 79 " ideal model delta sigma weight residual 119.70 126.86 -7.16 1.20e+00 6.94e-01 3.56e+01 angle pdb=" O5' U A 61 " pdb=" C5' U A 61 " pdb=" C4' U A 61 " ideal model delta sigma weight residual 109.40 113.63 -4.23 8.00e-01 1.56e+00 2.80e+01 angle pdb=" C1' U A 12 " pdb=" N1 U A 12 " pdb=" C2 U A 12 " ideal model delta sigma weight residual 117.70 123.93 -6.23 1.20e+00 6.94e-01 2.69e+01 angle pdb=" C5 G A 60 " pdb=" C4 G A 60 " pdb=" N3 G A 60 " ideal model delta sigma weight residual 128.60 126.26 2.34 5.00e-01 4.00e+00 2.18e+01 angle pdb=" C3' G A 60 " pdb=" O3' G A 60 " pdb=" P U A 61 " ideal model delta sigma weight residual 119.70 125.26 -5.56 1.20e+00 6.94e-01 2.15e+01 ... (remaining 28712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 12145 35.68 - 71.36: 500 71.36 - 107.04: 18 107.04 - 142.71: 2 142.71 - 178.39: 8 Dihedral angle restraints: 12673 sinusoidal: 6447 harmonic: 6226 Sorted by residual: dihedral pdb=" O4' U A 30 " pdb=" C1' U A 30 " pdb=" N1 U A 30 " pdb=" C2 U A 30 " ideal model delta sinusoidal sigma weight residual 232.00 64.36 167.64 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" O4' U A 80 " pdb=" C1' U A 80 " pdb=" N1 U A 80 " pdb=" C2 U A 80 " ideal model delta sinusoidal sigma weight residual -160.00 -88.86 -71.14 1 1.50e+01 4.44e-03 2.89e+01 dihedral pdb=" CA ASN E 84 " pdb=" C ASN E 84 " pdb=" N LYS E 85 " pdb=" CA LYS E 85 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 12670 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2853 0.071 - 0.142: 402 0.142 - 0.213: 24 0.213 - 0.285: 4 0.285 - 0.356: 1 Chirality restraints: 3284 Sorted by residual: chirality pdb=" C3' G A 60 " pdb=" C4' G A 60 " pdb=" O3' G A 60 " pdb=" C2' G A 60 " both_signs ideal model delta sigma weight residual False -2.48 -2.12 -0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" C1' U A 52 " pdb=" O4' U A 52 " pdb=" C2' U A 52 " pdb=" N1 U A 52 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C1' A A 22 " pdb=" O4' A A 22 " pdb=" C2' A A 22 " pdb=" N9 A A 22 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3281 not shown) Planarity restraints: 3117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A A 82 " -0.032 2.00e-02 2.50e+03 1.51e-02 6.29e+00 pdb=" N9 A A 82 " 0.037 2.00e-02 2.50e+03 pdb=" C8 A A 82 " 0.003 2.00e-02 2.50e+03 pdb=" N7 A A 82 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 82 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A A 82 " -0.001 2.00e-02 2.50e+03 pdb=" N6 A A 82 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A A 82 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A A 82 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A A 82 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A A 82 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U A 52 " -0.030 2.00e-02 2.50e+03 1.59e-02 5.67e+00 pdb=" N1 U A 52 " 0.036 2.00e-02 2.50e+03 pdb=" C2 U A 52 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U A 52 " 0.003 2.00e-02 2.50e+03 pdb=" N3 U A 52 " -0.003 2.00e-02 2.50e+03 pdb=" C4 U A 52 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U A 52 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U A 52 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U A 52 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 22 " 0.029 2.00e-02 2.50e+03 1.33e-02 4.90e+00 pdb=" N9 A A 22 " -0.031 2.00e-02 2.50e+03 pdb=" C8 A A 22 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A A 22 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A A 22 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A 22 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A A 22 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A A 22 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A A 22 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A A 22 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A A 22 " -0.004 2.00e-02 2.50e+03 ... (remaining 3114 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 8776 2.98 - 3.46: 18692 3.46 - 3.94: 32200 3.94 - 4.42: 36136 4.42 - 4.90: 59462 Nonbonded interactions: 155266 Sorted by model distance: nonbonded pdb=" O5' A A 81 " pdb=" O4' A A 81 " model vdw 2.504 2.432 nonbonded pdb=" O5' DG C 33 " pdb=" O4' DG C 33 " model vdw 2.516 2.432 nonbonded pdb=" O5' C A 17 " pdb=" O4' C A 17 " model vdw 2.555 2.432 nonbonded pdb=" O5' U A 12 " pdb=" O4' U A 12 " model vdw 2.557 2.432 nonbonded pdb=" O5' G A 60 " pdb=" O4' G A 60 " model vdw 2.561 2.432 ... (remaining 155261 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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 group one per residue 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: 3.320 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: 0.240 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.290 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.003 0.056 20788 Z= 0.245 Angle : 0.592 7.442 28717 Z= 0.468 Chirality : 0.048 0.356 3284 Planarity : 0.004 0.042 3117 Dihedral : 16.807 178.392 8647 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.18), residues: 2123 helix: 1.52 (0.19), residues: 710 sheet: 1.21 (0.21), residues: 556 loop : 0.43 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 39 TYR 0.012 0.001 TYR D 59 PHE 0.010 0.001 PHE G 14 TRP 0.006 0.001 TRP K 178 HIS 0.002 0.000 HIS N 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.24 (20788) covalent geometry : angle 0.59243 / 0.47 (28717) hydrogen bonds : bond 0.17030 / 18.34 ( 916) hydrogen bonds : angle 7.90469 / 10.25 ( 2675) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 669 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 PRO cc_start: 0.4589 (Cg_exo) cc_final: 0.4234 (Cg_endo) REVERT: E 61 ASP cc_start: 0.5621 (t70) cc_final: 0.5132 (t0) REVERT: E 94 ILE cc_start: 0.7058 (pt) cc_final: 0.6441 (mt) REVERT: E 103 MET cc_start: 0.5858 (ttt) cc_final: 0.5246 (mtp) REVERT: F 2 LYS cc_start: 0.6675 (mmtt) cc_final: 0.6151 (mmmt) REVERT: F 94 ILE cc_start: 0.8061 (pt) cc_final: 0.7689 (pt) REVERT: F 153 ASP cc_start: 0.5784 (t0) cc_final: 0.5456 (t0) REVERT: G 9 THR cc_start: 0.8521 (m) cc_final: 0.8286 (p) REVERT: G 135 MET cc_start: 0.8046 (tpt) cc_final: 0.7720 (tpt) REVERT: G 153 ASP cc_start: 0.8489 (t0) cc_final: 0.8138 (t0) REVERT: H 135 MET cc_start: 0.8561 (tpt) cc_final: 0.8102 (tpt) REVERT: I 31 TYR cc_start: 0.8727 (t80) cc_final: 0.8523 (t80) REVERT: I 85 LYS cc_start: 0.8010 (mttt) cc_final: 0.7503 (mmtm) REVERT: I 189 ILE cc_start: 0.7373 (mm) cc_final: 0.6690 (mt) REVERT: I 194 ASN cc_start: 0.7038 (m-40) cc_final: 0.6612 (t0) REVERT: N 88 LYS cc_start: 0.6924 (mmtm) cc_final: 0.6681 (mttt) REVERT: N 139 PRO cc_start: 0.6925 (Cg_exo) cc_final: 0.6706 (Cg_endo) outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.1445 time to fit residues: 147.2933 Evaluate side-chains 351 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [216, 98, 194, 107, 10, 66, 130, 124, 103, 200, 212] chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 20.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 32 HIS D 53 GLN E 84 ASN F 17 HIS G 53 GLN I 156 GLN J 5 ASN N 171 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.171338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117877 restraints weight = 32335.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115642 restraints weight = 20395.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118744 restraints weight = 17345.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118001 restraints weight = 14063.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.119116 restraints weight = 12904.758| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 20788 Z= 0.241 Angle : 0.681 9.817 28717 Z= 0.376 Chirality : 0.050 0.375 3284 Planarity : 0.005 0.051 3117 Dihedral : 20.863 179.857 4346 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.48 % Allowed : 12.42 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.18), residues: 2123 helix: 1.78 (0.20), residues: 697 sheet: 0.92 (0.21), residues: 558 loop : 0.28 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 142 TYR 0.021 0.002 TYR F 60 PHE 0.021 0.002 PHE M 121 TRP 0.013 0.002 TRP M 144 HIS 0.005 0.002 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (20788) covalent geometry : angle 0.68117 / 0.38 (28717) hydrogen bonds : bond 0.04987 / 5.50 ( 916) hydrogen bonds : angle 6.11714 / 7.92 ( 2675) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 362 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.3137 (ttt) cc_final: 0.2322 (mmt) REVERT: E 1 MET cc_start: 0.5524 (OUTLIER) cc_final: 0.5162 (mtp) REVERT: E 5 ASN cc_start: 0.5496 (t0) cc_final: 0.5252 (t0) REVERT: E 68 MET cc_start: 0.5918 (ttm) cc_final: 0.5348 (tmm) REVERT: E 84 ASN cc_start: 0.8556 (OUTLIER) cc_final: 0.8326 (t0) REVERT: E 103 MET cc_start: 0.6227 (ttt) cc_final: 0.4999 (mtp) REVERT: E 121 PHE cc_start: 0.3588 (m-80) cc_final: 0.3382 (m-80) REVERT: E 151 MET cc_start: 0.5880 (mtm) cc_final: 0.4737 (ttm) REVERT: E 164 MET cc_start: 0.6507 (mmm) cc_final: 0.6205 (mmm) REVERT: E 167 GLU cc_start: 0.5625 (tm-30) cc_final: 0.5233 (tm-30) REVERT: F 86 LEU cc_start: 0.8630 (mm) cc_final: 0.8173 (mp) REVERT: F 153 ASP cc_start: 0.5504 (t0) cc_final: 0.4993 (t0) REVERT: F 190 MET cc_start: 0.8537 (mmp) cc_final: 0.8190 (mmm) REVERT: G 9 THR cc_start: 0.8898 (m) cc_final: 0.8546 (p) REVERT: G 61 ASP cc_start: 0.7981 (t0) cc_final: 0.7746 (t0) REVERT: G 153 ASP cc_start: 0.8453 (t0) cc_final: 0.8181 (t0) REVERT: I 23 ASP cc_start: 0.8343 (t0) cc_final: 0.8099 (t0) REVERT: I 31 TYR cc_start: 0.8774 (t80) cc_final: 0.8503 (t80) REVERT: I 85 LYS cc_start: 0.8089 (mttt) cc_final: 0.7417 (mmtm) REVERT: I 129 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8184 (mt) REVERT: I 188 GLU cc_start: 0.6909 (tm-30) cc_final: 0.6653 (tm-30) REVERT: I 194 ASN cc_start: 0.7204 (m-40) cc_final: 0.6590 (t0) REVERT: J 107 ASN cc_start: 0.8186 (t0) cc_final: 0.7906 (t0) REVERT: K 157 ILE cc_start: 0.8795 (tt) cc_final: 0.8552 (tt) REVERT: L 190 MET cc_start: 0.8012 (mmm) cc_final: 0.7654 (mtt) REVERT: M 69 ASN cc_start: 0.7249 (t0) cc_final: 0.7009 (t0) REVERT: M 115 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7867 (tp) REVERT: M 118 ASN cc_start: 0.6731 (m-40) cc_final: 0.6442 (m110) REVERT: M 144 TRP cc_start: 0.7610 (p-90) cc_final: 0.7057 (p-90) REVERT: N 73 ILE cc_start: 0.7962 (mt) cc_final: 0.7713 (mt) REVERT: N 88 LYS cc_start: 0.7090 (mmtm) cc_final: 0.6735 (mttt) REVERT: N 151 MET cc_start: 0.7117 (mtm) cc_final: 0.6696 (mtm) outliers start: 47 outliers final: 32 residues processed: 385 average time/residue: 0.1373 time to fit residues: 83.4593 Evaluate side-chains 362 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 326 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain M residue 115 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [14, 183, 9, 189, 45, 16, 52, 213, 125, 40, 161] chunk 14 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 189 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.167770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114876 restraints weight = 32484.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112930 restraints weight = 21228.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.115612 restraints weight = 17104.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114895 restraints weight = 13984.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118804 restraints weight = 12985.299| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 20788 Z= 0.250 Angle : 0.674 11.208 28717 Z= 0.370 Chirality : 0.050 0.350 3284 Planarity : 0.005 0.044 3117 Dihedral : 20.930 179.826 4346 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.75 % Allowed : 12.74 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 2123 helix: 1.57 (0.19), residues: 731 sheet: 0.41 (0.21), residues: 578 loop : -0.25 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 142 TYR 0.027 0.002 TYR F 60 PHE 0.023 0.002 PHE G 14 TRP 0.010 0.002 TRP M 144 HIS 0.006 0.002 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.25 (20788) covalent geometry : angle 0.67384 / 0.37 (28717) hydrogen bonds : bond 0.04644 / 5.15 ( 916) hydrogen bonds : angle 5.66243 / 7.35 ( 2675) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 333 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.3101 (ttt) cc_final: 0.2410 (mmt) REVERT: D 84 ASN cc_start: 0.8146 (m110) cc_final: 0.7733 (m-40) REVERT: D 95 MET cc_start: 0.3346 (mpp) cc_final: 0.3124 (mpp) REVERT: E 68 MET cc_start: 0.6121 (ttm) cc_final: 0.5478 (tmm) REVERT: E 72 MET cc_start: 0.6976 (mtp) cc_final: 0.6406 (mtp) REVERT: E 103 MET cc_start: 0.6289 (ttt) cc_final: 0.5357 (mtp) REVERT: E 164 MET cc_start: 0.6436 (mmm) cc_final: 0.6213 (mmm) REVERT: E 167 GLU cc_start: 0.5568 (tm-30) cc_final: 0.5121 (tm-30) REVERT: F 63 GLN cc_start: 0.8102 (mp10) cc_final: 0.7813 (mm110) REVERT: F 103 MET cc_start: 0.5877 (ttt) cc_final: 0.5582 (ttt) REVERT: F 153 ASP cc_start: 0.5832 (t0) cc_final: 0.5382 (t0) REVERT: G 9 THR cc_start: 0.8921 (m) cc_final: 0.8577 (p) REVERT: G 61 ASP cc_start: 0.8104 (t0) cc_final: 0.7812 (t0) REVERT: G 153 ASP cc_start: 0.8414 (t0) cc_final: 0.8175 (t0) REVERT: H 23 ASP cc_start: 0.7988 (t0) cc_final: 0.7330 (p0) REVERT: H 45 ASP cc_start: 0.8254 (m-30) cc_final: 0.7988 (m-30) REVERT: I 31 TYR cc_start: 0.8779 (t80) cc_final: 0.8404 (t80) REVERT: I 85 LYS cc_start: 0.8497 (mttt) cc_final: 0.7898 (mmtm) REVERT: J 45 ASP cc_start: 0.7875 (m-30) cc_final: 0.7541 (m-30) REVERT: J 107 ASN cc_start: 0.8310 (t0) cc_final: 0.7903 (t0) REVERT: K 143 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7508 (t0) REVERT: K 157 ILE cc_start: 0.8882 (tt) cc_final: 0.8646 (tt) REVERT: L 1 MET cc_start: 0.7072 (mtm) cc_final: 0.6690 (mtp) REVERT: L 85 LYS cc_start: 0.8569 (mtpp) cc_final: 0.8244 (mttm) REVERT: L 135 MET cc_start: 0.8726 (mmm) cc_final: 0.8267 (mmm) REVERT: L 161 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7524 (mp0) REVERT: L 190 MET cc_start: 0.8132 (mmm) cc_final: 0.7768 (mtt) REVERT: M 115 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7939 (tp) REVERT: M 118 ASN cc_start: 0.6742 (m-40) cc_final: 0.6530 (m110) REVERT: M 153 ASP cc_start: 0.8014 (t0) cc_final: 0.7803 (t0) REVERT: N 1 MET cc_start: 0.7050 (tpp) cc_final: 0.6798 (tpp) REVERT: N 88 LYS cc_start: 0.7008 (mmtm) cc_final: 0.6636 (mttt) outliers start: 71 outliers final: 50 residues processed: 372 average time/residue: 0.1279 time to fit residues: 75.8665 Evaluate side-chains 373 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 321 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 68 MET Chi-restraints excluded: chain J residue 79 SER Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 29 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain M residue 115 LEU Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 122 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [102, 27, 167, 85, 124, 210, 153, 171, 126, 22, 65] chunk 102 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 167 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 210 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 53 GLN E 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.170594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.108540 restraints weight = 31958.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112664 restraints weight = 15695.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.113208 restraints weight = 10144.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113896 restraints weight = 9114.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114037 restraints weight = 8369.537| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20788 Z= 0.151 Angle : 0.580 8.655 28717 Z= 0.322 Chirality : 0.047 0.356 3284 Planarity : 0.004 0.048 3117 Dihedral : 20.899 177.972 4346 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.38 % Allowed : 14.22 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2123 helix: 1.77 (0.19), residues: 731 sheet: 0.44 (0.21), residues: 578 loop : -0.17 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 142 TYR 0.029 0.002 TYR F 60 PHE 0.016 0.002 PHE D 152 TRP 0.007 0.001 TRP K 178 HIS 0.002 0.001 HIS F 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (20788) covalent geometry : angle 0.57952 / 0.32 (28717) hydrogen bonds : bond 0.03813 / 4.20 ( 916) hydrogen bonds : angle 5.34860 / 6.95 ( 2675) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 351 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.3097 (ttt) cc_final: 0.2428 (mmt) REVERT: E 68 MET cc_start: 0.5477 (ttm) cc_final: 0.4861 (tmm) REVERT: E 103 MET cc_start: 0.6047 (ttt) cc_final: 0.5064 (mtp) REVERT: E 164 MET cc_start: 0.6800 (mmm) cc_final: 0.6493 (mmm) REVERT: E 167 GLU cc_start: 0.5641 (tm-30) cc_final: 0.5133 (tm-30) REVERT: F 63 GLN cc_start: 0.8148 (mp10) cc_final: 0.7889 (mm110) REVERT: F 153 ASP cc_start: 0.5609 (t0) cc_final: 0.5173 (t0) REVERT: F 179 ARG cc_start: 0.8139 (ptt90) cc_final: 0.7505 (ptt90) REVERT: G 9 THR cc_start: 0.8938 (m) cc_final: 0.8591 (p) REVERT: G 61 ASP cc_start: 0.8162 (t0) cc_final: 0.7828 (t0) REVERT: G 103 MET cc_start: 0.8522 (ttm) cc_final: 0.8292 (ttp) REVERT: G 153 ASP cc_start: 0.8427 (t0) cc_final: 0.8159 (t0) REVERT: G 163 LEU cc_start: 0.8191 (tt) cc_final: 0.7976 (tt) REVERT: H 23 ASP cc_start: 0.7910 (t0) cc_final: 0.7236 (p0) REVERT: H 39 ARG cc_start: 0.8502 (tpt170) cc_final: 0.8258 (tpt-90) REVERT: H 45 ASP cc_start: 0.8237 (m-30) cc_final: 0.7897 (m-30) REVERT: I 31 TYR cc_start: 0.8741 (t80) cc_final: 0.8347 (t80) REVERT: J 1 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7353 (ptt) REVERT: J 45 ASP cc_start: 0.7816 (m-30) cc_final: 0.7595 (m-30) REVERT: J 107 ASN cc_start: 0.8435 (t0) cc_final: 0.8076 (t0) REVERT: K 157 ILE cc_start: 0.8787 (tt) cc_final: 0.8581 (tt) REVERT: L 1 MET cc_start: 0.7018 (mtm) cc_final: 0.6630 (mtp) REVERT: L 190 MET cc_start: 0.8082 (mmm) cc_final: 0.7766 (mtt) REVERT: M 21 LEU cc_start: 0.8994 (mt) cc_final: 0.8675 (tt) REVERT: M 68 MET cc_start: 0.7486 (tmm) cc_final: 0.7208 (tmm) REVERT: N 15 LEU cc_start: 0.7910 (mt) cc_final: 0.7614 (mt) REVERT: N 88 LYS cc_start: 0.6948 (mmtm) cc_final: 0.6634 (mttt) outliers start: 64 outliers final: 46 residues processed: 383 average time/residue: 0.1284 time to fit residues: 78.3059 Evaluate side-chains 376 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 329 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 94 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [162, 198, 49, 168, 179, 124, 9, 197, 147, 7, 59] chunk 162 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 197 optimal weight: 2.9990 chunk 147 optimal weight: 0.0770 chunk 7 optimal weight: 50.0000 chunk 59 optimal weight: 2.9990 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 53 GLN M 53 GLN M 118 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.169372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110574 restraints weight = 31359.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.110430 restraints weight = 18178.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.111295 restraints weight = 12270.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.112342 restraints weight = 10807.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.112415 restraints weight = 9916.749| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20788 Z= 0.172 Angle : 0.596 10.262 28717 Z= 0.327 Chirality : 0.048 0.376 3284 Planarity : 0.005 0.046 3117 Dihedral : 20.884 178.701 4346 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.91 % Allowed : 15.06 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.18), residues: 2123 helix: 1.71 (0.19), residues: 735 sheet: 0.40 (0.22), residues: 578 loop : -0.29 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 142 TYR 0.031 0.002 TYR F 60 PHE 0.016 0.002 PHE E 148 TRP 0.007 0.001 TRP K 178 HIS 0.003 0.001 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (20788) covalent geometry : angle 0.59640 / 0.33 (28717) hydrogen bonds : bond 0.03804 / 4.20 ( 916) hydrogen bonds : angle 5.23552 / 6.80 ( 2675) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 338 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.2870 (ttt) cc_final: 0.2231 (mmt) REVERT: D 164 MET cc_start: 0.6966 (tmm) cc_final: 0.6599 (tmm) REVERT: E 68 MET cc_start: 0.5747 (ttm) cc_final: 0.5117 (tmm) REVERT: E 103 MET cc_start: 0.6205 (ttt) cc_final: 0.5218 (mtp) REVERT: E 164 MET cc_start: 0.6771 (mmm) cc_final: 0.5799 (tpp) REVERT: E 167 GLU cc_start: 0.5589 (tm-30) cc_final: 0.4986 (tm-30) REVERT: F 63 GLN cc_start: 0.8153 (mp10) cc_final: 0.7942 (mm110) REVERT: F 86 LEU cc_start: 0.8449 (mm) cc_final: 0.8175 (mp) REVERT: F 153 ASP cc_start: 0.5739 (t0) cc_final: 0.5294 (t0) REVERT: F 190 MET cc_start: 0.8176 (mmm) cc_final: 0.7897 (mmm) REVERT: G 9 THR cc_start: 0.8933 (m) cc_final: 0.8591 (p) REVERT: G 61 ASP cc_start: 0.8175 (t0) cc_final: 0.7797 (t0) REVERT: G 103 MET cc_start: 0.8515 (ttm) cc_final: 0.8257 (ttp) REVERT: G 153 ASP cc_start: 0.8439 (t0) cc_final: 0.8158 (t0) REVERT: G 163 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7922 (tt) REVERT: H 23 ASP cc_start: 0.7942 (t0) cc_final: 0.7220 (p0) REVERT: H 39 ARG cc_start: 0.8493 (tpt170) cc_final: 0.8260 (tpt-90) REVERT: H 45 ASP cc_start: 0.8253 (m-30) cc_final: 0.7876 (m-30) REVERT: I 31 TYR cc_start: 0.8747 (t80) cc_final: 0.8421 (t80) REVERT: J 45 ASP cc_start: 0.7866 (m-30) cc_final: 0.7632 (m-30) REVERT: J 107 ASN cc_start: 0.8407 (t0) cc_final: 0.8057 (t0) REVERT: K 40 LYS cc_start: 0.7606 (ttmm) cc_final: 0.7273 (ptmm) REVERT: K 68 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8067 (ttp) REVERT: K 143 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7590 (t0) REVERT: K 157 ILE cc_start: 0.8825 (tt) cc_final: 0.8622 (tt) REVERT: L 1 MET cc_start: 0.7061 (mtm) cc_final: 0.6665 (mtp) REVERT: L 190 MET cc_start: 0.8117 (mmm) cc_final: 0.7798 (mtt) REVERT: M 21 LEU cc_start: 0.9135 (mt) cc_final: 0.8804 (tt) REVERT: M 103 MET cc_start: 0.5763 (ttt) cc_final: 0.5365 (mtm) REVERT: M 114 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5840 (tm-30) REVERT: M 118 ASN cc_start: 0.6886 (m-40) cc_final: 0.6147 (m110) REVERT: M 151 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5660 (mpp) REVERT: N 1 MET cc_start: 0.7075 (tpp) cc_final: 0.6813 (tpp) REVERT: N 88 LYS cc_start: 0.7013 (mmtm) cc_final: 0.6642 (mttt) outliers start: 74 outliers final: 52 residues processed: 378 average time/residue: 0.1241 time to fit residues: 75.0243 Evaluate side-chains 383 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 326 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 95 MET Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 68 MET Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 49 LEU Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 94 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [109, 126, 130, 216, 218, 32, 171, 74, 91, 147, 133] chunk 109 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 130 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 218 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 171 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 133 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 53 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.171747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.113630 restraints weight = 31733.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.113741 restraints weight = 17309.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.114104 restraints weight = 13077.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.114661 restraints weight = 12074.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.114853 restraints weight = 10736.401| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20788 Z= 0.125 Angle : 0.552 8.383 28717 Z= 0.306 Chirality : 0.046 0.363 3284 Planarity : 0.004 0.046 3117 Dihedral : 20.858 177.043 4346 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.07 % Allowed : 16.07 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2123 helix: 1.82 (0.20), residues: 735 sheet: 0.52 (0.22), residues: 562 loop : -0.28 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.028 0.002 TYR F 60 PHE 0.025 0.001 PHE M 121 TRP 0.006 0.001 TRP K 178 HIS 0.002 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (20788) covalent geometry : angle 0.55230 / 0.31 (28717) hydrogen bonds : bond 0.03338 / 3.69 ( 916) hydrogen bonds : angle 5.00768 / 6.52 ( 2675) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.2966 (ttt) cc_final: 0.2348 (mmt) REVERT: D 164 MET cc_start: 0.6934 (tmm) cc_final: 0.6585 (tmm) REVERT: D 190 MET cc_start: 0.7038 (tmm) cc_final: 0.6624 (ppp) REVERT: E 68 MET cc_start: 0.5621 (ttm) cc_final: 0.4992 (tmm) REVERT: E 103 MET cc_start: 0.6238 (ttt) cc_final: 0.5269 (mtp) REVERT: E 164 MET cc_start: 0.6861 (mmm) cc_final: 0.6655 (mmm) REVERT: E 167 GLU cc_start: 0.5656 (tm-30) cc_final: 0.5121 (tm-30) REVERT: F 86 LEU cc_start: 0.8415 (mm) cc_final: 0.8146 (mp) REVERT: F 153 ASP cc_start: 0.5704 (t0) cc_final: 0.5252 (t0) REVERT: F 190 MET cc_start: 0.8201 (mmm) cc_final: 0.7892 (mmm) REVERT: G 1 MET cc_start: 0.7569 (OUTLIER) cc_final: 0.6956 (mmm) REVERT: G 9 THR cc_start: 0.8891 (m) cc_final: 0.8536 (p) REVERT: G 61 ASP cc_start: 0.8175 (t0) cc_final: 0.7808 (t0) REVERT: G 103 MET cc_start: 0.8479 (ttm) cc_final: 0.8185 (ttp) REVERT: G 163 LEU cc_start: 0.8203 (tt) cc_final: 0.7957 (tt) REVERT: H 23 ASP cc_start: 0.7926 (t0) cc_final: 0.7252 (p0) REVERT: H 39 ARG cc_start: 0.8574 (tpt170) cc_final: 0.8301 (tpt-90) REVERT: H 45 ASP cc_start: 0.8284 (m-30) cc_final: 0.7940 (m-30) REVERT: J 45 ASP cc_start: 0.7992 (m-30) cc_final: 0.7647 (m-30) REVERT: J 107 ASN cc_start: 0.8225 (t0) cc_final: 0.7940 (t0) REVERT: K 40 LYS cc_start: 0.7555 (ttmm) cc_final: 0.7187 (ptmm) REVERT: K 143 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7579 (t0) REVERT: L 1 MET cc_start: 0.7073 (mtm) cc_final: 0.6665 (mtp) REVERT: M 21 LEU cc_start: 0.9118 (mt) cc_final: 0.8879 (tt) REVERT: M 98 ASP cc_start: 0.8153 (t0) cc_final: 0.7852 (t0) REVERT: M 103 MET cc_start: 0.5845 (ttt) cc_final: 0.5428 (mtp) REVERT: M 120 ASP cc_start: 0.7881 (p0) cc_final: 0.7636 (p0) REVERT: M 151 MET cc_start: 0.5917 (OUTLIER) cc_final: 0.5571 (mpp) REVERT: N 15 LEU cc_start: 0.7514 (mt) cc_final: 0.7208 (mt) REVERT: N 88 LYS cc_start: 0.7074 (mmtm) cc_final: 0.6710 (mttt) outliers start: 58 outliers final: 38 residues processed: 368 average time/residue: 0.1300 time to fit residues: 76.4706 Evaluate side-chains 354 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 98 ASP Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [145, 39, 210, 45, 46, 154, 30, 97, 205, 40, 135] chunk 145 optimal weight: 0.5980 chunk 39 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 154 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 53 GLN E 156 GLN M 53 GLN M 118 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.167539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114100 restraints weight = 32070.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.112805 restraints weight = 20617.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.115336 restraints weight = 16170.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.114951 restraints weight = 12811.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.116005 restraints weight = 12350.677| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 20788 Z= 0.245 Angle : 0.667 13.316 28717 Z= 0.360 Chirality : 0.050 0.396 3284 Planarity : 0.005 0.045 3117 Dihedral : 20.912 179.955 4346 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.07 % Allowed : 16.07 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 2123 helix: 1.54 (0.19), residues: 735 sheet: 0.29 (0.22), residues: 578 loop : -0.43 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 142 TYR 0.027 0.002 TYR D 46 PHE 0.024 0.002 PHE G 14 TRP 0.009 0.002 TRP K 144 HIS 0.005 0.001 HIS K 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 (20788) covalent geometry : angle 0.66706 / 0.36 (28717) hydrogen bonds : bond 0.04223 / 4.64 ( 916) hydrogen bonds : angle 5.15350 / 6.69 ( 2675) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 312 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.2867 (ttt) cc_final: 0.2251 (mmt) REVERT: D 164 MET cc_start: 0.6877 (tmm) cc_final: 0.6476 (tmm) REVERT: D 190 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6355 (ppp) REVERT: E 68 MET cc_start: 0.6035 (ttm) cc_final: 0.5283 (tmm) REVERT: E 72 MET cc_start: 0.6726 (mtp) cc_final: 0.6181 (mtp) REVERT: E 103 MET cc_start: 0.6339 (ttt) cc_final: 0.5410 (mtp) REVERT: E 164 MET cc_start: 0.6624 (mmm) cc_final: 0.5875 (tpp) REVERT: E 167 GLU cc_start: 0.5532 (tm-30) cc_final: 0.4982 (tm-30) REVERT: F 153 ASP cc_start: 0.5589 (t0) cc_final: 0.5184 (t0) REVERT: G 61 ASP cc_start: 0.8272 (t0) cc_final: 0.7905 (t0) REVERT: G 103 MET cc_start: 0.8614 (ttm) cc_final: 0.8335 (ttp) REVERT: G 163 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8178 (tt) REVERT: H 23 ASP cc_start: 0.8054 (t0) cc_final: 0.7308 (p0) REVERT: H 39 ARG cc_start: 0.8556 (tpt170) cc_final: 0.8306 (tpt-90) REVERT: H 45 ASP cc_start: 0.8241 (m-30) cc_final: 0.7935 (m-30) REVERT: I 23 ASP cc_start: 0.8434 (t0) cc_final: 0.8098 (t0) REVERT: I 31 TYR cc_start: 0.8766 (t80) cc_final: 0.8544 (t80) REVERT: J 45 ASP cc_start: 0.8025 (m-30) cc_final: 0.7597 (m-30) REVERT: J 107 ASN cc_start: 0.8276 (t0) cc_final: 0.7962 (t0) REVERT: K 40 LYS cc_start: 0.7615 (ttmm) cc_final: 0.7381 (pttp) REVERT: K 143 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7564 (t0) REVERT: L 1 MET cc_start: 0.7325 (mtm) cc_final: 0.6818 (mtp) REVERT: L 190 MET cc_start: 0.8186 (mmm) cc_final: 0.7795 (mtt) REVERT: M 21 LEU cc_start: 0.9094 (mt) cc_final: 0.8759 (tt) REVERT: M 58 CYS cc_start: 0.7785 (m) cc_final: 0.7504 (t) REVERT: M 98 ASP cc_start: 0.8338 (t0) cc_final: 0.8002 (t0) REVERT: M 103 MET cc_start: 0.5768 (ttt) cc_final: 0.5533 (mtp) REVERT: M 114 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: M 120 ASP cc_start: 0.7663 (p0) cc_final: 0.7410 (p0) REVERT: M 148 PHE cc_start: 0.7757 (p90) cc_final: 0.7552 (p90) REVERT: M 151 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5719 (mpp) REVERT: N 1 MET cc_start: 0.6686 (tpp) cc_final: 0.6145 (tpp) REVERT: N 15 LEU cc_start: 0.7423 (mt) cc_final: 0.7115 (mt) REVERT: N 88 LYS cc_start: 0.6953 (mmtm) cc_final: 0.6599 (mttt) outliers start: 77 outliers final: 59 residues processed: 352 average time/residue: 0.1312 time to fit residues: 73.2879 Evaluate side-chains 371 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 122 ILE Chi-restraints excluded: chain F residue 135 MET Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 95 MET Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain M residue 9 THR Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 107 ASN Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [6, 192, 87, 133, 94, 53, 126, 7, 37, 66, 12] chunk 6 optimal weight: 50.0000 chunk 192 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 7 optimal weight: 50.0000 chunk 37 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 53 GLN G 63 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.169213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115235 restraints weight = 32059.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.114098 restraints weight = 19594.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.117494 restraints weight = 15741.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.116840 restraints weight = 12091.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117502 restraints weight = 11374.181| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20788 Z= 0.153 Angle : 0.606 13.754 28717 Z= 0.328 Chirality : 0.047 0.365 3284 Planarity : 0.004 0.045 3117 Dihedral : 20.894 176.653 4346 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.17 % Allowed : 17.49 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2123 helix: 1.65 (0.19), residues: 735 sheet: 0.34 (0.22), residues: 562 loop : -0.44 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.028 0.002 TYR D 46 PHE 0.021 0.002 PHE E 152 TRP 0.008 0.001 TRP E 178 HIS 0.003 0.001 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (20788) covalent geometry : angle 0.60601 / 0.33 (28717) hydrogen bonds : bond 0.03537 / 3.90 ( 916) hydrogen bonds : angle 5.00641 / 6.52 ( 2675) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 316 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.2921 (ttt) cc_final: 0.2332 (mmt) REVERT: D 164 MET cc_start: 0.6965 (tmm) cc_final: 0.6603 (tmm) REVERT: D 190 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6325 (ppp) REVERT: E 68 MET cc_start: 0.6078 (ttm) cc_final: 0.5450 (tmm) REVERT: E 72 MET cc_start: 0.6684 (mtp) cc_final: 0.6015 (mtp) REVERT: E 103 MET cc_start: 0.6328 (ttt) cc_final: 0.5424 (mtp) REVERT: E 164 MET cc_start: 0.6703 (mmm) cc_final: 0.5896 (tpp) REVERT: E 167 GLU cc_start: 0.5560 (tm-30) cc_final: 0.4942 (tm-30) REVERT: F 86 LEU cc_start: 0.8427 (mm) cc_final: 0.8138 (mp) REVERT: F 153 ASP cc_start: 0.5578 (t0) cc_final: 0.5187 (t0) REVERT: G 9 THR cc_start: 0.8935 (m) cc_final: 0.8543 (p) REVERT: G 61 ASP cc_start: 0.8255 (t0) cc_final: 0.7896 (t0) REVERT: G 103 MET cc_start: 0.8523 (ttm) cc_final: 0.8232 (ttp) REVERT: G 120 ASP cc_start: 0.7471 (m-30) cc_final: 0.7199 (m-30) REVERT: G 163 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8144 (tt) REVERT: H 23 ASP cc_start: 0.7995 (t0) cc_final: 0.7440 (p0) REVERT: H 39 ARG cc_start: 0.8556 (tpt170) cc_final: 0.8294 (tpt-90) REVERT: H 45 ASP cc_start: 0.8249 (m-30) cc_final: 0.7947 (m-30) REVERT: H 104 THR cc_start: 0.8657 (m) cc_final: 0.8417 (p) REVERT: I 31 TYR cc_start: 0.8720 (t80) cc_final: 0.8467 (t80) REVERT: J 45 ASP cc_start: 0.8058 (m-30) cc_final: 0.7641 (m-30) REVERT: J 107 ASN cc_start: 0.8315 (t0) cc_final: 0.8005 (t0) REVERT: K 40 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7377 (pttp) REVERT: K 143 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7580 (t0) REVERT: L 1 MET cc_start: 0.7315 (mtm) cc_final: 0.6763 (mtp) REVERT: M 58 CYS cc_start: 0.7778 (m) cc_final: 0.7450 (t) REVERT: M 91 ASP cc_start: 0.8200 (t0) cc_final: 0.7941 (t0) REVERT: M 98 ASP cc_start: 0.8345 (t0) cc_final: 0.7980 (t0) REVERT: M 103 MET cc_start: 0.5778 (ttt) cc_final: 0.5549 (mtp) REVERT: M 114 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6682 (tm-30) REVERT: M 144 TRP cc_start: 0.7420 (p-90) cc_final: 0.6791 (p-90) REVERT: M 151 MET cc_start: 0.6125 (OUTLIER) cc_final: 0.5696 (mpp) REVERT: N 1 MET cc_start: 0.6845 (tpp) cc_final: 0.6040 (tpp) REVERT: N 15 LEU cc_start: 0.7365 (mt) cc_final: 0.7061 (mt) REVERT: N 88 LYS cc_start: 0.6939 (mmtm) cc_final: 0.6589 (mttt) outliers start: 60 outliers final: 48 residues processed: 349 average time/residue: 0.1285 time to fit residues: 71.2361 Evaluate side-chains 358 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 305 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 151 MET Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [164, 71, 72, 176, 187, 5, 130, 182, 152, 26, 18] chunk 164 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 176 optimal weight: 0.0980 chunk 187 optimal weight: 0.9980 chunk 5 optimal weight: 40.0000 chunk 130 optimal weight: 2.9990 chunk 182 optimal weight: 4.9990 chunk 152 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 63 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.170309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.111718 restraints weight = 31860.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.111613 restraints weight = 18271.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.112660 restraints weight = 13597.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.113748 restraints weight = 11298.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.113790 restraints weight = 9781.791| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20788 Z= 0.128 Angle : 0.596 12.795 28717 Z= 0.322 Chirality : 0.046 0.370 3284 Planarity : 0.004 0.044 3117 Dihedral : 20.865 175.768 4346 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.80 % Allowed : 18.13 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.18), residues: 2123 helix: 1.70 (0.20), residues: 735 sheet: 0.40 (0.22), residues: 562 loop : -0.37 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 179 TYR 0.017 0.001 TYR M 31 PHE 0.024 0.001 PHE E 152 TRP 0.008 0.001 TRP E 178 HIS 0.002 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (20788) covalent geometry : angle 0.59601 / 0.32 (28717) hydrogen bonds : bond 0.03280 / 3.65 ( 916) hydrogen bonds : angle 4.92256 / 6.40 ( 2675) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 320 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.3025 (ttt) cc_final: 0.2393 (mmt) REVERT: E 68 MET cc_start: 0.5639 (ttm) cc_final: 0.4997 (tmm) REVERT: E 72 MET cc_start: 0.6446 (mtp) cc_final: 0.5811 (mtp) REVERT: E 164 MET cc_start: 0.6885 (mmm) cc_final: 0.5957 (tpp) REVERT: E 167 GLU cc_start: 0.5606 (tm-30) cc_final: 0.4940 (tm-30) REVERT: F 86 LEU cc_start: 0.8397 (mm) cc_final: 0.8120 (mp) REVERT: F 95 MET cc_start: 0.6679 (ptm) cc_final: 0.6080 (ttp) REVERT: F 153 ASP cc_start: 0.5411 (t0) cc_final: 0.5006 (t0) REVERT: G 9 THR cc_start: 0.8942 (m) cc_final: 0.8542 (p) REVERT: G 61 ASP cc_start: 0.8230 (t0) cc_final: 0.7800 (t0) REVERT: G 103 MET cc_start: 0.8435 (ttm) cc_final: 0.8112 (ttp) REVERT: G 120 ASP cc_start: 0.7461 (m-30) cc_final: 0.7235 (m-30) REVERT: G 163 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8070 (tt) REVERT: H 23 ASP cc_start: 0.7936 (t0) cc_final: 0.7427 (p0) REVERT: H 39 ARG cc_start: 0.8611 (tpt170) cc_final: 0.8312 (tpt-90) REVERT: H 45 ASP cc_start: 0.8261 (m-30) cc_final: 0.7956 (m-30) REVERT: H 104 THR cc_start: 0.8641 (m) cc_final: 0.8374 (p) REVERT: I 31 TYR cc_start: 0.8647 (t80) cc_final: 0.8336 (t80) REVERT: J 45 ASP cc_start: 0.8019 (m-30) cc_final: 0.7613 (m-30) REVERT: J 107 ASN cc_start: 0.8282 (t0) cc_final: 0.7986 (t0) REVERT: K 40 LYS cc_start: 0.7539 (ttmm) cc_final: 0.7293 (pttp) REVERT: K 143 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7575 (t0) REVERT: L 1 MET cc_start: 0.7210 (mtm) cc_final: 0.6701 (mtp) REVERT: M 1 MET cc_start: 0.7789 (tmm) cc_final: 0.7431 (tmm) REVERT: M 58 CYS cc_start: 0.7976 (m) cc_final: 0.7541 (t) REVERT: M 91 ASP cc_start: 0.8230 (t0) cc_final: 0.7937 (t0) REVERT: M 98 ASP cc_start: 0.8360 (t0) cc_final: 0.8071 (t0) REVERT: M 103 MET cc_start: 0.5873 (ttt) cc_final: 0.5644 (mtp) REVERT: M 114 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: M 144 TRP cc_start: 0.7249 (p-90) cc_final: 0.6716 (p-90) REVERT: N 1 MET cc_start: 0.7080 (tpp) cc_final: 0.6336 (tpp) REVERT: N 15 LEU cc_start: 0.7482 (mt) cc_final: 0.7137 (mt) REVERT: N 69 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.6843 (m-40) REVERT: N 88 LYS cc_start: 0.6881 (mmtm) cc_final: 0.6576 (mttt) REVERT: N 121 PHE cc_start: 0.6298 (m-80) cc_final: 0.5751 (t80) REVERT: N 164 MET cc_start: 0.7632 (pmm) cc_final: 0.7268 (pmm) outliers start: 53 outliers final: 45 residues processed: 348 average time/residue: 0.1306 time to fit residues: 72.1143 Evaluate side-chains 360 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 118 ASN Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 69 ASN Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [89, 177, 195, 123, 159, 112, 85, 54, 18, 124, 150] chunk 89 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 159 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 18 optimal weight: 10.0000 chunk 124 optimal weight: 0.5980 chunk 150 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 53 GLN N 171 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.170939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.116291 restraints weight = 32160.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115030 restraints weight = 18622.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118749 restraints weight = 15176.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.117993 restraints weight = 11848.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.118734 restraints weight = 10997.197| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20788 Z= 0.126 Angle : 0.597 14.083 28717 Z= 0.321 Chirality : 0.046 0.373 3284 Planarity : 0.004 0.044 3117 Dihedral : 20.840 175.639 4346 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.70 % Allowed : 18.29 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2123 helix: 1.72 (0.20), residues: 735 sheet: 0.39 (0.22), residues: 562 loop : -0.33 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 179 TYR 0.018 0.001 TYR F 31 PHE 0.021 0.001 PHE E 148 TRP 0.008 0.001 TRP E 178 HIS 0.002 0.001 HIS J 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (20788) covalent geometry : angle 0.59683 / 0.32 (28717) hydrogen bonds : bond 0.03216 / 3.60 ( 916) hydrogen bonds : angle 4.84089 / 6.32 ( 2675) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 327 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 MET cc_start: 0.2976 (ttt) cc_final: 0.2360 (mmt) REVERT: E 68 MET cc_start: 0.5889 (ttm) cc_final: 0.5304 (tmm) REVERT: E 72 MET cc_start: 0.6680 (mtp) cc_final: 0.6079 (mtp) REVERT: E 85 LYS cc_start: 0.7244 (mmtp) cc_final: 0.6868 (mmtt) REVERT: E 167 GLU cc_start: 0.5567 (tm-30) cc_final: 0.4958 (tm-30) REVERT: F 86 LEU cc_start: 0.8387 (mm) cc_final: 0.8123 (mp) REVERT: F 95 MET cc_start: 0.6573 (ptm) cc_final: 0.6055 (ttp) REVERT: F 153 ASP cc_start: 0.5482 (t0) cc_final: 0.5085 (t0) REVERT: G 9 THR cc_start: 0.8890 (m) cc_final: 0.8501 (p) REVERT: G 23 ASP cc_start: 0.8359 (t70) cc_final: 0.8069 (m-30) REVERT: G 61 ASP cc_start: 0.8220 (t0) cc_final: 0.7807 (t0) REVERT: G 103 MET cc_start: 0.8415 (ttm) cc_final: 0.8094 (ttp) REVERT: G 120 ASP cc_start: 0.7424 (m-30) cc_final: 0.7223 (m-30) REVERT: H 23 ASP cc_start: 0.7938 (t0) cc_final: 0.7465 (p0) REVERT: H 39 ARG cc_start: 0.8568 (tpt170) cc_final: 0.8288 (tpt-90) REVERT: H 45 ASP cc_start: 0.8194 (m-30) cc_final: 0.7954 (m-30) REVERT: H 104 THR cc_start: 0.8614 (m) cc_final: 0.8389 (p) REVERT: H 190 MET cc_start: 0.8249 (mmp) cc_final: 0.7801 (mmp) REVERT: I 31 TYR cc_start: 0.8618 (t80) cc_final: 0.8319 (t80) REVERT: J 107 ASN cc_start: 0.8301 (t0) cc_final: 0.8029 (t0) REVERT: K 40 LYS cc_start: 0.7561 (ttmm) cc_final: 0.7349 (pttp) REVERT: K 143 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7587 (t0) REVERT: L 1 MET cc_start: 0.7252 (mtm) cc_final: 0.6774 (mtp) REVERT: M 58 CYS cc_start: 0.7829 (m) cc_final: 0.7439 (t) REVERT: M 91 ASP cc_start: 0.8219 (t0) cc_final: 0.7868 (t0) REVERT: M 98 ASP cc_start: 0.8348 (t0) cc_final: 0.8067 (t0) REVERT: M 103 MET cc_start: 0.5795 (ttt) cc_final: 0.5582 (mtp) REVERT: M 114 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6653 (tm-30) REVERT: M 144 TRP cc_start: 0.7339 (p-90) cc_final: 0.6888 (p-90) REVERT: N 1 MET cc_start: 0.6687 (tpp) cc_final: 0.5959 (tpp) REVERT: N 15 LEU cc_start: 0.7390 (mt) cc_final: 0.7037 (mt) REVERT: N 88 LYS cc_start: 0.6887 (mmtm) cc_final: 0.6560 (mttt) REVERT: N 143 ASP cc_start: 0.4464 (p0) cc_final: 0.4123 (t0) outliers start: 51 outliers final: 44 residues processed: 354 average time/residue: 0.1386 time to fit residues: 77.7198 Evaluate side-chains 356 residues out of total 1892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain D residue 152 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 11 THR Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 146 VAL Chi-restraints excluded: chain F residue 163 LEU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 95 MET Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 151 MET Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 99 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 163 LEU Chi-restraints excluded: chain I residue 164 MET Chi-restraints excluded: chain I residue 187 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 120 ASP Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 95 MET Chi-restraints excluded: chain L residue 115 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 114 GLU Chi-restraints excluded: chain M residue 122 ILE Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 94 ILE Chi-restraints excluded: chain N residue 98 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: [219, 129, 146, 86, 105, 30, 213, 75, 197, 77, 17] chunk 219 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN G 63 GLN ** K 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 GLN M 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.168433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111361 restraints weight = 32126.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110515 restraints weight = 17307.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111380 restraints weight = 13843.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.111996 restraints weight = 11846.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.112041 restraints weight = 10701.537| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 20788 Z= 0.207 Angle : 0.661 14.535 28717 Z= 0.351 Chirality : 0.048 0.371 3284 Planarity : 0.005 0.044 3117 Dihedral : 20.875 177.898 4346 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.70 % Allowed : 18.55 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 2123 helix: 1.47 (0.19), residues: 741 sheet: 0.26 (0.22), residues: 559 loop : -0.52 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 179 TYR 0.020 0.002 TYR L 59 PHE 0.021 0.002 PHE E 148 TRP 0.011 0.001 TRP E 178 HIS 0.003 0.001 HIS G 17 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (20788) covalent geometry : angle 0.66140 / 0.35 (28717) hydrogen bonds : bond 0.03701 / 4.11 ( 916) hydrogen bonds : angle 4.99117 / 6.50 ( 2675) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3433.58 seconds wall clock time: 59 minutes 59.27 seconds (3599.27 seconds total)