Starting phenix.real_space_refine on Sun Jan 26 02:29:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zvi_11457/01_2025/6zvi_11457.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zvi_11457/01_2025/6zvi_11457.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/6zvi_11457/01_2025/6zvi_11457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zvi_11457/01_2025/6zvi_11457.map" model { file = "/net/cci-nas-00/data/ceres_data/6zvi_11457/01_2025/6zvi_11457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zvi_11457/01_2025/6zvi_11457.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1945 5.49 5 S 87 5.16 5 C 42916 2.51 5 N 14524 2.21 5 O 20614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 283 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 80088 Number of models: 1 Model: "" Number of chains: 40 Chain: "d" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1620 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 62} Chain: "e" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 33, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 66} Chain: "f" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 724 Classifications: {'RNA': 35} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 8, 'rna3p_pur': 7, 'rna3p_pyr': 17} Link IDs: {'rna2p': 10, 'rna3p': 24} Chain breaks: 1 Chain: "h" Number of atoms: 37455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1758, 37455 Classifications: {'RNA': 1758} Modifications used: {'rna2p_pur': 160, 'rna2p_pyr': 159, 'rna3p_pur': 763, 'rna3p_pyr': 676} Link IDs: {'rna2p': 318, 'rna3p': 1439} Chain breaks: 3 Chain: "i" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1583 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 189} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "j" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain: "k" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1635 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 13, 'TRANS': 203} Chain: "l" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1734 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 9, 'TRANS': 213} Chain: "m" Number of atoms: 2068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2068 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 12, 'TRANS': 247} Chain: "n" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1609 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 8, 'TRANS': 197} Chain: "o" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1755 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "p" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1486 Classifications: {'peptide': 185} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 172} Chain: "q" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1489 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 4, 'TRANS': 183} Chain breaks: 1 Chain: "r" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1494 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 8, 'TRANS': 176} Chain: "s" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 741 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 88} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "t" Number of atoms: 1168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1168 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 8, 'TRANS': 137} Chain: "u" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 890 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 121} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "v" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1192 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 7, 'TRANS': 142} Chain: "x" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 939 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "y" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1105 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "z" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "A" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1192 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "B" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 5, 'TRANS': 137} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 805 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 5, 'TRANS': 95} Chain: "D" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 684 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "E" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1021 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 1, 'TRANS': 125} Chain: "H" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1121 Classifications: {'peptide': 144} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 137} Chain: "I" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1073 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "J" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 558 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "L" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "N" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 497 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "P" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 370 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 3, 'TRANS': 42} Chain: "Q" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 556 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 69} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2403 Classifications: {'peptide': 313} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 304} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "T" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 870 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "O" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 442 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "w" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 949 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "K" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 769 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 6, 'TRANS': 90} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 72905 SG CYS L 37 131.695 137.283 13.608 1.00 84.30 S ATOM 73040 SG CYS L 56 131.313 138.938 16.262 1.00 81.20 S ATOM 78219 SG CYS O 39 86.835 63.630 119.914 1.00 30.18 S Time building chain proxies: 31.89, per 1000 atoms: 0.40 Number of scatterers: 80088 At special positions: 0 Unit cell: (238.275, 224.508, 201.21, 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) Zn 2 29.99 S 87 16.00 P 1945 15.00 O 20614 8.00 N 14524 7.00 C 42916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.07 Conformation dependent library (CDL) restraints added in 4.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 56 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 37 " pdb=" ZN O 101 " pdb="ZN ZN O 101 " - pdb=" SG CYS O 39 " 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9146 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 58 sheets defined 34.1% alpha, 17.8% beta 547 base pairs and 960 stacking pairs defined. Time for finding SS restraints: 26.95 Creating SS restraints... Processing helix chain 'i' and resid 4 through 8 removed outlier: 3.900A pdb=" N ASP i 8 " --> pdb=" O ALA i 5 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 20 Processing helix chain 'i' and resid 30 through 35 Proline residue: i 35 - end of helix Processing helix chain 'i' and resid 42 through 44 No H-bonds generated for 'chain 'i' and resid 42 through 44' Processing helix chain 'i' and resid 49 through 65 Processing helix chain 'i' and resid 69 through 71 No H-bonds generated for 'chain 'i' and resid 69 through 71' Processing helix chain 'i' and resid 79 through 81 No H-bonds generated for 'chain 'i' and resid 79 through 81' Processing helix chain 'i' and resid 82 through 88 Processing helix chain 'i' and resid 88 through 93 Processing helix chain 'i' and resid 129 through 137 Processing helix chain 'i' and resid 166 through 184 removed outlier: 4.097A pdb=" N ILE i 170 " --> pdb=" O GLY i 166 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY i 171 " --> pdb=" O LYS i 167 " (cutoff:3.500A) Processing helix chain 'i' and resid 198 through 203 removed outlier: 3.627A pdb=" N PHE i 203 " --> pdb=" O ASP i 200 " (cutoff:3.500A) Processing helix chain 'j' and resid 70 through 75 Processing helix chain 'j' and resid 76 through 80 removed outlier: 3.690A pdb=" N HIS j 79 " --> pdb=" O SER j 76 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 114 removed outlier: 3.625A pdb=" N ARG j 111 " --> pdb=" O THR j 107 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL j 114 " --> pdb=" O LEU j 110 " (cutoff:3.500A) Processing helix chain 'j' and resid 157 through 178 removed outlier: 3.551A pdb=" N ARG j 162 " --> pdb=" O SER j 158 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL j 176 " --> pdb=" O LEU j 172 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY j 178 " --> pdb=" O LYS j 174 " (cutoff:3.500A) Processing helix chain 'j' and resid 180 through 188 removed outlier: 3.915A pdb=" N SER j 186 " --> pdb=" O ALA j 182 " (cutoff:3.500A) Processing helix chain 'j' and resid 191 through 199 removed outlier: 3.511A pdb=" N LYS j 195 " --> pdb=" O GLU j 191 " (cutoff:3.500A) Processing helix chain 'j' and resid 224 through 232 removed outlier: 3.858A pdb=" N LEU j 228 " --> pdb=" O ASP j 224 " (cutoff:3.500A) Processing helix chain 'k' and resid 39 through 47 Processing helix chain 'k' and resid 53 through 60 Processing helix chain 'k' and resid 65 through 69 Processing helix chain 'k' and resid 120 through 135 Processing helix chain 'k' and resid 181 through 192 removed outlier: 3.548A pdb=" N LYS k 186 " --> pdb=" O PRO k 182 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU k 190 " --> pdb=" O LYS k 186 " (cutoff:3.500A) Processing helix chain 'k' and resid 206 through 220 Processing helix chain 'k' and resid 226 through 230 removed outlier: 3.714A pdb=" N TRP k 230 " --> pdb=" O PRO k 227 " (cutoff:3.500A) Processing helix chain 'k' and resid 238 through 243 Processing helix chain 'k' and resid 243 through 248 Processing helix chain 'l' and resid 6 through 29 Processing helix chain 'l' and resid 54 through 59 Processing helix chain 'l' and resid 60 through 64 removed outlier: 3.638A pdb=" N GLY l 63 " --> pdb=" O GLY l 60 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 77 Processing helix chain 'l' and resid 93 through 96 Processing helix chain 'l' and resid 97 through 111 Processing helix chain 'l' and resid 114 through 129 removed outlier: 3.627A pdb=" N VAL l 122 " --> pdb=" O ALA l 118 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR l 125 " --> pdb=" O GLY l 121 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 167 removed outlier: 4.021A pdb=" N ASN l 165 " --> pdb=" O GLY l 161 " (cutoff:3.500A) Processing helix chain 'm' and resid 15 through 19 Processing helix chain 'm' and resid 37 through 41 removed outlier: 4.047A pdb=" N SER m 41 " --> pdb=" O LEU m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 50 Processing helix chain 'm' and resid 58 through 66 removed outlier: 3.657A pdb=" N LYS m 62 " --> pdb=" O GLY m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 133 through 135 No H-bonds generated for 'chain 'm' and resid 133 through 135' Processing helix chain 'm' and resid 247 through 259 Processing helix chain 'n' and resid 30 through 35 removed outlier: 4.013A pdb=" N GLN n 34 " --> pdb=" O PRO n 30 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN n 35 " --> pdb=" O GLU n 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 30 through 35' Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'n' and resid 88 through 95 Processing helix chain 'n' and resid 106 through 125 removed outlier: 3.847A pdb=" N ARG n 112 " --> pdb=" O LEU n 108 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP n 119 " --> pdb=" O LYS n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 128 through 140 Processing helix chain 'n' and resid 163 through 183 Processing helix chain 'n' and resid 189 through 203 removed outlier: 3.708A pdb=" N LYS n 203 " --> pdb=" O ILE n 199 " (cutoff:3.500A) Processing helix chain 'n' and resid 208 through 224 removed outlier: 3.511A pdb=" N GLU n 216 " --> pdb=" O LYS n 212 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 26 removed outlier: 4.018A pdb=" N VAL o 26 " --> pdb=" O HIS o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 39 through 41 No H-bonds generated for 'chain 'o' and resid 39 through 41' Processing helix chain 'o' and resid 137 through 143 Processing helix chain 'o' and resid 152 through 156 removed outlier: 3.722A pdb=" N ASP o 155 " --> pdb=" O ASP o 152 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 216 removed outlier: 3.506A pdb=" N VAL o 195 " --> pdb=" O ARG o 191 " (cutoff:3.500A) Processing helix chain 'p' and resid 14 through 29 removed outlier: 4.207A pdb=" N LEU p 27 " --> pdb=" O ALA p 23 " (cutoff:3.500A) Processing helix chain 'p' and resid 33 through 37 Processing helix chain 'p' and resid 66 through 71 Processing helix chain 'p' and resid 73 through 83 removed outlier: 3.741A pdb=" N ARG p 79 " --> pdb=" O THR p 75 " (cutoff:3.500A) Processing helix chain 'p' and resid 113 through 116 Processing helix chain 'p' and resid 117 through 130 removed outlier: 3.809A pdb=" N ASP p 123 " --> pdb=" O THR p 119 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL p 130 " --> pdb=" O LEU p 126 " (cutoff:3.500A) Processing helix chain 'p' and resid 158 through 164 removed outlier: 3.818A pdb=" N GLN p 161 " --> pdb=" O ASP p 158 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP p 163 " --> pdb=" O GLN p 160 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N TYR p 164 " --> pdb=" O GLN p 161 " (cutoff:3.500A) Processing helix chain 'p' and resid 165 through 178 removed outlier: 3.885A pdb=" N ALA p 171 " --> pdb=" O GLU p 167 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 27 No H-bonds generated for 'chain 'q' and resid 25 through 27' Processing helix chain 'q' and resid 88 through 94 removed outlier: 3.550A pdb=" N ARG q 92 " --> pdb=" O ASN q 88 " (cutoff:3.500A) Processing helix chain 'q' and resid 106 through 117 removed outlier: 3.705A pdb=" N TRP q 112 " --> pdb=" O PRO q 108 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU q 114 " --> pdb=" O ARG q 110 " (cutoff:3.500A) Processing helix chain 'q' and resid 136 through 138 No H-bonds generated for 'chain 'q' and resid 136 through 138' Processing helix chain 'q' and resid 139 through 146 removed outlier: 3.645A pdb=" N TRP q 143 " --> pdb=" O ALA q 139 " (cutoff:3.500A) Processing helix chain 'q' and resid 153 through 158 Processing helix chain 'q' and resid 159 through 162 Processing helix chain 'q' and resid 172 through 177 Processing helix chain 'q' and resid 186 through 200 removed outlier: 3.670A pdb=" N ARG q 194 " --> pdb=" O ALA q 190 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS q 199 " --> pdb=" O ARG q 195 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 33 removed outlier: 4.196A pdb=" N LEU r 30 " --> pdb=" O ALA r 26 " (cutoff:3.500A) Processing helix chain 'r' and resid 39 through 62 removed outlier: 3.839A pdb=" N ILE r 45 " --> pdb=" O GLU r 41 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA r 55 " --> pdb=" O LYS r 51 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 83 Processing helix chain 'r' and resid 92 through 97 removed outlier: 3.797A pdb=" N LEU r 97 " --> pdb=" O LEU r 93 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 removed outlier: 3.687A pdb=" N LEU r 105 " --> pdb=" O VAL r 101 " (cutoff:3.500A) Processing helix chain 'r' and resid 108 through 116 removed outlier: 4.303A pdb=" N TYR r 114 " --> pdb=" O GLN r 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 121 through 131 removed outlier: 3.747A pdb=" N ARG r 126 " --> pdb=" O VAL r 122 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL r 127 " --> pdb=" O HIS r 123 " (cutoff:3.500A) Processing helix chain 'r' and resid 162 through 166 Processing helix chain 'r' and resid 170 through 182 removed outlier: 3.631A pdb=" N LYS r 180 " --> pdb=" O ASN r 176 " (cutoff:3.500A) Processing helix chain 's' and resid 4 through 19 removed outlier: 3.801A pdb=" N LYS s 10 " --> pdb=" O GLU s 6 " (cutoff:3.500A) Processing helix chain 's' and resid 38 through 53 removed outlier: 3.544A pdb=" N LEU s 46 " --> pdb=" O VAL s 42 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS s 52 " --> pdb=" O SER s 48 " (cutoff:3.500A) Processing helix chain 's' and resid 69 through 81 removed outlier: 4.024A pdb=" N GLU s 74 " --> pdb=" O GLU s 70 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR s 75 " --> pdb=" O GLU s 71 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU s 78 " --> pdb=" O GLU s 74 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR s 79 " --> pdb=" O TYR s 75 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 51 removed outlier: 3.627A pdb=" N ILE t 49 " --> pdb=" O PRO t 45 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 37 removed outlier: 3.650A pdb=" N THR u 34 " --> pdb=" O VAL u 30 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 44 through 53 removed outlier: 3.662A pdb=" N SER u 48 " --> pdb=" O GLY u 44 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR u 53 " --> pdb=" O THR u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 71 through 80 removed outlier: 3.617A pdb=" N LEU u 78 " --> pdb=" O LEU u 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 98 removed outlier: 3.714A pdb=" N GLN u 96 " --> pdb=" O ASP u 93 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY u 98 " --> pdb=" O LYS u 95 " (cutoff:3.500A) Processing helix chain 'u' and resid 130 through 142 removed outlier: 5.394A pdb=" N ILE u 136 " --> pdb=" O GLU u 132 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET u 137 " --> pdb=" O LEU u 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU u 138 " --> pdb=" O SER u 134 " (cutoff:3.500A) Processing helix chain 'v' and resid 31 through 42 Processing helix chain 'v' and resid 46 through 58 removed outlier: 3.543A pdb=" N VAL v 52 " --> pdb=" O SER v 48 " (cutoff:3.500A) Processing helix chain 'v' and resid 62 through 68 removed outlier: 3.881A pdb=" N ILE v 66 " --> pdb=" O GLN v 62 " (cutoff:3.500A) Processing helix chain 'v' and resid 70 through 78 Processing helix chain 'v' and resid 85 through 105 removed outlier: 3.899A pdb=" N LEU v 91 " --> pdb=" O ASP v 87 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG v 104 " --> pdb=" O LYS v 100 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN v 105 " --> pdb=" O HIS v 101 " (cutoff:3.500A) Processing helix chain 'v' and resid 108 through 132 removed outlier: 3.509A pdb=" N ILE v 116 " --> pdb=" O LYS v 112 " (cutoff:3.500A) Processing helix chain 'v' and resid 145 through 151 removed outlier: 3.668A pdb=" N LEU v 149 " --> pdb=" O THR v 145 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL v 150 " --> pdb=" O ALA v 146 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN v 151 " --> pdb=" O SER v 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 145 through 151' Processing helix chain 'x' and resid 21 through 27 removed outlier: 3.997A pdb=" N GLU x 27 " --> pdb=" O GLU x 23 " (cutoff:3.500A) Processing helix chain 'x' and resid 29 through 35 removed outlier: 3.580A pdb=" N VAL x 34 " --> pdb=" O THR x 30 " (cutoff:3.500A) Processing helix chain 'x' and resid 38 through 47 Processing helix chain 'x' and resid 53 through 65 removed outlier: 3.517A pdb=" N MET x 57 " --> pdb=" O PRO x 53 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS x 59 " --> pdb=" O GLY x 55 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG x 61 " --> pdb=" O MET x 57 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU x 65 " --> pdb=" O ARG x 61 " (cutoff:3.500A) Processing helix chain 'x' and resid 86 through 90 Processing helix chain 'x' and resid 108 through 112 removed outlier: 3.895A pdb=" N LEU x 112 " --> pdb=" O PRO x 109 " (cutoff:3.500A) Processing helix chain 'x' and resid 115 through 120 removed outlier: 3.709A pdb=" N SER x 120 " --> pdb=" O GLY x 117 " (cutoff:3.500A) Processing helix chain 'y' and resid 37 through 39 No H-bonds generated for 'chain 'y' and resid 37 through 39' Processing helix chain 'y' and resid 44 through 49 removed outlier: 3.591A pdb=" N VAL y 48 " --> pdb=" O ARG y 45 " (cutoff:3.500A) Processing helix chain 'y' and resid 56 through 61 removed outlier: 3.756A pdb=" N LYS y 59 " --> pdb=" O GLY y 56 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE y 60 " --> pdb=" O LEU y 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 73 through 97 removed outlier: 3.659A pdb=" N VAL y 78 " --> pdb=" O HIS y 74 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG y 82 " --> pdb=" O VAL y 78 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN y 83 " --> pdb=" O TYR y 79 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS y 95 " --> pdb=" O ALA y 91 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL y 97 " --> pdb=" O HIS y 93 " (cutoff:3.500A) Processing helix chain 'y' and resid 98 through 112 removed outlier: 3.565A pdb=" N LYS y 102 " --> pdb=" O ASP y 98 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN y 103 " --> pdb=" O GLU y 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU y 104 " --> pdb=" O GLN y 100 " (cutoff:3.500A) Processing helix chain 'z' and resid 6 through 18 removed outlier: 3.554A pdb=" N ARG z 11 " --> pdb=" O LYS z 7 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 24 Processing helix chain 'z' and resid 31 through 38 removed outlier: 3.635A pdb=" N ASP z 36 " --> pdb=" O LYS z 32 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 43 through 60 removed outlier: 3.617A pdb=" N ARG z 60 " --> pdb=" O HIS z 56 " (cutoff:3.500A) Processing helix chain 'z' and resid 73 through 81 removed outlier: 3.678A pdb=" N GLU z 77 " --> pdb=" O LEU z 73 " (cutoff:3.500A) Processing helix chain 'z' and resid 82 through 84 No H-bonds generated for 'chain 'z' and resid 82 through 84' Processing helix chain 'z' and resid 103 through 114 Processing helix chain 'A' and resid 27 through 33 removed outlier: 3.844A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 76 through 80 removed outlier: 3.669A pdb=" N LYS A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 3.835A pdb=" N SER A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'B' and resid 5 through 9 Processing helix chain 'B' and resid 10 through 26 removed outlier: 3.521A pdb=" N ALA B 17 " --> pdb=" O ASP B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 68 removed outlier: 3.582A pdb=" N LYS B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 removed outlier: 3.515A pdb=" N LYS B 78 " --> pdb=" O GLY B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 111 removed outlier: 3.889A pdb=" N ASN B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 141 removed outlier: 3.523A pdb=" N ARG B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 135 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU B 140 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 removed outlier: 3.903A pdb=" N ASN C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL C 37 " --> pdb=" O GLN C 33 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS C 48 " --> pdb=" O ASN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 107 removed outlier: 3.640A pdb=" N VAL C 100 " --> pdb=" O PRO C 96 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG C 102 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR C 107 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 63 Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'E' and resid 5 through 21 removed outlier: 3.750A pdb=" N ASP E 9 " --> pdb=" O SER E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 removed outlier: 3.553A pdb=" N HIS E 44 " --> pdb=" O VAL E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 94 removed outlier: 3.664A pdb=" N ASN E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.506A pdb=" N ARG E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 24 removed outlier: 3.544A pdb=" N LEU H 15 " --> pdb=" O SER H 11 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TRP H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 35 removed outlier: 3.596A pdb=" N LYS H 31 " --> pdb=" O ASN H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 40 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 132 through 137 Processing helix chain 'I' and resid 16 through 18 No H-bonds generated for 'chain 'I' and resid 16 through 18' Processing helix chain 'I' and resid 36 through 49 removed outlier: 3.955A pdb=" N LEU I 40 " --> pdb=" O SER I 36 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL I 47 " --> pdb=" O LYS I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 85 removed outlier: 3.592A pdb=" N PHE I 85 " --> pdb=" O GLU I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 94 removed outlier: 3.599A pdb=" N ARG I 93 " --> pdb=" O TYR I 89 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR I 94 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 116 removed outlier: 3.709A pdb=" N LYS I 112 " --> pdb=" O ARG I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 135 removed outlier: 3.745A pdb=" N LYS I 127 " --> pdb=" O LYS I 123 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS I 128 " --> pdb=" O ARG I 124 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG I 131 " --> pdb=" O LYS I 127 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG I 132 " --> pdb=" O LYS I 128 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 52 Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 61 through 69 Processing helix chain 'J' and resid 75 through 86 removed outlier: 4.176A pdb=" N ARG J 81 " --> pdb=" O ARG J 77 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU J 84 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU J 86 " --> pdb=" O HIS J 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 18 Processing helix chain 'P' and resid 32 through 43 removed outlier: 3.698A pdb=" N LYS P 36 " --> pdb=" O GLY P 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 164 removed outlier: 4.115A pdb=" N ASP R 163 " --> pdb=" O GLU R 160 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP R 164 " --> pdb=" O ALA R 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 160 through 164' Processing helix chain 'T' and resid 33 through 37 removed outlier: 4.001A pdb=" N ARG T 37 " --> pdb=" O ALA T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 68 removed outlier: 3.663A pdb=" N LYS T 64 " --> pdb=" O GLN T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 91 removed outlier: 4.125A pdb=" N ARG T 83 " --> pdb=" O PRO T 79 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE T 85 " --> pdb=" O VAL T 81 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG T 87 " --> pdb=" O ARG T 83 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 103 removed outlier: 3.563A pdb=" N THR T 101 " --> pdb=" O LYS T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 110 through 114 Processing helix chain 'T' and resid 121 through 133 removed outlier: 3.784A pdb=" N LEU T 132 " --> pdb=" O LEU T 128 " (cutoff:3.500A) Processing helix chain 'O' and resid 32 through 36 removed outlier: 3.810A pdb=" N GLY O 35 " --> pdb=" O ARG O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 40 through 46 removed outlier: 3.538A pdb=" N GLU O 45 " --> pdb=" O GLN O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 51 Processing helix chain 'w' and resid 45 through 47 No H-bonds generated for 'chain 'w' and resid 45 through 47' Processing helix chain 'w' and resid 56 through 75 removed outlier: 3.551A pdb=" N ALA w 63 " --> pdb=" O ALA w 59 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 108 removed outlier: 4.437A pdb=" N ALA w 100 " --> pdb=" O PRO w 96 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA w 106 " --> pdb=" O LEU w 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 56 removed outlier: 4.467A pdb=" N GLU K 55 " --> pdb=" O ARG K 51 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 56' Processing helix chain 'K' and resid 74 through 81 Processing helix chain 'K' and resid 90 through 94 removed outlier: 3.551A pdb=" N LYS K 93 " --> pdb=" O GLU K 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'i' and resid 37 through 40 removed outlier: 6.673A pdb=" N VAL i 47 " --> pdb=" O PHE i 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'i' and resid 97 through 99 removed outlier: 7.462A pdb=" N ILE i 98 " --> pdb=" O VAL i 73 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA i 75 " --> pdb=" O ILE i 98 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL i 74 " --> pdb=" O ILE i 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'j' and resid 42 through 46 removed outlier: 4.052A pdb=" N GLY j 44 " --> pdb=" O ILE j 32 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LEU j 96 " --> pdb=" O VAL j 91 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL j 91 " --> pdb=" O LEU j 96 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N THR j 98 " --> pdb=" O ASP j 89 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP j 89 " --> pdb=" O THR j 98 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N PHE j 100 " --> pdb=" O ARG j 87 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ARG j 87 " --> pdb=" O PHE j 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'j' and resid 42 through 46 removed outlier: 4.052A pdb=" N GLY j 44 " --> pdb=" O ILE j 32 " (cutoff:3.500A) removed outlier: 13.457A pdb=" N ASN j 99 " --> pdb=" O LYS j 219 " (cutoff:3.500A) removed outlier: 13.454A pdb=" N LYS j 219 " --> pdb=" O ASN j 99 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N HIS j 101 " --> pdb=" O LEU j 217 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU j 217 " --> pdb=" O HIS j 101 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET j 103 " --> pdb=" O VAL j 215 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ARG j 213 " --> pdb=" O PHE j 105 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE j 210 " --> pdb=" O PHE j 142 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N PHE j 142 " --> pdb=" O ILE j 210 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL j 212 " --> pdb=" O ILE j 140 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE j 140 " --> pdb=" O VAL j 212 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS j 214 " --> pdb=" O PHE j 138 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL j 134 " --> pdb=" O LEU j 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'k' and resid 77 through 89 removed outlier: 3.679A pdb=" N GLN k 77 " --> pdb=" O GLY k 105 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL k 101 " --> pdb=" O MET k 81 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE k 83 " --> pdb=" O LYS k 99 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LYS k 99 " --> pdb=" O ILE k 83 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG k 97 " --> pdb=" O PRO k 85 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLN k 87 " --> pdb=" O ARG k 95 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG k 95 " --> pdb=" O GLN k 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'k' and resid 141 through 142 Processing sheet with id=AA7, first strand: chain 'k' and resid 158 through 162 removed outlier: 3.623A pdb=" N VAL k 165 " --> pdb=" O CYS k 162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR k 166 " --> pdb=" O ASN k 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 34 through 40 removed outlier: 6.499A pdb=" N ARG l 51 " --> pdb=" O SER l 35 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL l 37 " --> pdb=" O ILE l 49 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE l 49 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL l 39 " --> pdb=" O GLU l 47 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU l 47 " --> pdb=" O VAL l 39 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR l 46 " --> pdb=" O VAL l 85 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N TYR l 87 " --> pdb=" O THR l 46 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL l 48 " --> pdb=" O TYR l 87 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N GLU l 89 " --> pdb=" O VAL l 48 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE l 50 " --> pdb=" O GLU l 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'l' and resid 148 through 155 Processing sheet with id=AB1, first strand: chain 'l' and resid 207 through 208 Processing sheet with id=AB2, first strand: chain 'l' and resid 221 through 224 removed outlier: 6.639A pdb=" N ALA R 180 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASP R 191 " --> pdb=" O VAL R 178 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL R 178 " --> pdb=" O ASP R 191 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR R 168 " --> pdb=" O VAL R 157 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLN R 153 " --> pdb=" O ALA R 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'm' and resid 42 through 43 Processing sheet with id=AB4, first strand: chain 'm' and resid 75 through 76 removed outlier: 4.192A pdb=" N ASN m 98 " --> pdb=" O ILE m 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'm' and resid 146 through 148 removed outlier: 5.654A pdb=" N VAL m 136 " --> pdb=" O LEU m 131 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LEU m 131 " --> pdb=" O VAL m 136 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR m 138 " --> pdb=" O VAL m 129 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N VAL m 129 " --> pdb=" O TYR m 138 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL m 140 " --> pdb=" O LYS m 127 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N THR m 159 " --> pdb=" O PHE m 172 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N PHE m 172 " --> pdb=" O THR m 159 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS m 161 " --> pdb=" O THR m 170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'm' and resid 179 through 183 removed outlier: 3.722A pdb=" N GLY m 229 " --> pdb=" O LEU m 180 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR m 182 " --> pdb=" O VAL m 227 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N VAL m 227 " --> pdb=" O TYR m 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'm' and resid 197 through 199 removed outlier: 3.525A pdb=" N HIS m 197 " --> pdb=" O HIS m 209 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'n' and resid 145 through 148 Processing sheet with id=AB9, first strand: chain 'o' and resid 12 through 17 removed outlier: 6.280A pdb=" N LYS o 2 " --> pdb=" O LEU o 109 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU o 111 " --> pdb=" O LYS o 2 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASN o 4 " --> pdb=" O LEU o 111 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE o 113 " --> pdb=" O ASN o 4 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N SER o 6 " --> pdb=" O ILE o 113 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N LYS o 115 " --> pdb=" O SER o 6 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL o 112 " --> pdb=" O ILE o 52 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N ILE o 52 " --> pdb=" O VAL o 112 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL o 114 " --> pdb=" O PHE o 50 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE o 50 " --> pdb=" O VAL o 114 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'o' and resid 73 through 77 Processing sheet with id=AC2, first strand: chain 'o' and resid 160 through 163 Processing sheet with id=AC3, first strand: chain 'p' and resid 45 through 50 removed outlier: 3.940A pdb=" N SER p 45 " --> pdb=" O PHE p 61 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG p 47 " --> pdb=" O ALA p 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 180 through 184 removed outlier: 4.487A pdb=" N GLN p 180 " --> pdb=" O LYS p 148 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY p 137 " --> pdb=" O LEU p 153 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LYS p 138 " --> pdb=" O ASP E 54 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE E 50 " --> pdb=" O TYR p 142 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 3 through 4 removed outlier: 3.669A pdb=" N ILE q 3 " --> pdb=" O GLY q 30 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'q' and resid 37 through 38 removed outlier: 6.537A pdb=" N ARG q 42 " --> pdb=" O LEU q 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'q' and resid 72 through 76 removed outlier: 3.563A pdb=" N ILE q 72 " --> pdb=" O TRP q 67 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN q 64 " --> pdb=" O GLY q 181 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N ILE q 183 " --> pdb=" O ASN q 64 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER q 66 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE q 101 " --> pdb=" O VAL q 82 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY q 80 " --> pdb=" O GLN q 103 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP q 105 " --> pdb=" O ILE q 78 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE q 78 " --> pdb=" O ASP q 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'r' and resid 139 through 140 Processing sheet with id=AC9, first strand: chain 's' and resid 20 through 21 Processing sheet with id=AD1, first strand: chain 't' and resid 70 through 77 removed outlier: 17.903A pdb=" N ILE t 70 " --> pdb=" O LEU t 91 " (cutoff:3.500A) removed outlier: 15.404A pdb=" N LEU t 91 " --> pdb=" O ILE t 70 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N THR t 72 " --> pdb=" O ALA t 89 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA t 89 " --> pdb=" O THR t 72 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL t 85 " --> pdb=" O VAL t 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG t 99 " --> pdb=" O ILE t 94 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N PHE t 137 " --> pdb=" O PRO t 108 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR t 124 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N VAL t 142 " --> pdb=" O ILE t 122 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE t 122 " --> pdb=" O VAL t 142 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N ASP t 121 " --> pdb=" O VAL t 75 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL t 75 " --> pdb=" O ASP t 121 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'u' and resid 41 through 43 removed outlier: 3.696A pdb=" N VAL u 121 " --> pdb=" O VAL u 61 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL u 123 " --> pdb=" O LEU u 59 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU u 59 " --> pdb=" O VAL u 123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'x' and resid 76 through 78 Processing sheet with id=AD4, first strand: chain 'y' and resid 6 through 13 removed outlier: 3.631A pdb=" N THR y 70 " --> pdb=" O THR y 17 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS y 30 " --> pdb=" O VAL y 67 " (cutoff:3.500A) removed outlier: 8.266A pdb=" N VAL y 69 " --> pdb=" O LYS y 30 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AD6, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AD7, first strand: chain 'B' and resid 83 through 86 removed outlier: 3.778A pdb=" N LYS B 92 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ARG B 86 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AD9, first strand: chain 'C' and resid 20 through 21 Processing sheet with id=AE1, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.726A pdb=" N TYR C 90 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 56 through 57 removed outlier: 3.726A pdb=" N TYR C 90 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 32 through 37 Processing sheet with id=AE4, first strand: chain 'E' and resid 72 through 74 Processing sheet with id=AE5, first strand: chain 'E' and resid 72 through 74 removed outlier: 6.716A pdb=" N ILE E 103 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE E 128 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TYR E 101 " --> pdb=" O PHE E 128 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 48 through 57 removed outlier: 6.703A pdb=" N ARG H 73 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS H 56 " --> pdb=" O CYS H 71 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS H 71 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N PHE H 122 " --> pdb=" O THR H 84 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU H 103 " --> pdb=" O VAL H 125 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 6 through 15 removed outlier: 3.524A pdb=" N THR I 6 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL I 12 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN I 22 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N SER I 14 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG I 20 " --> pdb=" O SER I 14 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 6 through 15 removed outlier: 3.524A pdb=" N THR I 6 " --> pdb=" O LEU I 28 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL I 12 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN I 22 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N SER I 14 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ARG I 20 " --> pdb=" O SER I 14 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 89 through 95 removed outlier: 7.097A pdb=" N ILE J 100 " --> pdb=" O ILE J 92 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LYS J 94 " --> pdb=" O GLN J 98 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLN J 98 " --> pdb=" O LYS J 94 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 44 through 47 removed outlier: 4.013A pdb=" N THR L 44 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER L 78 " --> pdb=" O LYS L 36 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 64 through 65 Processing sheet with id=AF3, first strand: chain 'N' and resid 39 through 44 removed outlier: 7.208A pdb=" N VAL N 25 " --> pdb=" O GLY N 17 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY N 17 " --> pdb=" O VAL N 25 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN N 27 " --> pdb=" O VAL N 15 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL N 15 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG N 29 " --> pdb=" O ILE N 13 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'R' and resid 8 through 13 removed outlier: 3.802A pdb=" N ARG R 10 " --> pdb=" O VAL R 312 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL R 312 " --> pdb=" O ARG R 10 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR R 12 " --> pdb=" O ILE R 310 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE R 310 " --> pdb=" O THR R 12 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N THR R 300 " --> pdb=" O TRP R 294 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TRP R 294 " --> pdb=" O THR R 300 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N PHE R 302 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU R 292 " --> pdb=" O PHE R 302 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY R 304 " --> pdb=" O VAL R 290 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'R' and resid 20 through 25 removed outlier: 3.958A pdb=" N LEU R 33 " --> pdb=" O TRP R 45 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG R 59 " --> pdb=" O SER R 44 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS R 46 " --> pdb=" O PRO R 57 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 68 through 73 removed outlier: 3.549A pdb=" N SER R 84 " --> pdb=" O THR R 88 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR R 88 " --> pdb=" O SER R 84 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN R 101 " --> pdb=" O LEU R 91 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASP R 93 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N THR R 99 " --> pdb=" O ASP R 93 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 110 through 115 removed outlier: 3.654A pdb=" N SER R 112 " --> pdb=" O GLY R 125 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE R 131 " --> pdb=" O THR R 143 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR R 143 " --> pdb=" O ILE R 131 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL R 133 " --> pdb=" O LEU R 141 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'R' and resid 201 through 204 removed outlier: 3.505A pdb=" N THR R 201 " --> pdb=" O ALA R 214 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR R 232 " --> pdb=" O LEU R 222 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASN R 224 " --> pdb=" O ALA R 230 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ALA R 230 " --> pdb=" O ASN R 224 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 240 through 245 removed outlier: 3.676A pdb=" N ASP R 272 " --> pdb=" O VAL R 262 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N SER R 264 " --> pdb=" O LEU R 270 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU R 270 " --> pdb=" O SER R 264 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 30 through 31 Processing sheet with id=AG2, first strand: chain 'w' and resid 40 through 43 removed outlier: 6.302A pdb=" N GLY w 15 " --> pdb=" O HIS w 80 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LYS w 82 " --> pdb=" O GLY w 15 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA w 17 " --> pdb=" O LYS w 82 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ARG w 84 " --> pdb=" O ALA w 17 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE w 19 " --> pdb=" O ARG w 84 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL w 81 " --> pdb=" O GLY w 113 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE w 115 " --> pdb=" O VAL w 81 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE w 83 " --> pdb=" O ILE w 115 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ASP w 117 " --> pdb=" O ILE w 83 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 20 through 22 Processing sheet with id=AG4, first strand: chain 'K' and resid 37 through 43 1344 hydrogen bonds defined for protein. 3750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1345 hydrogen bonds 2172 hydrogen bond angles 0 basepair planarities 547 basepair parallelities 960 stacking parallelities Total time for adding SS restraints: 64.34 Time building geometry restraints manager: 16.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10217 1.32 - 1.45: 33654 1.45 - 1.57: 37728 1.57 - 1.70: 3883 1.70 - 1.83: 137 Bond restraints: 85619 Sorted by residual: bond pdb=" CA LYS B 27 " pdb=" CB LYS B 27 " ideal model delta sigma weight residual 1.528 1.635 -0.107 2.61e-02 1.47e+03 1.67e+01 bond pdb=" CA LEU I 28 " pdb=" CB LEU I 28 " ideal model delta sigma weight residual 1.527 1.482 0.045 1.75e-02 3.27e+03 6.49e+00 bond pdb=" C2 G h 976 " pdb=" N3 G h 976 " ideal model delta sigma weight residual 1.323 1.280 0.043 2.00e-02 2.50e+03 4.66e+00 bond pdb=" CB VAL t 135 " pdb=" CG2 VAL t 135 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.25e+00 bond pdb=" N3 U h1012 " pdb=" C4 U h1012 " ideal model delta sigma weight residual 1.380 1.339 0.041 2.00e-02 2.50e+03 4.21e+00 ... (remaining 85614 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 122823 3.00 - 6.00: 1938 6.00 - 9.00: 275 9.00 - 12.00: 38 12.00 - 15.00: 11 Bond angle restraints: 125085 Sorted by residual: angle pdb=" C ILE u 89 " pdb=" N LYS u 90 " pdb=" CA LYS u 90 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" N THR w 91 " pdb=" CA THR w 91 " pdb=" C THR w 91 " ideal model delta sigma weight residual 111.28 117.42 -6.14 1.09e+00 8.42e-01 3.17e+01 angle pdb=" CA GLU N 62 " pdb=" CB GLU N 62 " pdb=" CG GLU N 62 " ideal model delta sigma weight residual 114.10 124.58 -10.48 2.00e+00 2.50e-01 2.75e+01 angle pdb=" C ASN I 34 " pdb=" N VAL I 35 " pdb=" CA VAL I 35 " ideal model delta sigma weight residual 122.14 116.63 5.51 1.11e+00 8.12e-01 2.46e+01 angle pdb=" CA LYS Q 136 " pdb=" CB LYS Q 136 " pdb=" CG LYS Q 136 " ideal model delta sigma weight residual 114.10 123.95 -9.85 2.00e+00 2.50e-01 2.43e+01 ... (remaining 125080 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 48860 35.96 - 71.92: 4819 71.92 - 107.88: 517 107.88 - 143.83: 26 143.83 - 179.79: 56 Dihedral angle restraints: 54278 sinusoidal: 40108 harmonic: 14170 Sorted by residual: dihedral pdb=" CA VAL p 64 " pdb=" C VAL p 64 " pdb=" N PRO p 65 " pdb=" CA PRO p 65 " ideal model delta harmonic sigma weight residual 180.00 123.55 56.45 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA SER u 119 " pdb=" C SER u 119 " pdb=" N VAL u 120 " pdb=" CA VAL u 120 " ideal model delta harmonic sigma weight residual 180.00 124.39 55.61 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" CA ALA s 23 " pdb=" C ALA s 23 " pdb=" N LYS s 24 " pdb=" CA LYS s 24 " ideal model delta harmonic sigma weight residual 180.00 130.09 49.91 0 5.00e+00 4.00e-02 9.96e+01 ... (remaining 54275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 14582 0.097 - 0.194: 1019 0.194 - 0.291: 80 0.291 - 0.388: 24 0.388 - 0.485: 3 Chirality restraints: 15708 Sorted by residual: chirality pdb=" C3' C h 408 " pdb=" C4' C h 408 " pdb=" O3' C h 408 " pdb=" C2' C h 408 " both_signs ideal model delta sigma weight residual False -2.74 -2.26 -0.48 2.00e-01 2.50e+01 5.87e+00 chirality pdb=" C3' G h 925 " pdb=" C4' G h 925 " pdb=" O3' G h 925 " pdb=" C2' G h 925 " both_signs ideal model delta sigma weight residual False -2.48 -2.06 -0.41 2.00e-01 2.50e+01 4.29e+00 chirality pdb=" CB VAL p 64 " pdb=" CA VAL p 64 " pdb=" CG1 VAL p 64 " pdb=" CG2 VAL p 64 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 15705 not shown) Planarity restraints: 8721 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G h 287 " -0.059 2.00e-02 2.50e+03 2.66e-02 2.13e+01 pdb=" N9 G h 287 " 0.068 2.00e-02 2.50e+03 pdb=" C8 G h 287 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G h 287 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G h 287 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G h 287 " -0.009 2.00e-02 2.50e+03 pdb=" O6 G h 287 " -0.011 2.00e-02 2.50e+03 pdb=" N1 G h 287 " -0.004 2.00e-02 2.50e+03 pdb=" C2 G h 287 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G h 287 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G h 287 " 0.008 2.00e-02 2.50e+03 pdb=" C4 G h 287 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL p 64 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO p 65 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO p 65 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO p 65 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A h1039 " -0.055 2.00e-02 2.50e+03 2.53e-02 1.76e+01 pdb=" N9 A h1039 " 0.060 2.00e-02 2.50e+03 pdb=" C8 A h1039 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A h1039 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A h1039 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A h1039 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A h1039 " -0.019 2.00e-02 2.50e+03 pdb=" N1 A h1039 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A h1039 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A h1039 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A h1039 " 0.008 2.00e-02 2.50e+03 ... (remaining 8718 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 489 2.51 - 3.11: 53166 3.11 - 3.71: 142295 3.71 - 4.30: 206722 4.30 - 4.90: 295020 Nonbonded interactions: 697692 Sorted by model distance: nonbonded pdb=" N1 G h 976 " pdb=" C2 A h1027 " model vdw 1.914 3.420 nonbonded pdb=" CA CYS O 39 " pdb="ZN ZN O 101 " model vdw 2.037 2.128 nonbonded pdb=" O2' G h 991 " pdb=" O2' U h1785 " model vdw 2.157 3.040 nonbonded pdb=" OP1 G h 925 " pdb=" O2' G h 986 " model vdw 2.180 3.040 nonbonded pdb=" O2' C h1729 " pdb=" O GLY q 2 " model vdw 2.182 3.040 ... (remaining 697687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 2.350 Check model and map are aligned: 0.440 Set scattering table: 0.560 Process input model: 191.900 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.230 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: 0.020 Load rotamer database and sin/cos tables:10.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 211.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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 : 0.007 0.107 85619 Z= 0.444 Angle : 0.973 14.996 125085 Z= 0.504 Chirality : 0.053 0.485 15708 Planarity : 0.006 0.113 8721 Dihedral : 23.039 179.792 45132 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.16 % Favored : 94.64 % Rotamer: Outliers : 0.02 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 2.04 % Twisted General : 0.45 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.11), residues: 4848 helix: -2.56 (0.10), residues: 1387 sheet: -0.80 (0.17), residues: 885 loop : -1.86 (0.11), residues: 2576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP v 139 HIS 0.023 0.002 HIS R 288 PHE 0.066 0.003 PHE H 107 TYR 0.065 0.003 TYR Q 148 ARG 0.019 0.001 ARG j 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 656 time to evaluate : 4.490 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: o 89 ASP cc_start: 0.7201 (p0) cc_final: 0.6878 (p0) REVERT: J 67 ASP cc_start: 0.8079 (t0) cc_final: 0.7777 (t0) outliers start: 1 outliers final: 0 residues processed: 657 average time/residue: 1.5419 time to fit residues: 1364.1384 Evaluate side-chains 538 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 564 optimal weight: 8.9990 chunk 506 optimal weight: 0.6980 chunk 280 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 341 optimal weight: 8.9990 chunk 270 optimal weight: 0.3980 chunk 523 optimal weight: 0.0670 chunk 202 optimal weight: 5.9990 chunk 318 optimal weight: 5.9990 chunk 389 optimal weight: 5.9990 chunk 606 optimal weight: 10.0000 overall best weight: 2.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: j 79 HIS k 228 ASN l 67 ASN m 98 ASN n 66 GLN n 127 GLN n 131 GLN p 110 GLN r 48 GLN v 58 HIS v 62 GLN z 48 ASN A 19 ASN A 71 GLN B 129 GLN I 77 ASN L 5 GLN L 26 GLN N 51 ASN ** T 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.096383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.068610 restraints weight = 206216.556| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.50 r_work: 0.2984 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 85619 Z= 0.180 Angle : 0.680 16.456 125085 Z= 0.349 Chirality : 0.040 0.326 15708 Planarity : 0.005 0.088 8721 Dihedral : 23.981 179.778 35509 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.57 % Favored : 92.29 % Rotamer: Outliers : 1.53 % Allowed : 11.05 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.11), residues: 4848 helix: -0.94 (0.13), residues: 1448 sheet: -0.69 (0.17), residues: 902 loop : -1.75 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP u 100 HIS 0.006 0.001 HIS R 288 PHE 0.026 0.001 PHE H 107 TYR 0.033 0.001 TYR R 250 ARG 0.011 0.001 ARG J 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 639 time to evaluate : 4.552 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: i 200 ASP cc_start: 0.8994 (m-30) cc_final: 0.8756 (m-30) REVERT: k 246 GLU cc_start: 0.8625 (mp0) cc_final: 0.8407 (mp0) REVERT: l 93 ASP cc_start: 0.6920 (t0) cc_final: 0.6640 (t0) REVERT: n 41 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7815 (ptmm) REVERT: n 65 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7520 (mmt180) REVERT: o 25 ARG cc_start: 0.8244 (ttp-110) cc_final: 0.8009 (ttp-110) REVERT: p 22 GLN cc_start: 0.9356 (mp-120) cc_final: 0.9023 (mm110) REVERT: p 83 LYS cc_start: 0.9020 (ptpp) cc_final: 0.8603 (pttm) REVERT: u 76 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9189 (pm20) REVERT: y 120 ASP cc_start: 0.8522 (p0) cc_final: 0.8308 (p0) REVERT: z 18 GLU cc_start: 0.8540 (pp20) cc_final: 0.8184 (tm-30) REVERT: z 82 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8197 (t0) REVERT: B 23 GLN cc_start: 0.8727 (tt0) cc_final: 0.8421 (tt0) REVERT: B 35 ASP cc_start: 0.8844 (p0) cc_final: 0.8544 (p0) REVERT: C 33 GLN cc_start: 0.8712 (mp10) cc_final: 0.8443 (mp10) REVERT: C 48 HIS cc_start: 0.8395 (OUTLIER) cc_final: 0.7768 (p-80) REVERT: J 45 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8168 (tm-30) REVERT: J 53 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8281 (mt-10) REVERT: J 67 ASP cc_start: 0.8489 (t0) cc_final: 0.8237 (t0) REVERT: J 82 HIS cc_start: 0.9157 (t70) cc_final: 0.8945 (t70) REVERT: N 38 ARG cc_start: 0.7397 (mtp180) cc_final: 0.7189 (mtp180) REVERT: Q 116 LYS cc_start: 0.8220 (mmpt) cc_final: 0.6961 (mmtt) REVERT: Q 123 ASN cc_start: 0.8335 (t0) cc_final: 0.8108 (t0) REVERT: R 121 MET cc_start: 0.8812 (mpp) cc_final: 0.8552 (mpp) REVERT: R 155 ARG cc_start: 0.8279 (tpp80) cc_final: 0.8038 (mmt-90) REVERT: R 231 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8108 (mtm) REVERT: K 87 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.6875 (ptm-80) REVERT: K 91 ASP cc_start: 0.8895 (m-30) cc_final: 0.8683 (m-30) outliers start: 63 outliers final: 15 residues processed: 659 average time/residue: 1.5164 time to fit residues: 1348.6488 Evaluate side-chains 589 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 567 time to evaluate : 4.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 196 SER Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain n residue 41 LYS Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain p residue 157 LYS Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain u residue 76 GLU Chi-restraints excluded: chain z residue 79 GLU Chi-restraints excluded: chain z residue 82 ASP Chi-restraints excluded: chain z residue 113 LEU Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 477 optimal weight: 9.9990 chunk 355 optimal weight: 10.0000 chunk 557 optimal weight: 8.9990 chunk 234 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 275 optimal weight: 40.0000 chunk 537 optimal weight: 7.9990 chunk 479 optimal weight: 5.9990 chunk 472 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 563 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** i 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN n 66 GLN ** p 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 111 GLN ** q 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 74 ASN v 36 GLN v 58 HIS A 19 ASN A 71 GLN B 129 GLN I 77 ASN N 51 ASN R 288 HIS ** T 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.093648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.065387 restraints weight = 205635.457| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.66 r_work: 0.2890 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 85619 Z= 0.380 Angle : 0.754 21.822 125085 Z= 0.385 Chirality : 0.045 0.327 15708 Planarity : 0.006 0.093 8721 Dihedral : 23.878 179.822 35509 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.46 % Favored : 91.42 % Rotamer: Outliers : 2.93 % Allowed : 15.22 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 1.53 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.12), residues: 4848 helix: -0.46 (0.13), residues: 1479 sheet: -0.79 (0.17), residues: 897 loop : -1.75 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP q 112 HIS 0.007 0.001 HIS p 122 PHE 0.041 0.002 PHE H 107 TYR 0.021 0.002 TYR y 79 ARG 0.010 0.001 ARG t 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 604 time to evaluate : 4.583 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: i 200 ASP cc_start: 0.9133 (m-30) cc_final: 0.8809 (m-30) REVERT: j 92 GLN cc_start: 0.8776 (pt0) cc_final: 0.8443 (pp30) REVERT: k 199 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.7717 (mm-40) REVERT: l 56 GLN cc_start: 0.8433 (pm20) cc_final: 0.8156 (pm20) REVERT: l 105 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8010 (tpp) REVERT: l 215 GLU cc_start: 0.8570 (mp0) cc_final: 0.7910 (tm-30) REVERT: n 65 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7532 (mmt180) REVERT: p 22 GLN cc_start: 0.9327 (mp-120) cc_final: 0.8832 (mm110) REVERT: q 111 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8698 (pm20) REVERT: u 33 ARG cc_start: 0.8976 (mmp80) cc_final: 0.8602 (mmp80) REVERT: u 139 HIS cc_start: 0.8316 (t-90) cc_final: 0.7983 (t-90) REVERT: x 57 MET cc_start: 0.8965 (mmm) cc_final: 0.8718 (mmm) REVERT: y 83 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8366 (mm-40) REVERT: z 18 GLU cc_start: 0.8695 (pp20) cc_final: 0.8346 (tm-30) REVERT: z 82 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8173 (t0) REVERT: A 60 GLU cc_start: 0.8717 (mp0) cc_final: 0.8508 (mp0) REVERT: B 35 ASP cc_start: 0.8947 (p0) cc_final: 0.8599 (p0) REVERT: C 33 GLN cc_start: 0.8788 (mp10) cc_final: 0.8580 (mp10) REVERT: C 48 HIS cc_start: 0.8538 (OUTLIER) cc_final: 0.7918 (p-80) REVERT: D 38 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8444 (mtpt) REVERT: J 53 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8350 (mt-10) REVERT: J 67 ASP cc_start: 0.8523 (t0) cc_final: 0.8242 (t0) REVERT: Q 123 ASN cc_start: 0.8417 (t0) cc_final: 0.8117 (t0) REVERT: R 121 MET cc_start: 0.8940 (mpp) cc_final: 0.8629 (mpp) REVERT: R 155 ARG cc_start: 0.8269 (tpp80) cc_final: 0.7902 (mmt-90) REVERT: R 231 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7837 (mpp) REVERT: R 250 TYR cc_start: 0.7499 (t80) cc_final: 0.7189 (t80) REVERT: w 61 MET cc_start: 0.8390 (ptt) cc_final: 0.8148 (ptm) REVERT: w 81 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8864 (m) REVERT: w 124 ASP cc_start: 0.6488 (p0) cc_final: 0.6257 (p0) REVERT: K 87 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8113 (ptm-80) outliers start: 121 outliers final: 42 residues processed: 661 average time/residue: 1.5414 time to fit residues: 1378.4287 Evaluate side-chains 612 residues out of total 4165 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 559 time to evaluate : 4.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 9 LEU Chi-restraints excluded: chain i residue 77 SER Chi-restraints excluded: chain i residue 169 SER Chi-restraints excluded: chain i residue 196 SER Chi-restraints excluded: chain j residue 24 PHE Chi-restraints excluded: chain k residue 51 THR Chi-restraints excluded: chain k residue 111 VAL Chi-restraints excluded: chain k residue 146 THR Chi-restraints excluded: chain k residue 199 GLN Chi-restraints excluded: chain l residue 105 MET Chi-restraints excluded: chain l residue 175 VAL Chi-restraints excluded: chain m residue 140 VAL Chi-restraints excluded: chain n residue 40 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain o residue 6 SER Chi-restraints excluded: chain o residue 12 SER Chi-restraints excluded: chain q residue 91 VAL Chi-restraints excluded: chain q residue 111 GLN Chi-restraints excluded: chain r residue 138 LYS Chi-restraints excluded: chain r residue 161 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 21 VAL Chi-restraints excluded: chain t residue 83 THR Chi-restraints excluded: chain u residue 26 ASP Chi-restraints excluded: chain y residue 83 GLN Chi-restraints excluded: chain z residue 17 ILE Chi-restraints excluded: chain z residue 25 THR Chi-restraints excluded: chain z residue 79 GLU Chi-restraints excluded: chain z residue 82 ASP Chi-restraints excluded: chain z residue 112 SER Chi-restraints excluded: chain z residue 117 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain D residue 32 VAL Chi-restraints excluded: chain D residue 38 LYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain E residue 85 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain J residue 56 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 41 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 150 VAL Chi-restraints excluded: chain R residue 231 MET Chi-restraints excluded: chain T residue 51 THR Chi-restraints excluded: chain w residue 81 VAL Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.4064 > 50: distance: 33 - 100: 19.459 distance: 48 - 103: 29.933 distance: 83 - 89: 20.770 distance: 89 - 90: 13.769 distance: 90 - 91: 15.476 distance: 90 - 93: 9.325 distance: 91 - 92: 25.375 distance: 91 - 100: 24.267 distance: 93 - 94: 14.474 distance: 94 - 95: 18.565 distance: 94 - 96: 14.239 distance: 95 - 97: 19.838 distance: 96 - 98: 27.436 distance: 97 - 99: 13.709 distance: 98 - 99: 10.494 distance: 100 - 101: 26.463 distance: 101 - 102: 35.701 distance: 101 - 104: 30.434 distance: 102 - 103: 55.409 distance: 102 - 108: 34.418 distance: 104 - 105: 21.807 distance: 105 - 106: 9.960 distance: 105 - 107: 5.142 distance: 108 - 109: 29.487 distance: 109 - 110: 14.156 distance: 109 - 112: 40.603 distance: 110 - 111: 15.788 distance: 110 - 113: 22.305 distance: 113 - 114: 24.439 distance: 114 - 115: 38.557 distance: 114 - 117: 27.010 distance: 115 - 116: 10.610 distance: 115 - 122: 18.496 distance: 117 - 118: 22.010 distance: 118 - 119: 8.645 distance: 119 - 120: 13.125 distance: 119 - 121: 18.124 distance: 122 - 123: 16.320 distance: 123 - 124: 20.305 distance: 123 - 126: 26.480 distance: 124 - 125: 10.153 distance: 124 - 133: 30.694 distance: 126 - 127: 24.995 distance: 127 - 128: 5.893 distance: 128 - 129: 8.483 distance: 133 - 134: 5.027 distance: 134 - 135: 10.282 distance: 134 - 137: 43.035 distance: 135 - 136: 14.525 distance: 135 - 144: 12.700 distance: 137 - 138: 23.746 distance: 138 - 139: 21.433 distance: 139 - 140: 3.762 distance: 140 - 141: 5.280 distance: 141 - 142: 5.067 distance: 141 - 143: 5.016 distance: 144 - 145: 5.829 distance: 145 - 146: 31.688 distance: 145 - 148: 24.699 distance: 146 - 147: 40.287 distance: 146 - 152: 21.428 distance: 148 - 149: 22.483 distance: 148 - 150: 17.464 distance: 149 - 151: 24.236 distance: 152 - 153: 15.999 distance: 153 - 154: 31.287 distance: 153 - 156: 43.735 distance: 154 - 155: 15.952 distance: 154 - 160: 12.089 distance: 156 - 157: 25.579 distance: 157 - 158: 36.049 distance: 157 - 159: 30.865 distance: 160 - 161: 10.872 distance: 160 - 166: 20.048 distance: 161 - 162: 18.458 distance: 161 - 164: 20.221 distance: 162 - 163: 38.304 distance: 162 - 167: 34.838 distance: 164 - 165: 15.532 distance: 165 - 166: 23.636 distance: 167 - 168: 22.613 distance: 168 - 169: 12.914 distance: 168 - 171: 11.109 distance: 169 - 170: 15.228 distance: 169 - 176: 22.484 distance: 171 - 172: 13.505 distance: 172 - 173: 6.988 distance: 173 - 174: 5.580 distance: 174 - 175: 3.335