Starting phenix.real_space_refine on Wed Aug 27 03:08:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ghu_40051/08_2025/8ghu_40051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ghu_40051/08_2025/8ghu_40051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ghu_40051/08_2025/8ghu_40051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ghu_40051/08_2025/8ghu_40051.map" model { file = "/net/cci-nas-00/data/ceres_data/8ghu_40051/08_2025/8ghu_40051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ghu_40051/08_2025/8ghu_40051.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 57 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 1531 5.49 5 Mg 83 5.21 5 S 53 5.16 5 C 23726 2.51 5 N 8745 2.21 5 O 13270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 47408 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2260 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 268} Chain: "a" Number of atoms: 30099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1403, 30099 Classifications: {'RNA': 1403} Modifications used: {'5*END': 1, 'rna2p_pur': 122, 'rna2p_pyr': 103, 'rna3p_pur': 677, 'rna3p_pyr': 501} Link IDs: {'rna2p': 224, 'rna3p': 1178} Chain: "a" Number of atoms: 2801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2801 Unusual residues: {'ZIV': 1} Classifications: {'RNA': 128, 'undetermined': 1} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 63, 'rna3p_pyr': 46} Link IDs: {'rna2p': 19, 'rna3p': 108, None: 1} Not linked: pdbres="ZIV a1405 " pdbres=" U a1406 " Chain: "c" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1106 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "f" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "g" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "h" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "l" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "m" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "o" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "p" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "q" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "r" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "a" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 79 Unusual residues: {' MG': 79} Classifications: {'undetermined': 79} Link IDs: {None: 78} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 470 residue: pdb=" P C a 930 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 930 " occ=0.00 residue: pdb=" P C a 931 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 931 " occ=0.00 residue: pdb=" P C a 932 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 932 " occ=0.00 residue: pdb=" P G a 933 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G a 933 " occ=0.00 residue: pdb=" P C a 934 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 934 " occ=0.00 residue: pdb=" P A a 935 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A a 935 " occ=0.00 residue: pdb=" P C a 936 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 936 " occ=0.00 residue: pdb=" P A a 937 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A a 937 " occ=0.00 residue: pdb=" P A a 938 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A a 938 " occ=0.00 residue: pdb=" P G a 939 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G a 939 " occ=0.00 residue: pdb=" P C a 940 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C a 940 " occ=0.00 residue: pdb=" P G a 941 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G a 941 " occ=0.00 ... (remaining 458 not shown) Time building chain proxies: 10.11, per 1000 atoms: 0.21 Number of scatterers: 47408 At special positions: 0 Unit cell: (185.229, 240.318, 156.486, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 1531 15.00 Mg 83 11.99 O 13270 8.00 N 8745 7.00 C 23726 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3396 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 19 sheets defined 31.5% alpha, 11.2% beta 140 base pairs and 754 stacking pairs defined. Time for finding SS restraints: 6.35 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 8 through 18 removed outlier: 4.241A pdb=" N LYS A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 36 removed outlier: 3.565A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 36 " --> pdb=" O VAL A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.873A pdb=" N HIS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 removed outlier: 3.608A pdb=" N TRP A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 111 through 115 removed outlier: 3.943A pdb=" N TYR A 115 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.903A pdb=" N THR A 126 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.920A pdb=" N ALA A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 151 " --> pdb=" O PHE A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.965A pdb=" N ALA A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS A 171 " --> pdb=" O GLU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.583A pdb=" N THR A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 3.571A pdb=" N GLU A 213 " --> pdb=" O LEU A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 223 removed outlier: 4.350A pdb=" N GLN A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 255 removed outlier: 4.227A pdb=" N VAL A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N PHE A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 247 through 255' Processing helix chain 'c' and resid 32 through 35 removed outlier: 3.764A pdb=" N ASP c 35 " --> pdb=" O LEU c 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 32 through 35' Processing helix chain 'c' and resid 36 through 44 removed outlier: 3.536A pdb=" N GLN c 40 " --> pdb=" O PHE c 36 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 95 removed outlier: 3.641A pdb=" N ARG c 87 " --> pdb=" O VAL c 83 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL c 89 " --> pdb=" O LYS c 85 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL c 90 " --> pdb=" O LEU c 86 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP c 92 " --> pdb=" O LYS c 88 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ILE c 93 " --> pdb=" O VAL c 89 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA c 94 " --> pdb=" O VAL c 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY c 95 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 113 through 123 removed outlier: 3.735A pdb=" N ILE c 119 " --> pdb=" O VAL c 115 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN c 122 " --> pdb=" O SER c 118 " (cutoff:3.500A) Processing helix chain 'c' and resid 124 through 126 No H-bonds generated for 'chain 'c' and resid 124 through 126' Processing helix chain 'c' and resid 128 through 142 removed outlier: 3.777A pdb=" N MET c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N VAL c 137 " --> pdb=" O MET c 133 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN c 138 " --> pdb=" O LYS c 134 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ALA c 140 " --> pdb=" O ALA c 136 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ARG c 142 " --> pdb=" O GLN c 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 11 removed outlier: 3.517A pdb=" N LEU d 10 " --> pdb=" O PRO d 6 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER d 11 " --> pdb=" O LYS d 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 6 through 11' Processing helix chain 'd' and resid 48 through 65 removed outlier: 3.644A pdb=" N GLN d 53 " --> pdb=" O ASP d 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG d 55 " --> pdb=" O GLY d 51 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU d 56 " --> pdb=" O VAL d 52 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS d 57 " --> pdb=" O GLN d 53 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL d 60 " --> pdb=" O GLU d 56 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE d 63 " --> pdb=" O LYS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 67 through 79 removed outlier: 4.030A pdb=" N ASN d 73 " --> pdb=" O ARG d 69 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR d 74 " --> pdb=" O GLN d 70 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS d 76 " --> pdb=" O ARG d 72 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA d 79 " --> pdb=" O TYR d 75 " (cutoff:3.500A) Processing helix chain 'd' and resid 84 through 95 removed outlier: 4.029A pdb=" N LEU d 90 " --> pdb=" O GLY d 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA d 91 " --> pdb=" O GLU d 87 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU d 92 " --> pdb=" O ASN d 88 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY d 95 " --> pdb=" O ALA d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 96 through 101 removed outlier: 3.529A pdb=" N VAL d 100 " --> pdb=" O ARG d 96 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL d 101 " --> pdb=" O LEU d 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 96 through 101' Processing helix chain 'd' and resid 102 through 105 removed outlier: 3.756A pdb=" N GLY d 105 " --> pdb=" O TYR d 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 102 through 105' Processing helix chain 'd' and resid 109 through 117 removed outlier: 3.528A pdb=" N ALA d 113 " --> pdb=" O THR d 109 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG d 114 " --> pdb=" O ARG d 110 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN d 115 " --> pdb=" O ALA d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 156 removed outlier: 3.804A pdb=" N ALA d 156 " --> pdb=" O SER d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 159 No H-bonds generated for 'chain 'd' and resid 157 through 159' Processing helix chain 'e' and resid 54 through 68 removed outlier: 3.504A pdb=" N ALA e 62 " --> pdb=" O ALA e 58 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET e 63 " --> pdb=" O ILE e 59 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU e 64 " --> pdb=" O GLN e 60 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS e 65 " --> pdb=" O LYS e 61 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA e 66 " --> pdb=" O ALA e 62 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG e 67 " --> pdb=" O MET e 63 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG e 68 " --> pdb=" O GLU e 64 " (cutoff:3.500A) Processing helix chain 'e' and resid 110 through 118 removed outlier: 3.685A pdb=" N ALA e 117 " --> pdb=" O VAL e 113 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 136 removed outlier: 3.748A pdb=" N VAL e 136 " --> pdb=" O PRO e 132 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 143 Processing helix chain 'e' and resid 148 through 154 removed outlier: 3.639A pdb=" N ALA e 154 " --> pdb=" O GLU e 150 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 22 removed outlier: 3.759A pdb=" N ILE f 22 " --> pdb=" O VAL f 18 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 75 removed outlier: 3.511A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP f 72 " --> pdb=" O GLN f 68 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) Processing helix chain 'f' and resid 76 through 81 removed outlier: 3.804A pdb=" N PHE f 80 " --> pdb=" O THR f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 59 through 67 removed outlier: 3.784A pdb=" N ALA g 64 " --> pdb=" O ALA g 60 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU g 65 " --> pdb=" O PHE g 61 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN g 67 " --> pdb=" O VAL g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 100 through 107 removed outlier: 3.964A pdb=" N VAL g 104 " --> pdb=" O MET g 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU g 105 " --> pdb=" O ARG g 101 " (cutoff:3.500A) Processing helix chain 'g' and resid 114 through 119 removed outlier: 4.196A pdb=" N ARG g 118 " --> pdb=" O SER g 114 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU g 119 " --> pdb=" O MET g 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 114 through 119' Processing helix chain 'g' and resid 137 through 144 removed outlier: 4.348A pdb=" N HIS g 141 " --> pdb=" O ARG g 137 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 20 removed outlier: 3.676A pdb=" N ASP h 8 " --> pdb=" O ASP h 4 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET h 9 " --> pdb=" O PRO h 5 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE h 13 " --> pdb=" O MET h 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN h 17 " --> pdb=" O ILE h 13 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA h 18 " --> pdb=" O ARG h 14 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA h 19 " --> pdb=" O ASN h 15 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 42 removed outlier: 3.802A pdb=" N ALA h 34 " --> pdb=" O LYS h 30 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU h 41 " --> pdb=" O ASN h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 91 removed outlier: 4.066A pdb=" N LEU h 91 " --> pdb=" O LYS h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 98 removed outlier: 3.600A pdb=" N ALA h 96 " --> pdb=" O LYS h 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 6 Processing helix chain 'm' and resid 44 through 48 Processing helix chain 'm' and resid 49 through 51 No H-bonds generated for 'chain 'm' and resid 49 through 51' Processing helix chain 'm' and resid 52 through 58 removed outlier: 3.605A pdb=" N LEU m 56 " --> pdb=" O GLN m 52 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP m 58 " --> pdb=" O ASP m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 68 through 73 removed outlier: 3.985A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 92 removed outlier: 3.606A pdb=" N ARG m 90 " --> pdb=" O TYR m 86 " (cutoff:3.500A) Processing helix chain 'o' and resid 8 through 13 removed outlier: 4.347A pdb=" N VAL o 12 " --> pdb=" O THR o 8 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER o 13 " --> pdb=" O ALA o 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 8 through 13' Processing helix chain 'o' and resid 26 through 41 removed outlier: 4.230A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU o 32 " --> pdb=" O GLN o 28 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA o 34 " --> pdb=" O ALA o 30 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN o 35 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU o 39 " --> pdb=" O GLN o 35 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 44 No H-bonds generated for 'chain 'o' and resid 42 through 44' Processing helix chain 'o' and resid 50 through 55 Processing helix chain 'o' and resid 56 through 61 removed outlier: 3.932A pdb=" N SER o 61 " --> pdb=" O LEU o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 61 through 68 removed outlier: 4.098A pdb=" N LYS o 65 " --> pdb=" O SER o 61 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASP o 68 " --> pdb=" O ARG o 64 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 76 No H-bonds generated for 'chain 'o' and resid 74 through 76' Processing helix chain 'o' and resid 77 through 85 removed outlier: 3.963A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU o 83 " --> pdb=" O THR o 79 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 58 removed outlier: 3.912A pdb=" N ALA p 58 " --> pdb=" O LEU p 54 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 75 removed outlier: 3.588A pdb=" N ALA p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU p 74 " --> pdb=" O ARG p 70 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE p 75 " --> pdb=" O VAL p 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 27 through 31 removed outlier: 4.173A pdb=" N ASN r 30 " --> pdb=" O THR r 27 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR r 31 " --> pdb=" O LEU r 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 27 through 31' Processing helix chain 'r' and resid 57 through 63 removed outlier: 3.501A pdb=" N ARG r 60 " --> pdb=" O ALA r 57 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR r 63 " --> pdb=" O ARG r 60 " (cutoff:3.500A) Processing helix chain 't' and resid 3 through 25 removed outlier: 3.990A pdb=" N ARG t 9 " --> pdb=" O SER t 5 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE t 11 " --> pdb=" O LYS t 7 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS t 18 " --> pdb=" O GLU t 14 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA t 21 " --> pdb=" O ARG t 17 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER t 22 " --> pdb=" O LYS t 18 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG t 23 " --> pdb=" O HIS t 19 " (cutoff:3.500A) Processing helix chain 't' and resid 25 through 41 removed outlier: 3.831A pdb=" N THR t 29 " --> pdb=" O SER t 25 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE t 30 " --> pdb=" O MET t 26 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS t 33 " --> pdb=" O THR t 29 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL t 34 " --> pdb=" O PHE t 30 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR t 35 " --> pdb=" O ILE t 31 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA t 36 " --> pdb=" O LYS t 32 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE t 38 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU t 39 " --> pdb=" O TYR t 35 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY t 41 " --> pdb=" O ALA t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 49 removed outlier: 3.919A pdb=" N LYS t 48 " --> pdb=" O ALA t 44 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA t 49 " --> pdb=" O ALA t 45 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 44 through 49' Processing helix chain 't' and resid 49 through 58 removed outlier: 3.627A pdb=" N GLN t 54 " --> pdb=" O PHE t 50 " (cutoff:3.500A) Proline residue: t 55 - end of helix Processing helix chain 't' and resid 69 through 78 removed outlier: 3.554A pdb=" N ARG t 73 " --> pdb=" O ASN t 69 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU t 78 " --> pdb=" O HIS t 74 " (cutoff:3.500A) Processing helix chain 't' and resid 78 through 86 removed outlier: 3.574A pdb=" N ILE t 82 " --> pdb=" O LEU t 78 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 159 removed outlier: 8.587A pdb=" N PHE A 159 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ASP A 134 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 230 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 195 through 196 removed outlier: 6.635A pdb=" N GLY A 195 " --> pdb=" O LYS A 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 267 removed outlier: 7.019A pdb=" N ILE A 277 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 19 through 20 removed outlier: 4.138A pdb=" N THR c 20 " --> pdb=" O ILE c 56 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL c 55 " --> pdb=" O THR c 66 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL c 65 " --> pdb=" O ASN c 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 148 through 151 removed outlier: 4.083A pdb=" N ILE c 201 " --> pdb=" O ASP c 182 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ASP c 182 " --> pdb=" O ILE c 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 127 through 128 removed outlier: 3.980A pdb=" N ASP d 140 " --> pdb=" O PHE d 181 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE d 181 " --> pdb=" O ASP d 140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 18 through 21 Processing sheet with id=AA8, first strand: chain 'e' and resid 35 through 38 removed outlier: 3.723A pdb=" N VAL e 38 " --> pdb=" O GLY e 46 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY e 46 " --> pdb=" O VAL e 38 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.532A pdb=" N VAL e 84 " --> pdb=" O MET e 95 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET e 95 " --> pdb=" O VAL e 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.532A pdb=" N VAL e 84 " --> pdb=" O MET e 95 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET e 95 " --> pdb=" O VAL e 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'f' and resid 36 through 44 removed outlier: 3.940A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU f 61 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TRP f 42 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE f 8 " --> pdb=" O VAL f 60 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET f 62 " --> pdb=" O ILE f 6 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE f 6 " --> pdb=" O MET f 62 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL f 64 " --> pdb=" O TYR f 4 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TYR f 4 " --> pdb=" O VAL f 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'h' and resid 26 through 27 removed outlier: 6.124A pdb=" N GLU h 57 " --> pdb=" O VAL h 50 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL h 50 " --> pdb=" O GLU h 57 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU h 59 " --> pdb=" O PHE h 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE h 48 " --> pdb=" O GLU h 59 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N THR h 61 " --> pdb=" O GLU h 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 64 through 65 removed outlier: 3.515A pdb=" N PHE h 65 " --> pdb=" O LYS h 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'h' and resid 109 through 110 removed outlier: 7.165A pdb=" N ILE h 100 " --> pdb=" O TYR h 127 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N TYR h 127 " --> pdb=" O ILE h 100 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N VAL h 102 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'l' and resid 61 through 63 removed outlier: 3.821A pdb=" N VAL l 62 " --> pdb=" O VAL l 54 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL l 54 " --> pdb=" O VAL l 62 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG l 82 " --> pdb=" O HIS l 95 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS l 95 " --> pdb=" O ARG l 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'p' and resid 32 through 37 removed outlier: 6.912A pdb=" N VAL p 21 " --> pdb=" O ILE p 33 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ARG p 35 " --> pdb=" O VAL p 19 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N VAL p 19 " --> pdb=" O ARG p 35 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLY p 37 " --> pdb=" O TYR p 17 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N TYR p 17 " --> pdb=" O GLY p 37 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL p 20 " --> pdb=" O ARG p 5 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG p 5 " --> pdb=" O VAL p 20 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA p 22 " --> pdb=" O THR p 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'q' and resid 6 through 7 removed outlier: 3.872A pdb=" N ASP q 56 " --> pdb=" O VAL q 11 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL q 21 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU q 43 " --> pdb=" O VAL q 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'q' and resid 6 through 7 removed outlier: 8.230A pdb=" N VAL q 57 " --> pdb=" O VAL q 77 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL q 77 " --> pdb=" O VAL q 57 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N GLU q 59 " --> pdb=" O VAL q 75 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL q 75 " --> pdb=" O GLU q 59 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG q 61 " --> pdb=" O THR q 73 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR q 73 " --> pdb=" O ARG q 61 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N SER q 71 " --> pdb=" O CYS q 63 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 25 through 29 removed outlier: 3.952A pdb=" N VAL q 28 " --> pdb=" O ILE q 37 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE q 37 " --> pdb=" O VAL q 28 " (cutoff:3.500A) 232 hydrogen bonds defined for protein. 630 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 510 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 754 stacking parallelities Total time for adding SS restraints: 19.25 Time building geometry restraints manager: 5.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3842 1.29 - 1.42: 22420 1.42 - 1.55: 22049 1.55 - 1.68: 3064 1.68 - 1.81: 95 Bond restraints: 51470 Sorted by residual: bond pdb=" C17 ZIV a1405 " pdb=" C19 ZIV a1405 " ideal model delta sigma weight residual 1.535 1.280 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C35 ZIV a1405 " pdb=" C45 ZIV a1405 " ideal model delta sigma weight residual 1.553 1.372 0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" C35 ZIV a1405 " pdb=" O36 ZIV a1405 " ideal model delta sigma weight residual 1.431 1.600 -0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" C16 ZIV a1405 " pdb=" O32 ZIV a1405 " ideal model delta sigma weight residual 1.445 1.288 0.157 2.00e-02 2.50e+03 6.17e+01 bond pdb=" C49 ZIV a1405 " pdb=" N51 ZIV a1405 " ideal model delta sigma weight residual 1.309 1.466 -0.157 2.00e-02 2.50e+03 6.14e+01 ... (remaining 51465 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.43: 76847 4.43 - 8.87: 258 8.87 - 13.30: 11 13.30 - 17.74: 2 17.74 - 22.17: 2 Bond angle restraints: 77120 Sorted by residual: angle pdb=" N TYR A 60 " pdb=" CA TYR A 60 " pdb=" C TYR A 60 " ideal model delta sigma weight residual 113.23 101.44 11.79 1.24e+00 6.50e-01 9.04e+01 angle pdb=" O3' G a1530 " pdb=" C3' G a1530 " pdb=" C2' G a1530 " ideal model delta sigma weight residual 109.50 121.19 -11.69 1.50e+00 4.44e-01 6.08e+01 angle pdb=" N PRO A 41 " pdb=" CA PRO A 41 " pdb=" C PRO A 41 " ideal model delta sigma weight residual 110.70 119.85 -9.15 1.22e+00 6.72e-01 5.63e+01 angle pdb=" C45 ZIV a1405 " pdb=" C35 ZIV a1405 " pdb=" N34 ZIV a1405 " ideal model delta sigma weight residual 116.46 94.29 22.17 3.00e+00 1.11e-01 5.46e+01 angle pdb=" O3' C a1210 " pdb=" C3' C a1210 " pdb=" C2' C a1210 " ideal model delta sigma weight residual 109.50 120.42 -10.92 1.50e+00 4.44e-01 5.30e+01 ... (remaining 77115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 29282 35.97 - 71.94: 3363 71.94 - 107.91: 404 107.91 - 143.88: 5 143.88 - 179.84: 18 Dihedral angle restraints: 33072 sinusoidal: 27810 harmonic: 5262 Sorted by residual: dihedral pdb=" C4' C a1038 " pdb=" C3' C a1038 " pdb=" C2' C a1038 " pdb=" C1' C a1038 " ideal model delta sinusoidal sigma weight residual -35.00 31.77 -66.77 1 8.00e+00 1.56e-02 9.08e+01 dihedral pdb=" C5' C a1038 " pdb=" C4' C a1038 " pdb=" C3' C a1038 " pdb=" O3' C a1038 " ideal model delta sinusoidal sigma weight residual 147.00 81.93 65.07 1 8.00e+00 1.56e-02 8.68e+01 dihedral pdb=" C5' C a1404 " pdb=" C4' C a1404 " pdb=" C3' C a1404 " pdb=" O3' C a1404 " ideal model delta sinusoidal sigma weight residual 147.00 83.66 63.34 1 8.00e+00 1.56e-02 8.27e+01 ... (remaining 33069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 9445 0.143 - 0.285: 368 0.285 - 0.428: 54 0.428 - 0.571: 4 0.571 - 0.713: 2 Chirality restraints: 9873 Sorted by residual: chirality pdb=" C3' C a1210 " pdb=" C4' C a1210 " pdb=" O3' C a1210 " pdb=" C2' C a1210 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" C3' U a1049 " pdb=" C4' U a1049 " pdb=" O3' U a1049 " pdb=" C2' U a1049 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.14e+00 chirality pdb=" C3' G a1530 " pdb=" C4' G a1530 " pdb=" O3' G a1530 " pdb=" C2' G a1530 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.51 2.00e-01 2.50e+01 6.51e+00 ... (remaining 9870 not shown) Planarity restraints: 4071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA e 98 " 0.025 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C ALA e 98 " -0.086 2.00e-02 2.50e+03 pdb=" O ALA e 98 " 0.032 2.00e-02 2.50e+03 pdb=" N SER e 99 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 230 " -0.018 2.00e-02 2.50e+03 3.48e-02 1.21e+01 pdb=" C VAL A 230 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL A 230 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE A 231 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 191 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.91e+00 pdb=" C SER A 191 " 0.052 2.00e-02 2.50e+03 pdb=" O SER A 191 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A 192 " -0.017 2.00e-02 2.50e+03 ... (remaining 4068 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4702 2.73 - 3.27: 39149 3.27 - 3.82: 84434 3.82 - 4.36: 109606 4.36 - 4.90: 147394 Nonbonded interactions: 385285 Sorted by model distance: nonbonded pdb=" O18 ZIV a1405 " pdb=" O20 ZIV a1405 " model vdw 2.190 2.432 nonbonded pdb=" N1 G a 413 " pdb=" CE LYS d 32 " model vdw 2.200 3.520 nonbonded pdb=" O LEU A 257 " pdb=" CD2 LEU A 257 " model vdw 2.235 3.460 nonbonded pdb=" O2' A a 563 " pdb=" O2' G a 566 " model vdw 2.254 3.040 nonbonded pdb=" O4 U a 652 " pdb=" O2' G a 752 " model vdw 2.264 3.040 ... (remaining 385280 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.79 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.030 Extract box with map and model: 0.730 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 53.400 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5155 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 : 0.006 0.255 51472 Z= 0.387 Angle : 0.740 22.175 77120 Z= 0.483 Chirality : 0.055 0.713 9873 Planarity : 0.003 0.050 4071 Dihedral : 22.474 179.845 29676 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.06 % Favored : 88.89 % Rotamer: Outliers : 3.01 % Allowed : 9.24 % Favored : 87.75 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.69 (0.15), residues: 1800 helix: -4.66 (0.11), residues: 379 sheet: -2.31 (0.37), residues: 176 loop : -2.91 (0.14), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG g 108 TYR 0.016 0.001 TYR A 275 PHE 0.016 0.001 PHE A 37 TRP 0.011 0.001 TRP A 224 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00583 (51470) covalent geometry : angle 0.74037 (77120) hydrogen bonds : bond 0.31219 ( 546) hydrogen bonds : angle 11.59241 ( 1140) Misc. bond : bond 0.06642 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 448 time to evaluate : 0.984 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5928 (mmm) cc_final: 0.5505 (mmm) REVERT: A 49 VAL cc_start: 0.3873 (p) cc_final: 0.3579 (t) REVERT: A 57 TYR cc_start: 0.5633 (t80) cc_final: 0.5298 (t80) REVERT: A 124 GLU cc_start: 0.4024 (OUTLIER) cc_final: 0.3202 (pm20) REVERT: A 188 ASP cc_start: 0.4955 (OUTLIER) cc_final: 0.4286 (t0) REVERT: A 206 TYR cc_start: -0.2419 (m-80) cc_final: -0.2891 (m-10) REVERT: A 246 GLU cc_start: -0.0320 (OUTLIER) cc_final: -0.1842 (tm-30) REVERT: c 54 ILE cc_start: 0.6423 (OUTLIER) cc_final: 0.6037 (pp) REVERT: c 104 GLU cc_start: 0.4286 (mp0) cc_final: 0.3796 (tp30) REVERT: c 120 THR cc_start: 0.5671 (m) cc_final: 0.4854 (t) REVERT: d 123 MET cc_start: 0.7500 (mtt) cc_final: 0.7255 (mtp) REVERT: d 150 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6809 (pptt) REVERT: d 182 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.5646 (tmtt) REVERT: e 60 GLN cc_start: 0.8542 (tm-30) cc_final: 0.8163 (tm-30) REVERT: f 4 TYR cc_start: 0.6648 (m-80) cc_final: 0.6204 (m-80) REVERT: f 42 TRP cc_start: 0.5375 (m100) cc_final: 0.4783 (m100) REVERT: f 88 MET cc_start: 0.6983 (tpp) cc_final: 0.6321 (mtt) REVERT: g 110 ARG cc_start: 0.2715 (tpt170) cc_final: 0.2456 (ptm160) REVERT: g 115 MET cc_start: -0.2632 (ptm) cc_final: -0.3075 (pmm) REVERT: h 33 VAL cc_start: 0.8425 (t) cc_final: 0.8043 (t) REVERT: m 31 LYS cc_start: 0.4603 (pttp) cc_final: 0.4131 (tppt) REVERT: o 26 GLU cc_start: 0.5115 (mt-10) cc_final: 0.4899 (mp0) REVERT: o 51 HIS cc_start: 0.7657 (t70) cc_final: 0.7407 (m90) REVERT: o 79 THR cc_start: 0.8178 (p) cc_final: 0.7710 (p) outliers start: 46 outliers final: 5 residues processed: 480 average time/residue: 0.9623 time to fit residues: 551.4651 Evaluate side-chains 223 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 213 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain c residue 13 ILE Chi-restraints excluded: chain c residue 54 ILE Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 182 LYS Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain g residue 123 LEU Chi-restraints excluded: chain q residue 48 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 155 GLN A 212 GLN c 40 GLN ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 184 ASN d 39 GLN d 53 GLN d 58 GLN d 115 GLN d 119 HIS d 197 HIS e 88 HIS e 120 HIS f 55 HIS ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 ASN h 37 ASN l 4 ASN m 14 HIS m 91 HIS q 30 HIS r 51 GLN t 2 ASN t 54 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4858 r_free = 0.4858 target = 0.187014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.163731 restraints weight = 165815.498| |-----------------------------------------------------------------------------| r_work (start): 0.4579 rms_B_bonded: 3.47 r_work: 0.4492 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5305 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 51472 Z= 0.124 Angle : 0.555 9.759 77120 Z= 0.278 Chirality : 0.031 0.367 9873 Planarity : 0.004 0.057 4071 Dihedral : 22.927 179.770 26061 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.17 % Favored : 96.78 % Rotamer: Outliers : 5.11 % Allowed : 21.30 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -4.04 (0.16), residues: 1800 helix: -3.56 (0.16), residues: 455 sheet: -1.64 (0.35), residues: 191 loop : -2.61 (0.16), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG d 183 TYR 0.017 0.001 TYR A 25 PHE 0.024 0.002 PHE d 181 TRP 0.011 0.001 TRP A 224 HIS 0.004 0.001 HIS c 68 Details of bonding type rmsd covalent geometry : bond 0.00256 (51470) covalent geometry : angle 0.55539 (77120) hydrogen bonds : bond 0.07593 ( 546) hydrogen bonds : angle 4.56732 ( 1140) Misc. bond : bond 0.00267 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 262 time to evaluate : 0.926 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: symmetry clash revert: symmetry clash REVERT: c 190 THR cc_start: -0.1576 (p) cc_final: -0.1832 (m) REVERT: d 123 MET cc_start: 0.7757 (mtt) cc_final: 0.7417 (mtp) REVERT: d 141 VAL cc_start: 0.7741 (t) cc_final: 0.7417 (p) REVERT: d 150 LYS cc_start: 0.7456 (mmtt) cc_final: 0.6925 (pttm) REVERT: e 150 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8049 (pp20) REVERT: f 4 TYR cc_start: 0.6003 (m-80) cc_final: 0.5564 (m-80) REVERT: f 9 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6620 (mtm) REVERT: f 42 TRP cc_start: 0.5839 (m100) cc_final: 0.4737 (m100) REVERT: f 46 GLN cc_start: 0.8142 (tp-100) cc_final: 0.7733 (mm-40) REVERT: f 78 PHE cc_start: 0.7592 (m-10) cc_final: 0.7376 (m-10) REVERT: f 88 MET cc_start: 0.7096 (tpp) cc_final: 0.6450 (mtt) REVERT: g 9 ARG cc_start: 0.0308 (mtt180) cc_final: -0.0328 (ttt-90) REVERT: g 108 ARG cc_start: 0.3149 (OUTLIER) cc_final: 0.1507 (mtt180) REVERT: g 110 ARG cc_start: 0.2859 (tpt170) cc_final: 0.2575 (ptm160) REVERT: g 143 MET cc_start: 0.1520 (ppp) cc_final: 0.0349 (mtm) REVERT: h 55 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5453 (mtmt) REVERT: m 31 LYS cc_start: 0.4804 (pttp) cc_final: 0.4357 (tppt) REVERT: o 26 GLU cc_start: 0.5998 (mt-10) cc_final: 0.5383 (mp0) REVERT: o 51 HIS cc_start: 0.7493 (t70) cc_final: 0.7169 (m90) REVERT: q 10 ARG cc_start: 0.7501 (tpp-160) cc_final: 0.7288 (tpp-160) REVERT: q 46 HIS cc_start: 0.5754 (OUTLIER) cc_final: 0.5193 (t70) REVERT: t 53 MET cc_start: 0.8462 (tmm) cc_final: 0.7604 (tpp) outliers start: 78 outliers final: 25 residues processed: 318 average time/residue: 0.8387 time to fit residues: 327.3004 Evaluate side-chains 228 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 203 PHE Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 41 TYR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 183 TYR Chi-restraints excluded: chain d residue 137 SER Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain f residue 9 MET Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain h residue 55 LYS Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 33 CYS Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 46 HIS Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 236 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 268 optimal weight: 0.7980 chunk 56 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 chunk 285 optimal weight: 7.9990 chunk 132 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 overall best weight: 6.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 GLN A 109 ASN A 212 GLN ** c 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 70 GLN d 119 HIS e 69 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN h 37 ASN o 51 HIS ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 73 HIS t 12 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.161866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.136218 restraints weight = 154218.685| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.87 r_work: 0.3855 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5666 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 51472 Z= 0.375 Angle : 0.838 15.378 77120 Z= 0.418 Chirality : 0.041 0.388 9873 Planarity : 0.007 0.087 4071 Dihedral : 23.692 179.643 26038 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 7.86 % Allowed : 21.30 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.99 (0.17), residues: 1800 helix: -3.41 (0.16), residues: 524 sheet: -1.66 (0.32), residues: 237 loop : -2.53 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG d 183 TYR 0.032 0.003 TYR r 69 PHE 0.026 0.003 PHE d 181 TRP 0.027 0.003 TRP c 200 HIS 0.013 0.003 HIS o 50 Details of bonding type rmsd covalent geometry : bond 0.00738 (51470) covalent geometry : angle 0.83838 (77120) hydrogen bonds : bond 0.08884 ( 546) hydrogen bonds : angle 4.86790 ( 1140) Misc. bond : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 266 time to evaluate : 0.987 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: A 60 TYR cc_start: 0.0277 (OUTLIER) cc_final: -0.0070 (m-10) REVERT: A 208 LEU cc_start: 0.7102 (pp) cc_final: 0.6752 (pt) REVERT: c 45 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6979 (pm20) REVERT: c 129 PHE cc_start: 0.5144 (OUTLIER) cc_final: 0.4380 (p90) REVERT: c 148 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7276 (mp) REVERT: c 190 THR cc_start: -0.0832 (p) cc_final: -0.1248 (m) REVERT: d 47 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8013 (pp) REVERT: d 123 MET cc_start: 0.8458 (mtt) cc_final: 0.7942 (mtp) REVERT: d 150 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7320 (pttm) REVERT: e 13 LYS cc_start: 0.8494 (ptmm) cc_final: 0.8079 (ptpp) REVERT: e 31 SER cc_start: 0.8715 (m) cc_final: 0.8304 (t) REVERT: e 64 GLU cc_start: 0.8459 (pm20) cc_final: 0.8185 (pm20) REVERT: e 102 THR cc_start: 0.9019 (m) cc_final: 0.8785 (p) REVERT: e 148 SER cc_start: 0.8615 (m) cc_final: 0.8305 (t) REVERT: e 151 MET cc_start: 0.8141 (ppp) cc_final: 0.7749 (ppp) REVERT: f 2 ARG cc_start: 0.6736 (mpp80) cc_final: 0.6439 (mtt180) REVERT: f 3 HIS cc_start: 0.7493 (m-70) cc_final: 0.7133 (m170) REVERT: f 38 ARG cc_start: 0.5647 (ptm160) cc_final: 0.5335 (ptm160) REVERT: f 42 TRP cc_start: 0.6691 (m100) cc_final: 0.6385 (m100) REVERT: f 49 TYR cc_start: 0.3251 (OUTLIER) cc_final: 0.1953 (p90) REVERT: f 62 MET cc_start: 0.8752 (ppp) cc_final: 0.7994 (ppp) REVERT: f 65 GLU cc_start: 0.7756 (mp0) cc_final: 0.7310 (mp0) REVERT: f 84 VAL cc_start: 0.6463 (t) cc_final: 0.6175 (p) REVERT: g 9 ARG cc_start: 0.0743 (mtt180) cc_final: 0.0026 (ttt-90) REVERT: g 108 ARG cc_start: 0.2343 (OUTLIER) cc_final: 0.1102 (mtt180) REVERT: g 110 ARG cc_start: 0.2835 (tpt170) cc_final: 0.2591 (mtp-110) REVERT: g 122 GLU cc_start: 0.4923 (mt-10) cc_final: 0.4473 (mm-30) REVERT: g 143 MET cc_start: 0.1697 (ppp) cc_final: 0.0400 (mtt) REVERT: h 46 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8065 (mt-10) REVERT: h 55 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6922 (mtmt) REVERT: h 59 GLU cc_start: 0.8435 (tt0) cc_final: 0.8104 (mm-30) REVERT: h 95 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8264 (ttp) REVERT: h 127 TYR cc_start: 0.8423 (m-10) cc_final: 0.8192 (m-10) REVERT: h 128 VAL cc_start: 0.8938 (t) cc_final: 0.8621 (p) REVERT: l 43 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7928 (tppt) REVERT: l 69 GLU cc_start: 0.7846 (mp0) cc_final: 0.7420 (mp0) REVERT: o 36 ILE cc_start: 0.7281 (mt) cc_final: 0.6867 (mt) REVERT: p 51 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7732 (ptp-110) REVERT: q 13 SER cc_start: 0.8640 (m) cc_final: 0.7837 (t) outliers start: 120 outliers final: 37 residues processed: 349 average time/residue: 0.7289 time to fit residues: 311.7131 Evaluate side-chains 241 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 194 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 60 TYR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain d residue 47 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 199 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain f residue 49 TYR Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 55 LYS Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 82 LEU Chi-restraints excluded: chain h residue 95 MET Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 56 ASP Chi-restraints excluded: chain r residue 71 ASP Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 22 SER Chi-restraints excluded: chain t residue 52 GLU Chi-restraints excluded: chain t residue 67 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 36 optimal weight: 40.0000 chunk 157 optimal weight: 30.0000 chunk 9 optimal weight: 40.0000 chunk 303 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 256 optimal weight: 5.9990 chunk 305 optimal weight: 0.0010 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 119 HIS e 60 GLN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4581 r_free = 0.4581 target = 0.172461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.147119 restraints weight = 157613.732| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.58 r_work: 0.3936 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 51472 Z= 0.135 Angle : 0.535 9.057 77120 Z= 0.273 Chirality : 0.032 0.328 9873 Planarity : 0.005 0.064 4071 Dihedral : 23.439 179.436 26038 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.91 % Allowed : 26.47 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.37 (0.18), residues: 1800 helix: -2.84 (0.19), residues: 511 sheet: -1.27 (0.33), residues: 236 loop : -2.20 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 80 TYR 0.023 0.002 TYR c 41 PHE 0.024 0.002 PHE A 146 TRP 0.019 0.001 TRP c 200 HIS 0.006 0.001 HIS l 76 Details of bonding type rmsd covalent geometry : bond 0.00267 (51470) covalent geometry : angle 0.53500 (77120) hydrogen bonds : bond 0.06371 ( 546) hydrogen bonds : angle 4.09058 ( 1140) Misc. bond : bond 0.00037 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 224 time to evaluate : 2.403 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: A 257 LEU cc_start: 0.4458 (OUTLIER) cc_final: 0.3816 (tm) REVERT: c 129 PHE cc_start: 0.5327 (OUTLIER) cc_final: 0.4256 (p90) REVERT: c 148 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7097 (mp) REVERT: c 150 VAL cc_start: 0.7232 (t) cc_final: 0.6958 (t) REVERT: c 190 THR cc_start: -0.0887 (p) cc_final: -0.1305 (m) REVERT: d 150 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7265 (pttm) REVERT: e 53 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7560 (mmm160) REVERT: e 54 GLU cc_start: 0.7917 (pm20) cc_final: 0.7598 (tp30) REVERT: e 60 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8109 (tp-100) REVERT: e 64 GLU cc_start: 0.8461 (pm20) cc_final: 0.8241 (pm20) REVERT: e 68 ARG cc_start: 0.8810 (mtm180) cc_final: 0.8549 (mtm-85) REVERT: e 92 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.8040 (mpp80) REVERT: g 9 ARG cc_start: 0.0781 (mtt180) cc_final: -0.0006 (ttt-90) REVERT: g 110 ARG cc_start: 0.2803 (tpt170) cc_final: 0.2577 (ptm160) REVERT: g 122 GLU cc_start: 0.4877 (mt-10) cc_final: 0.4010 (mp0) REVERT: g 136 LYS cc_start: 0.6708 (mmmt) cc_final: 0.6453 (mttp) REVERT: g 143 MET cc_start: 0.1508 (ppp) cc_final: 0.0215 (mtm) REVERT: h 2 MET cc_start: 0.7652 (tpp) cc_final: 0.7301 (tpt) REVERT: h 59 GLU cc_start: 0.8530 (tt0) cc_final: 0.8254 (mm-30) REVERT: h 63 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7846 (ptpt) REVERT: h 95 MET cc_start: 0.8328 (mmm) cc_final: 0.8116 (mtp) REVERT: h 100 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8084 (pt) REVERT: h 128 VAL cc_start: 0.9013 (t) cc_final: 0.8811 (t) REVERT: l 76 HIS cc_start: 0.8902 (m-70) cc_final: 0.8544 (m-70) REVERT: o 26 GLU cc_start: 0.7422 (mt-10) cc_final: 0.6768 (mp0) REVERT: o 36 ILE cc_start: 0.7082 (mt) cc_final: 0.6793 (mt) REVERT: o 53 ARG cc_start: 0.6597 (mtp-110) cc_final: 0.6332 (mmp-170) REVERT: q 13 SER cc_start: 0.8517 (m) cc_final: 0.7670 (t) REVERT: q 15 LYS cc_start: 0.9338 (mmtt) cc_final: 0.9038 (mtmt) REVERT: t 7 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9114 (ttpt) outliers start: 75 outliers final: 21 residues processed: 274 average time/residue: 0.6705 time to fit residues: 227.4758 Evaluate side-chains 220 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 92 ARG Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 108 ARG Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 63 LYS Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain t residue 7 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 31 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 130 optimal weight: 40.0000 chunk 21 optimal weight: 0.7980 chunk 230 optimal weight: 8.9990 chunk 262 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 122 GLN d 40 HIS ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 46 GLN ** f 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 147 ASN ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 44 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.133432 restraints weight = 157324.602| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.61 r_work: 0.3736 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5452 moved from start: 0.8240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 51472 Z= 0.333 Angle : 0.766 16.730 77120 Z= 0.386 Chirality : 0.040 0.308 9873 Planarity : 0.006 0.070 4071 Dihedral : 23.950 179.582 26038 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.94 % Favored : 92.00 % Rotamer: Outliers : 6.95 % Allowed : 26.02 % Favored : 67.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.57 (0.17), residues: 1800 helix: -2.92 (0.17), residues: 533 sheet: -1.30 (0.30), residues: 279 loop : -2.39 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG o 63 TYR 0.027 0.003 TYR r 31 PHE 0.028 0.003 PHE A 146 TRP 0.019 0.002 TRP c 200 HIS 0.011 0.002 HIS t 67 Details of bonding type rmsd covalent geometry : bond 0.00651 (51470) covalent geometry : angle 0.76639 (77120) hydrogen bonds : bond 0.09255 ( 546) hydrogen bonds : angle 4.54738 ( 1140) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 221 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 TYR cc_start: 0.5569 (t80) cc_final: 0.5294 (t80) REVERT: A 39 ARG cc_start: 0.4591 (tpp-160) cc_final: 0.4184 (tpp-160) REVERT: A 230 VAL cc_start: 0.3365 (t) cc_final: 0.2882 (m) REVERT: c 17 TRP cc_start: 0.4926 (m100) cc_final: 0.4044 (m-90) REVERT: c 125 ARG cc_start: 0.8021 (mtt180) cc_final: 0.7462 (tpt90) REVERT: c 148 ILE cc_start: 0.7214 (OUTLIER) cc_final: 0.6985 (mp) REVERT: d 17 ASP cc_start: 0.8522 (t0) cc_final: 0.8246 (t0) REVERT: d 150 LYS cc_start: 0.7793 (mmtt) cc_final: 0.7398 (pttm) REVERT: d 182 LYS cc_start: 0.8294 (tmtt) cc_final: 0.7993 (tttp) REVERT: d 194 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7384 (mt) REVERT: e 54 GLU cc_start: 0.8075 (pm20) cc_final: 0.7841 (tp30) REVERT: e 68 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8481 (mtm-85) REVERT: f 3 HIS cc_start: 0.6963 (m-70) cc_final: 0.6747 (m-70) REVERT: f 44 ARG cc_start: 0.8457 (mtm-85) cc_final: 0.7260 (ptm160) REVERT: f 62 MET cc_start: 0.8482 (ppp) cc_final: 0.8188 (ppp) REVERT: f 63 ASN cc_start: 0.7918 (OUTLIER) cc_final: 0.7493 (m110) REVERT: f 84 VAL cc_start: 0.6766 (OUTLIER) cc_final: 0.6526 (p) REVERT: g 9 ARG cc_start: 0.1092 (mtt180) cc_final: 0.0151 (ttt180) REVERT: g 143 MET cc_start: 0.1823 (ppp) cc_final: 0.0589 (mtt) REVERT: h 100 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8147 (tt) REVERT: l 17 LYS cc_start: 0.8972 (tppp) cc_final: 0.8313 (tttt) REVERT: l 43 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8097 (tppt) REVERT: l 69 GLU cc_start: 0.7926 (mp0) cc_final: 0.7389 (mp0) REVERT: l 74 GLN cc_start: 0.8534 (mm110) cc_final: 0.8290 (mm110) REVERT: m 4 ILE cc_start: 0.7782 (mm) cc_final: 0.7454 (pp) REVERT: o 26 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7574 (mp0) REVERT: o 42 HIS cc_start: 0.4979 (OUTLIER) cc_final: 0.3544 (t70) REVERT: o 45 GLU cc_start: 0.5406 (pm20) cc_final: 0.5204 (pt0) REVERT: o 53 ARG cc_start: 0.7981 (mtp-110) cc_final: 0.6578 (mmp-170) REVERT: p 51 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7523 (ptp-110) REVERT: p 76 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8420 (ttpt) REVERT: q 13 SER cc_start: 0.8558 (m) cc_final: 0.7914 (t) REVERT: t 7 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9155 (ttpt) outliers start: 106 outliers final: 33 residues processed: 288 average time/residue: 0.4842 time to fit residues: 174.9247 Evaluate side-chains 241 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 148 ILE Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 194 ILE Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain e residue 68 ARG Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain g residue 114 SER Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 100 ILE Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain o residue 42 HIS Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain p residue 76 LYS Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 79 optimal weight: 10.0000 chunk 10 optimal weight: 40.0000 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 20.0000 chunk 247 optimal weight: 20.0000 chunk 200 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 152 optimal weight: 30.0000 chunk 300 optimal weight: 0.0570 chunk 230 optimal weight: 4.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 115 GLN d 130 ASN e 60 GLN e 69 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 HIS f 46 GLN f 55 HIS f 58 HIS f 68 GLN h 37 ASN ** o 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 73 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.166172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.140009 restraints weight = 158414.610| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.55 r_work: 0.3780 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 moved from start: 0.8392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 51472 Z= 0.209 Angle : 0.584 10.513 77120 Z= 0.298 Chirality : 0.034 0.266 9873 Planarity : 0.005 0.050 4071 Dihedral : 23.752 179.866 26034 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 5.90 % Allowed : 27.65 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.22 (0.18), residues: 1800 helix: -2.52 (0.19), residues: 541 sheet: -1.13 (0.32), residues: 272 loop : -2.23 (0.18), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG d 80 TYR 0.025 0.002 TYR r 31 PHE 0.029 0.002 PHE f 8 TRP 0.019 0.001 TRP c 200 HIS 0.008 0.001 HIS t 67 Details of bonding type rmsd covalent geometry : bond 0.00407 (51470) covalent geometry : angle 0.58379 (77120) hydrogen bonds : bond 0.07026 ( 546) hydrogen bonds : angle 4.18228 ( 1140) Misc. bond : bond 0.00093 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 210 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 17 TRP cc_start: 0.4951 (m100) cc_final: 0.4106 (m-90) REVERT: d 150 LYS cc_start: 0.7762 (mmtt) cc_final: 0.7340 (pttm) REVERT: e 42 ASN cc_start: 0.8436 (p0) cc_final: 0.8162 (p0) REVERT: e 51 LYS cc_start: 0.8090 (ttpp) cc_final: 0.7713 (mtpp) REVERT: e 53 ARG cc_start: 0.7791 (mmm160) cc_final: 0.7519 (mmm160) REVERT: e 68 ARG cc_start: 0.8824 (mtm180) cc_final: 0.8612 (mtm-85) REVERT: e 150 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8375 (pp20) REVERT: f 3 HIS cc_start: 0.7031 (m-70) cc_final: 0.6757 (m170) REVERT: f 44 ARG cc_start: 0.8547 (mtm-85) cc_final: 0.7292 (ptm-80) REVERT: f 62 MET cc_start: 0.8500 (ppp) cc_final: 0.8271 (ppp) REVERT: f 63 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7779 (m-40) REVERT: f 65 GLU cc_start: 0.7718 (mp0) cc_final: 0.7289 (mp0) REVERT: g 9 ARG cc_start: 0.1294 (mtt180) cc_final: 0.0206 (ttt180) REVERT: g 143 MET cc_start: 0.1901 (ppp) cc_final: 0.0608 (mtm) REVERT: h 66 GLN cc_start: 0.9033 (mm-40) cc_final: 0.8768 (mm-40) REVERT: l 17 LYS cc_start: 0.8963 (tppp) cc_final: 0.8375 (tttt) REVERT: l 37 TYR cc_start: 0.8256 (p90) cc_final: 0.8052 (p90) REVERT: l 43 LYS cc_start: 0.8635 (pttp) cc_final: 0.7939 (tppt) REVERT: l 69 GLU cc_start: 0.7809 (mp0) cc_final: 0.7405 (mp0) REVERT: o 26 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7541 (mp0) REVERT: o 42 HIS cc_start: 0.5663 (OUTLIER) cc_final: 0.4471 (t70) REVERT: o 48 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6225 (mmmm) REVERT: o 53 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.6710 (mmp-170) REVERT: o 63 ARG cc_start: 0.7473 (mmp80) cc_final: 0.6883 (mpt-90) REVERT: o 74 ASP cc_start: 0.6101 (t0) cc_final: 0.5893 (t0) REVERT: p 51 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7773 (ptp-170) REVERT: q 13 SER cc_start: 0.8583 (m) cc_final: 0.7837 (t) REVERT: q 56 ASP cc_start: 0.7813 (m-30) cc_final: 0.7495 (m-30) REVERT: q 80 LYS cc_start: 0.8877 (tttt) cc_final: 0.8231 (tptm) REVERT: t 7 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9189 (ttpt) REVERT: t 9 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.5705 (tpt170) outliers start: 90 outliers final: 37 residues processed: 272 average time/residue: 0.5024 time to fit residues: 169.9783 Evaluate side-chains 230 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 115 GLU Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 150 GLU Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 55 HIS Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain o residue 42 HIS Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 99 optimal weight: 10.0000 chunk 223 optimal weight: 0.0020 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 249 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 258 optimal weight: 50.0000 chunk 162 optimal weight: 40.0000 chunk 214 optimal weight: 0.8980 chunk 172 optimal weight: 20.0000 overall best weight: 5.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 115 GLN d 130 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 HIS h 37 ASN o 42 HIS ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.158051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.133417 restraints weight = 155936.983| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.55 r_work: 0.3703 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.8984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 51472 Z= 0.304 Angle : 0.670 9.388 77120 Z= 0.339 Chirality : 0.037 0.346 9873 Planarity : 0.005 0.051 4071 Dihedral : 23.903 179.775 26034 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.28 % Favored : 92.67 % Rotamer: Outliers : 5.96 % Allowed : 27.85 % Favored : 66.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.31 (0.18), residues: 1800 helix: -2.46 (0.19), residues: 558 sheet: -1.23 (0.32), residues: 269 loop : -2.34 (0.18), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A 39 TYR 0.038 0.002 TYR r 31 PHE 0.020 0.002 PHE p 32 TRP 0.019 0.002 TRP c 200 HIS 0.019 0.002 HIS f 55 Details of bonding type rmsd covalent geometry : bond 0.00596 (51470) covalent geometry : angle 0.66980 (77120) hydrogen bonds : bond 0.08092 ( 546) hydrogen bonds : angle 4.39258 ( 1140) Misc. bond : bond 0.00126 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 216 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.4199 (tpp-160) cc_final: 0.3920 (tpp-160) REVERT: c 2 GLN cc_start: 0.7831 (mt0) cc_final: 0.7349 (mm-40) REVERT: c 17 TRP cc_start: 0.4829 (m100) cc_final: 0.4048 (m-90) REVERT: c 129 PHE cc_start: 0.5469 (OUTLIER) cc_final: 0.4527 (p90) REVERT: c 190 THR cc_start: 0.0110 (OUTLIER) cc_final: -0.0660 (m) REVERT: d 150 LYS cc_start: 0.7757 (mmtt) cc_final: 0.7385 (pttm) REVERT: d 205 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7812 (ttmm) REVERT: f 3 HIS cc_start: 0.6911 (m-70) cc_final: 0.6655 (m170) REVERT: f 44 ARG cc_start: 0.8661 (mtm-85) cc_final: 0.7450 (ptm160) REVERT: f 49 TYR cc_start: 0.2074 (OUTLIER) cc_final: 0.0385 (p90) REVERT: f 62 MET cc_start: 0.8397 (ppp) cc_final: 0.8175 (ppp) REVERT: f 63 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7726 (m-40) REVERT: f 65 GLU cc_start: 0.7637 (mp0) cc_final: 0.7298 (mp0) REVERT: g 9 ARG cc_start: 0.1374 (mtt180) cc_final: 0.0058 (ttt-90) REVERT: g 143 MET cc_start: 0.2285 (ppp) cc_final: 0.0963 (mtm) REVERT: h 66 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8969 (mm110) REVERT: h 95 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.7966 (ttp) REVERT: l 17 LYS cc_start: 0.8906 (tppp) cc_final: 0.8312 (tttt) REVERT: l 37 TYR cc_start: 0.8091 (p90) cc_final: 0.7862 (p90) REVERT: l 43 LYS cc_start: 0.8713 (pttp) cc_final: 0.7974 (tppt) REVERT: l 69 GLU cc_start: 0.7886 (mp0) cc_final: 0.7448 (mp0) REVERT: o 42 HIS cc_start: 0.5673 (OUTLIER) cc_final: 0.5373 (t-170) REVERT: o 48 LYS cc_start: 0.7228 (OUTLIER) cc_final: 0.6257 (mmmm) REVERT: o 54 ARG cc_start: 0.8242 (ttt90) cc_final: 0.8019 (ttt-90) REVERT: o 63 ARG cc_start: 0.7288 (mmp80) cc_final: 0.6285 (mtt90) REVERT: o 64 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7197 (mpt180) REVERT: o 74 ASP cc_start: 0.6238 (t0) cc_final: 0.5970 (t0) REVERT: p 51 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7589 (ptp-170) REVERT: q 13 SER cc_start: 0.8354 (m) cc_final: 0.7680 (t) REVERT: q 56 ASP cc_start: 0.7653 (m-30) cc_final: 0.7009 (m-30) REVERT: q 80 LYS cc_start: 0.8772 (tttt) cc_final: 0.8022 (tptt) REVERT: t 7 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9042 (ttpt) REVERT: t 9 ARG cc_start: 0.7273 (ttp-170) cc_final: 0.5417 (tpt170) outliers start: 91 outliers final: 42 residues processed: 279 average time/residue: 0.4921 time to fit residues: 169.8539 Evaluate side-chains 255 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 204 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 274 MET Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 143 LEU Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain d residue 204 SER Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 120 HIS Chi-restraints excluded: chain e residue 151 MET Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 49 TYR Chi-restraints excluded: chain f residue 63 ASN Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 89 ASP Chi-restraints excluded: chain h residue 95 MET Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain o residue 42 HIS Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 146 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 190 optimal weight: 40.0000 chunk 309 optimal weight: 6.9990 chunk 248 optimal weight: 0.0370 chunk 41 optimal weight: 8.9990 chunk 13 optimal weight: 40.0000 overall best weight: 5.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN e 69 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 27 ASN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 73 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.155918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.131297 restraints weight = 154281.875| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.49 r_work: 0.3702 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5249 moved from start: 0.9511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 51472 Z= 0.295 Angle : 0.667 12.644 77120 Z= 0.338 Chirality : 0.037 0.241 9873 Planarity : 0.005 0.076 4071 Dihedral : 24.008 179.967 26034 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.83 % Favored : 93.11 % Rotamer: Outliers : 5.77 % Allowed : 29.10 % Favored : 65.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.33 (0.18), residues: 1800 helix: -2.45 (0.19), residues: 579 sheet: -1.29 (0.33), residues: 269 loop : -2.33 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 39 TYR 0.025 0.002 TYR f 59 PHE 0.041 0.002 PHE o 43 TRP 0.022 0.002 TRP c 21 HIS 0.053 0.002 HIS o 42 Details of bonding type rmsd covalent geometry : bond 0.00576 (51470) covalent geometry : angle 0.66684 (77120) hydrogen bonds : bond 0.08074 ( 546) hydrogen bonds : angle 4.46417 ( 1140) Misc. bond : bond 0.00156 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 215 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.4002 (tpp-160) cc_final: 0.3030 (tpp-160) REVERT: A 225 LYS cc_start: 0.4541 (tttt) cc_final: 0.4153 (pmmt) REVERT: c 2 GLN cc_start: 0.8051 (mt0) cc_final: 0.7552 (mm-40) REVERT: c 15 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5169 (ptmm) REVERT: c 17 TRP cc_start: 0.4570 (m100) cc_final: 0.3928 (m-90) REVERT: c 125 ARG cc_start: 0.7730 (mtt180) cc_final: 0.7480 (tpt90) REVERT: c 190 THR cc_start: 0.0394 (OUTLIER) cc_final: -0.0541 (m) REVERT: d 150 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7197 (pttm) REVERT: d 205 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7804 (ttmm) REVERT: e 31 SER cc_start: 0.8383 (m) cc_final: 0.8029 (t) REVERT: e 51 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7208 (mtpp) REVERT: f 44 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8167 (mtp-110) REVERT: f 65 GLU cc_start: 0.7570 (mp0) cc_final: 0.7188 (mp0) REVERT: g 9 ARG cc_start: 0.1828 (mtt180) cc_final: 0.0387 (ttp-170) REVERT: g 27 ASN cc_start: 0.5903 (OUTLIER) cc_final: 0.5678 (t0) REVERT: g 143 MET cc_start: 0.2545 (ppp) cc_final: 0.1175 (mtm) REVERT: h 57 GLU cc_start: 0.8688 (tp30) cc_final: 0.8314 (tm-30) REVERT: h 95 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7878 (ttp) REVERT: l 17 LYS cc_start: 0.8848 (tppp) cc_final: 0.8325 (tttt) REVERT: l 43 LYS cc_start: 0.8718 (pttp) cc_final: 0.7968 (tppt) REVERT: l 69 GLU cc_start: 0.7803 (mp0) cc_final: 0.7393 (mp0) REVERT: l 75 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7844 (mm-30) REVERT: o 26 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7799 (mp0) REVERT: o 54 ARG cc_start: 0.8230 (ttt90) cc_final: 0.7961 (ttt-90) REVERT: o 63 ARG cc_start: 0.7253 (mmp80) cc_final: 0.6264 (mtt90) REVERT: o 64 ARG cc_start: 0.7602 (mtt180) cc_final: 0.7214 (mpt180) REVERT: o 74 ASP cc_start: 0.6599 (t0) cc_final: 0.6321 (t0) REVERT: p 51 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7597 (ptp-170) REVERT: p 55 ASP cc_start: 0.9306 (t0) cc_final: 0.9078 (t0) REVERT: q 3 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7815 (tptp) REVERT: q 13 SER cc_start: 0.8370 (m) cc_final: 0.7657 (t) REVERT: q 42 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8473 (mtmt) REVERT: q 47 ASP cc_start: 0.8268 (p0) cc_final: 0.8029 (p0) REVERT: q 56 ASP cc_start: 0.7683 (m-30) cc_final: 0.7178 (m-30) REVERT: q 80 LYS cc_start: 0.8748 (tttt) cc_final: 0.8007 (tptm) REVERT: r 30 ASN cc_start: 0.9328 (m-40) cc_final: 0.9096 (p0) REVERT: t 7 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9017 (ttpt) REVERT: t 9 ARG cc_start: 0.7264 (ttp-170) cc_final: 0.5485 (tpp80) outliers start: 88 outliers final: 40 residues processed: 280 average time/residue: 0.4937 time to fit residues: 169.6785 Evaluate side-chains 243 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 196 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 15 LYS Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 190 LEU Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain g residue 27 ASN Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain g residue 63 VAL Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 95 MET Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 48 GLU Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 3 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 160 optimal weight: 40.0000 chunk 279 optimal weight: 6.9990 chunk 13 optimal weight: 50.0000 chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 217 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 GLN e 69 ASN e 72 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 HIS e 121 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.157017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.132623 restraints weight = 155478.561| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.51 r_work: 0.3700 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5229 moved from start: 1.0013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 51472 Z= 0.311 Angle : 0.699 11.388 77120 Z= 0.353 Chirality : 0.038 0.396 9873 Planarity : 0.006 0.076 4071 Dihedral : 24.127 179.902 26034 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 4.65 % Allowed : 30.80 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.18), residues: 1800 helix: -2.47 (0.19), residues: 596 sheet: -1.38 (0.32), residues: 284 loop : -2.44 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG o 72 TYR 0.047 0.003 TYR r 31 PHE 0.017 0.002 PHE p 32 TRP 0.018 0.002 TRP c 200 HIS 0.020 0.002 HIS f 3 Details of bonding type rmsd covalent geometry : bond 0.00610 (51470) covalent geometry : angle 0.69872 (77120) hydrogen bonds : bond 0.08608 ( 546) hydrogen bonds : angle 4.51696 ( 1140) Misc. bond : bond 0.00185 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 202 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.4401 (tttt) cc_final: 0.4080 (pmmt) REVERT: c 2 GLN cc_start: 0.8168 (mt0) cc_final: 0.7831 (mm-40) REVERT: c 15 LYS cc_start: 0.5718 (OUTLIER) cc_final: 0.5271 (ptmm) REVERT: c 17 TRP cc_start: 0.4304 (m100) cc_final: 0.3736 (m-90) REVERT: c 125 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7479 (tpt90) REVERT: c 129 PHE cc_start: 0.5451 (OUTLIER) cc_final: 0.4518 (p90) REVERT: c 178 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.7107 (ptm-80) REVERT: c 190 THR cc_start: 0.0380 (OUTLIER) cc_final: -0.0598 (m) REVERT: d 150 LYS cc_start: 0.7604 (mmtt) cc_final: 0.7111 (pttm) REVERT: d 205 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7808 (ttmm) REVERT: f 44 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8162 (mtp-110) REVERT: g 9 ARG cc_start: 0.1820 (mtt180) cc_final: 0.0283 (ttp-170) REVERT: g 143 MET cc_start: 0.2736 (ppp) cc_final: 0.1417 (mtm) REVERT: h 95 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7914 (ttp) REVERT: l 17 LYS cc_start: 0.8933 (tppp) cc_final: 0.8428 (tmtt) REVERT: l 43 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7975 (tppt) REVERT: l 69 GLU cc_start: 0.7917 (mp0) cc_final: 0.7401 (mp0) REVERT: l 75 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7740 (mm-30) REVERT: o 26 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7700 (mp0) REVERT: o 47 LYS cc_start: 0.7574 (mttt) cc_final: 0.7280 (mtmp) REVERT: o 48 LYS cc_start: 0.7718 (mmmt) cc_final: 0.6266 (mtpt) REVERT: o 54 ARG cc_start: 0.8368 (ttt90) cc_final: 0.8106 (ttt-90) REVERT: o 63 ARG cc_start: 0.7252 (mmp80) cc_final: 0.6340 (mtt90) REVERT: o 64 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7348 (mpt180) REVERT: o 74 ASP cc_start: 0.6710 (t0) cc_final: 0.6452 (t0) REVERT: p 51 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7525 (ptp-170) REVERT: p 55 ASP cc_start: 0.9313 (t0) cc_final: 0.9102 (t0) REVERT: q 3 LYS cc_start: 0.8192 (mtpt) cc_final: 0.7886 (tptp) REVERT: q 13 SER cc_start: 0.8367 (m) cc_final: 0.7809 (t) REVERT: q 42 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8478 (mtmt) REVERT: q 47 ASP cc_start: 0.8229 (p0) cc_final: 0.7921 (p0) REVERT: q 56 ASP cc_start: 0.7680 (m-30) cc_final: 0.7060 (m-30) REVERT: q 80 LYS cc_start: 0.8747 (tttt) cc_final: 0.7969 (tptt) REVERT: r 60 ARG cc_start: 0.3901 (mtt180) cc_final: 0.3662 (tpt-90) REVERT: t 7 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8999 (ttpt) REVERT: t 9 ARG cc_start: 0.7268 (ttp-170) cc_final: 0.5522 (tpt170) REVERT: t 14 GLU cc_start: 0.7642 (pp20) cc_final: 0.7423 (pp20) outliers start: 71 outliers final: 40 residues processed: 256 average time/residue: 0.4832 time to fit residues: 152.3753 Evaluate side-chains 240 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 15 LYS Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 115 GLN Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 69 ASN Chi-restraints excluded: chain e residue 141 ASP Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain f residue 88 MET Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 95 MET Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain q residue 42 LYS Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 62 optimal weight: 10.0000 chunk 86 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 158 optimal weight: 40.0000 chunk 19 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 257 optimal weight: 30.0000 chunk 32 optimal weight: 6.9990 chunk 176 optimal weight: 30.0000 chunk 139 optimal weight: 20.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 69 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.157802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.133434 restraints weight = 156679.183| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.44 r_work: 0.3709 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5241 moved from start: 1.0105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 51472 Z= 0.251 Angle : 0.652 12.647 77120 Z= 0.330 Chirality : 0.036 0.387 9873 Planarity : 0.005 0.072 4071 Dihedral : 24.117 179.836 26034 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 4.00 % Allowed : 31.59 % Favored : 64.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.39 (0.18), residues: 1800 helix: -2.41 (0.19), residues: 601 sheet: -1.30 (0.32), residues: 278 loop : -2.44 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 39 TYR 0.033 0.002 TYR f 59 PHE 0.029 0.002 PHE f 8 TRP 0.019 0.002 TRP c 200 HIS 0.014 0.002 HIS f 3 Details of bonding type rmsd covalent geometry : bond 0.00494 (51470) covalent geometry : angle 0.65248 (77120) hydrogen bonds : bond 0.08073 ( 546) hydrogen bonds : angle 4.37027 ( 1140) Misc. bond : bond 0.00168 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3600 Ramachandran restraints generated. 1800 Oldfield, 0 Emsley, 1800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 202 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.4459 (tttt) cc_final: 0.4101 (pmmt) REVERT: c 2 GLN cc_start: 0.8169 (mt0) cc_final: 0.7720 (mm-40) REVERT: c 15 LYS cc_start: 0.5800 (OUTLIER) cc_final: 0.5371 (ptmm) REVERT: c 17 TRP cc_start: 0.4258 (m100) cc_final: 0.3701 (m-90) REVERT: c 125 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7477 (tpt90) REVERT: c 129 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.4531 (p90) REVERT: c 178 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.7118 (ptm-80) REVERT: c 190 THR cc_start: 0.0518 (OUTLIER) cc_final: -0.0464 (m) REVERT: d 150 LYS cc_start: 0.7594 (mmtt) cc_final: 0.7095 (pttm) REVERT: d 205 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7822 (ttmm) REVERT: e 51 LYS cc_start: 0.7805 (ttpp) cc_final: 0.7224 (mtpp) REVERT: f 44 ARG cc_start: 0.8611 (mtm-85) cc_final: 0.8202 (mtp-110) REVERT: f 49 TYR cc_start: 0.1799 (OUTLIER) cc_final: -0.0095 (p90) REVERT: g 9 ARG cc_start: 0.1887 (mtt180) cc_final: 0.0352 (ttt-90) REVERT: g 143 MET cc_start: 0.2893 (ppp) cc_final: 0.1559 (mtm) REVERT: h 57 GLU cc_start: 0.8599 (tp30) cc_final: 0.8306 (tm-30) REVERT: h 95 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7854 (ttp) REVERT: l 17 LYS cc_start: 0.8903 (tppp) cc_final: 0.8456 (tttt) REVERT: l 19 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7898 (t0) REVERT: l 37 TYR cc_start: 0.8156 (p90) cc_final: 0.7898 (p90) REVERT: l 43 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7952 (tppt) REVERT: l 69 GLU cc_start: 0.7797 (mp0) cc_final: 0.7394 (mp0) REVERT: l 104 SER cc_start: 0.8836 (t) cc_final: 0.8043 (p) REVERT: o 26 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7825 (mp0) REVERT: o 47 LYS cc_start: 0.7810 (mttt) cc_final: 0.7402 (mtmp) REVERT: o 48 LYS cc_start: 0.8003 (mmmt) cc_final: 0.6501 (mtpt) REVERT: o 63 ARG cc_start: 0.7269 (mmp80) cc_final: 0.6349 (mtt90) REVERT: o 64 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7383 (mpt180) REVERT: o 72 ARG cc_start: 0.8798 (mtm110) cc_final: 0.8208 (mtm-85) REVERT: o 74 ASP cc_start: 0.6704 (t0) cc_final: 0.6391 (t0) REVERT: p 51 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7574 (ptp-170) REVERT: p 55 ASP cc_start: 0.9311 (t0) cc_final: 0.9095 (t0) REVERT: q 3 LYS cc_start: 0.8195 (mtpt) cc_final: 0.7893 (tptp) REVERT: q 13 SER cc_start: 0.8407 (m) cc_final: 0.7860 (t) REVERT: q 47 ASP cc_start: 0.8087 (p0) cc_final: 0.7824 (p0) REVERT: q 56 ASP cc_start: 0.7696 (m-30) cc_final: 0.7218 (m-30) REVERT: q 80 LYS cc_start: 0.8719 (tttt) cc_final: 0.7995 (tptm) REVERT: r 60 ARG cc_start: 0.4003 (mtt180) cc_final: 0.3735 (tpt-90) REVERT: t 7 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9016 (ttpt) REVERT: t 9 ARG cc_start: 0.7255 (ttp-170) cc_final: 0.5570 (tpp80) outliers start: 61 outliers final: 40 residues processed: 245 average time/residue: 0.4871 time to fit residues: 146.3260 Evaluate side-chains 241 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 15 LYS Chi-restraints excluded: chain c residue 22 PHE Chi-restraints excluded: chain c residue 38 VAL Chi-restraints excluded: chain c residue 129 PHE Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 4 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 29 ILE Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 35 LEU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 55 VAL Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 39 LEU Chi-restraints excluded: chain f residue 41 ASP Chi-restraints excluded: chain f residue 49 TYR Chi-restraints excluded: chain f residue 76 THR Chi-restraints excluded: chain g residue 37 THR Chi-restraints excluded: chain h residue 25 THR Chi-restraints excluded: chain h residue 28 SER Chi-restraints excluded: chain h residue 33 VAL Chi-restraints excluded: chain h residue 54 THR Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 95 MET Chi-restraints excluded: chain h residue 110 MET Chi-restraints excluded: chain l residue 3 VAL Chi-restraints excluded: chain l residue 19 ASN Chi-restraints excluded: chain l residue 32 VAL Chi-restraints excluded: chain l residue 43 LYS Chi-restraints excluded: chain l residue 61 GLU Chi-restraints excluded: chain l residue 63 THR Chi-restraints excluded: chain l residue 86 VAL Chi-restraints excluded: chain l residue 101 LEU Chi-restraints excluded: chain o residue 36 ILE Chi-restraints excluded: chain p residue 24 SER Chi-restraints excluded: chain p residue 51 ARG Chi-restraints excluded: chain p residue 61 VAL Chi-restraints excluded: chain q residue 43 LEU Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain t residue 3 ILE Chi-restraints excluded: chain t residue 7 LYS Chi-restraints excluded: chain t residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 236 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 176 optimal weight: 30.0000 chunk 63 optimal weight: 7.9990 chunk 162 optimal weight: 40.0000 chunk 205 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 221 optimal weight: 4.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 ASN ** e 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 49 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.154817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.129942 restraints weight = 149674.997| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.87 r_work: 0.3658 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5259 moved from start: 1.0405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 51472 Z= 0.254 Angle : 0.659 13.404 77120 Z= 0.332 Chirality : 0.036 0.312 9873 Planarity : 0.005 0.052 4071 Dihedral : 24.141 179.484 26034 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 4.13 % Allowed : 31.91 % Favored : 63.96 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.39 (0.18), residues: 1800 helix: -2.42 (0.19), residues: 615 sheet: -1.26 (0.33), residues: 268 loop : -2.43 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 39 TYR 0.048 0.003 TYR r 31 PHE 0.048 0.002 PHE h 65 TRP 0.018 0.001 TRP c 200 HIS 0.010 0.001 HIS f 3 Details of bonding type rmsd covalent geometry : bond 0.00502 (51470) covalent geometry : angle 0.65861 (77120) hydrogen bonds : bond 0.08202 ( 546) hydrogen bonds : angle 4.32824 ( 1140) Misc. bond : bond 0.00148 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11051.24 seconds wall clock time: 188 minutes 36.15 seconds (11316.15 seconds total)