Starting phenix.real_space_refine (version: 1.21rc1) on Wed May 17 03:14:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/05_2023/6em1_3893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/05_2023/6em1_3893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/05_2023/6em1_3893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/05_2023/6em1_3893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/05_2023/6em1_3893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6em1_3893/05_2023/6em1_3893.pdb" } resolution = 3.6 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 2008 5.49 5 S 142 5.16 5 C 55494 2.51 5 N 18143 2.21 5 O 24191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "x ARG 51": "NH1" <-> "NH2" Residue "x ARG 64": "NH1" <-> "NH2" Residue "x ARG 272": "NH1" <-> "NH2" Residue "x TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "3 ARG 123": "NH1" <-> "NH2" Residue "4 PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 60": "NH1" <-> "NH2" Residue "4 PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ASP 223": "OD1" <-> "OD2" Residue "4 TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 252": "NH1" <-> "NH2" Residue "5 PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 300": "NH1" <-> "NH2" Residue "5 ARG 382": "NH1" <-> "NH2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "b ARG 24": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 34": "NH1" <-> "NH2" Residue "b ARG 43": "NH1" <-> "NH2" Residue "b ARG 79": "NH1" <-> "NH2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 135": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "b ARG 302": "NH1" <-> "NH2" Residue "b ARG 332": "NH1" <-> "NH2" Residue "J ARG 258": "NH1" <-> "NH2" Residue "r ARG 9": "NH1" <-> "NH2" Residue "r ARG 30": "NH1" <-> "NH2" Residue "u ARG 2": "NH1" <-> "NH2" Residue "u ARG 23": "NH1" <-> "NH2" Residue "u ARG 33": "NH1" <-> "NH2" Residue "u ARG 43": "NH1" <-> "NH2" Residue "u ARG 44": "NH1" <-> "NH2" Residue "u ARG 56": "NH1" <-> "NH2" Residue "u ARG 75": "NH1" <-> "NH2" Residue "u ARG 80": "NH1" <-> "NH2" Residue "u ARG 83": "NH1" <-> "NH2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u ARG 111": "NH1" <-> "NH2" Residue "u ARG 113": "NH1" <-> "NH2" Residue "v ARG 7": "NH1" <-> "NH2" Residue "W ARG 31": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 81": "NH1" <-> "NH2" Residue "W ARG 166": "NH1" <-> "NH2" Residue "W ARG 198": "NH1" <-> "NH2" Residue "y ARG 85": "NH1" <-> "NH2" Residue "y ARG 100": "NH1" <-> "NH2" Residue "z ARG 6": "NH1" <-> "NH2" Residue "z ARG 29": "NH1" <-> "NH2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 48": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "h ARG 105": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 91": "NH1" <-> "NH2" Residue "H ARG 166": "NH1" <-> "NH2" Residue "H ARG 168": "NH1" <-> "NH2" Residue "H ARG 173": "NH1" <-> "NH2" Residue "j ARG 63": "NH1" <-> "NH2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "M ARG 19": "NH1" <-> "NH2" Residue "M ARG 108": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "P TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "Q ARG 92": "NH1" <-> "NH2" Residue "S ARG 28": "NH1" <-> "NH2" Residue "S ARG 117": "NH1" <-> "NH2" Residue "S TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 70": "NH1" <-> "NH2" Residue "V ARG 88": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 121": "NH1" <-> "NH2" Residue "K ARG 34": "NH1" <-> "NH2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K ARG 240": "NH1" <-> "NH2" Residue "K ARG 277": "NH1" <-> "NH2" Residue "K ARG 285": "NH1" <-> "NH2" Residue "m ARG 362": "NH1" <-> "NH2" Residue "D TYR 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 97": "NH1" <-> "NH2" Residue "o ARG 121": "NH1" <-> "NH2" Residue "o PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 207": "NH1" <-> "NH2" Residue "n ARG 18": "NH1" <-> "NH2" Residue "n ARG 34": "NH1" <-> "NH2" Residue "n ARG 88": "NH1" <-> "NH2" Residue "n ARG 92": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 104": "NH1" <-> "NH2" Residue "n ARG 109": "NH1" <-> "NH2" Residue "n ARG 174": "NH1" <-> "NH2" Residue "n TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 369": "NH1" <-> "NH2" Residue "n ARG 414": "NH1" <-> "NH2" Residue "n ARG 424": "NH1" <-> "NH2" Residue "t ARG 74": "NH1" <-> "NH2" Residue "t ARG 77": "NH1" <-> "NH2" Residue "t PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ARG 130": "NH1" <-> "NH2" Residue "t ARG 146": "NH1" <-> "NH2" Residue "t ARG 148": "NH1" <-> "NH2" Residue "t ARG 205": "NH1" <-> "NH2" Residue "t ARG 211": "NH1" <-> "NH2" Residue "t ARG 213": "NH1" <-> "NH2" Residue "t ARG 275": "NH1" <-> "NH2" Residue "t ARG 299": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 99980 Number of models: 1 Model: "" Number of chains: 45 Chain: "x" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2268 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 12, 'TRANS': 254} Chain breaks: 2 Chain: "F" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1936 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "3" Number of atoms: 1434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1434 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 5, 'TRANS': 167} Chain: "4" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1853 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 7, 'TRANS': 209} Chain breaks: 3 Chain: "5" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3055 Classifications: {'peptide': 385} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 372} Chain breaks: 3 Chain: "A" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1211 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 10, 'TRANS': 134} Chain breaks: 2 Chain: "b" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3410 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 20, 'TRANS': 400} Chain breaks: 3 Chain: "J" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 549 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 1, 'TRANS': 64} Chain: "r" Number of atoms: 628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 628 Classifications: {'peptide': 73} Link IDs: {'TRANS': 72} Chain: "s" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 224 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "u" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 976 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "v" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1087 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain breaks: 2 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1870 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "y" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 444 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "B" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2646 Classifications: {'peptide': 333} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2611 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain: "e" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1009 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "E" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1205 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Chain breaks: 1 Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "G" Number of atoms: 1231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1231 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 8, 'TRANS': 150} Chain breaks: 1 Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "H" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1510 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "i" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 594 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "j" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 566 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'TRANS': 69} Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 864 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "N" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1513 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "O" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 188} Chain: "P" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1062 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Chain: "Q" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1009 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "S" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1432 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "V" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 936 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 7, 'TRANS': 118} Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "1" Number of atoms: 38221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1785, 38221 Classifications: {'RNA': 1785} Modifications used: {'rna2p_pur': 183, 'rna2p_pyr': 122, 'rna3p_pur': 816, 'rna3p_pyr': 664} Link IDs: {'rna2p': 305, 'rna3p': 1479} Chain breaks: 12 Chain: "2" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 17, 'rna2p_pyr': 14, 'rna3p_pur': 61, 'rna3p_pyr': 66} Link IDs: {'rna2p': 30, 'rna3p': 127} Chain breaks: 6 Chain: "6" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1370 Classifications: {'RNA': 65} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 20, 'rna3p_pur': 21, 'rna3p_pyr': 16} Link IDs: {'rna2p': 27, 'rna3p': 37} Chain breaks: 1 Chain: "K" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2073 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 10, 'TRANS': 246} Chain breaks: 1 Chain: "m" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1362 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 17, 'TRANS': 143} Chain: "D" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1590 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 9, 'TRANS': 184} Chain breaks: 2 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "n" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2734 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Chain: "t" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1935 Classifications: {'peptide': 244} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 234} Chain breaks: 1 Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" 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 16649 SG CYS u 9 171.889 57.042 205.116 1.00221.58 S ATOM 16834 SG CYS u 32 169.526 58.134 207.535 1.00299.18 S ATOM 16866 SG CYS u 36 168.450 56.825 203.872 1.00197.00 S ATOM 35308 SG CYS j 19 110.585 101.946 134.325 1.00109.48 S ATOM 35333 SG CYS j 22 110.012 104.578 137.086 1.00 87.45 S ATOM 35433 SG CYS j 34 108.834 101.124 137.532 1.00 98.44 S ATOM 35451 SG CYS j 37 107.354 103.379 135.144 1.00 75.92 S Residues with excluded nonbonded symmetry interactions: 202 residue: pdb=" N ASP 4 57 " occ=0.52 ... (6 atoms not shown) pdb=" OD2 ASP 4 57 " occ=0.52 residue: pdb=" N VAL O 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 3 " occ=0.50 residue: pdb=" N GLU O 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU O 4 " occ=0.50 residue: pdb=" N PRO O 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD PRO O 5 " occ=0.50 residue: pdb=" N VAL O 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 6 " occ=0.50 residue: pdb=" N VAL O 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 7 " occ=0.50 residue: pdb=" N VAL O 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 VAL O 8 " occ=0.50 residue: pdb=" N ILE O 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1 ILE O 9 " occ=0.50 residue: pdb=" N ASP O 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP O 10 " occ=0.50 residue: pdb=" N GLY O 11 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 11 " occ=0.50 residue: pdb=" N LYS O 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS O 12 " occ=0.50 residue: pdb=" N GLY O 13 " occ=0.50 ... (2 atoms not shown) pdb=" O GLY O 13 " occ=0.50 ... (remaining 190 not shown) Time building chain proxies: 37.15, per 1000 atoms: 0.37 Number of scatterers: 99980 At special positions: 0 Unit cell: (215.716, 228.724, 328.452, 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 142 16.00 P 2008 15.00 O 24191 8.00 N 18143 7.00 C 55494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 3 28 " - pdb=" SG CYS 3 38 " distance=2.72 Simple disulfide: pdb=" SG CYS 3 28 " - pdb=" SG CYS 3 43 " distance=2.61 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 80398 O5' G 13199 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.55 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 9 " Number of angles added : 6 13872 Ramachandran restraints generated. 6936 Oldfield, 0 Emsley, 6936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13416 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 75 sheets defined 39.7% alpha, 13.9% beta 600 base pairs and 1018 stacking pairs defined. Time for finding SS restraints: 29.10 Creating SS restraints... Processing helix chain 'x' and resid 12 through 19 Processing helix chain 'x' and resid 21 through 44 removed outlier: 4.356A pdb=" N ASN x 27 " --> pdb=" O LYS x 23 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS x 28 " --> pdb=" O HIS x 24 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU x 40 " --> pdb=" O LYS x 36 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU x 43 " --> pdb=" O LYS x 39 " (cutoff:3.500A) Processing helix chain 'x' and resid 45 through 50 removed outlier: 3.638A pdb=" N GLN x 50 " --> pdb=" O GLU x 46 " (cutoff:3.500A) Processing helix chain 'x' and resid 50 through 55 removed outlier: 3.735A pdb=" N GLU x 54 " --> pdb=" O GLN x 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 79 through 86 removed outlier: 3.995A pdb=" N ARG x 83 " --> pdb=" O ASP x 79 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN x 86 " --> pdb=" O MET x 82 " (cutoff:3.500A) Processing helix chain 'x' and resid 104 through 118 removed outlier: 3.703A pdb=" N TYR x 108 " --> pdb=" O LYS x 104 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE x 113 " --> pdb=" O GLU x 109 " (cutoff:3.500A) Processing helix chain 'x' and resid 132 through 142 Processing helix chain 'x' and resid 206 through 218 removed outlier: 3.703A pdb=" N VAL x 210 " --> pdb=" O LEU x 206 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG x 212 " --> pdb=" O GLN x 208 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER x 216 " --> pdb=" O ARG x 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 72 removed outlier: 3.612A pdb=" N SER F 16 " --> pdb=" O GLN F 12 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS F 21 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLN F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 28 " --> pdb=" O GLU F 24 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 35 " --> pdb=" O ALA F 31 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS F 70 " --> pdb=" O LYS F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.764A pdb=" N VAL F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 130 removed outlier: 3.506A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS F 128 " --> pdb=" O LEU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 133 No H-bonds generated for 'chain 'F' and resid 131 through 133' Processing helix chain 'F' and resid 140 through 152 removed outlier: 3.912A pdb=" N ILE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 Processing helix chain 'F' and resid 174 through 177 removed outlier: 3.657A pdb=" N GLY F 177 " --> pdb=" O GLY F 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 174 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 222 through 226 Processing helix chain 'F' and resid 235 through 244 removed outlier: 3.545A pdb=" N SER F 242 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 12 removed outlier: 3.915A pdb=" N GLN 3 8 " --> pdb=" O GLU 3 4 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL 3 9 " --> pdb=" O ILE 3 5 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN 3 12 " --> pdb=" O GLN 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 67 through 72 removed outlier: 3.642A pdb=" N ALA 3 70 " --> pdb=" O PRO 3 67 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N HIS 3 71 " --> pdb=" O GLU 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 98 removed outlier: 3.620A pdb=" N GLN 3 91 " --> pdb=" O THR 3 87 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS 3 96 " --> pdb=" O GLN 3 92 " (cutoff:3.500A) Processing helix chain '3' and resid 101 through 117 removed outlier: 4.439A pdb=" N LYS 3 109 " --> pdb=" O ARG 3 105 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 126 Processing helix chain '3' and resid 140 through 145 Processing helix chain '3' and resid 146 through 157 removed outlier: 3.760A pdb=" N ARG 3 150 " --> pdb=" O GLN 3 146 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS 3 151 " --> pdb=" O ASN 3 147 " (cutoff:3.500A) Processing helix chain '3' and resid 157 through 168 removed outlier: 3.613A pdb=" N ALA 3 161 " --> pdb=" O LYS 3 157 " (cutoff:3.500A) Processing helix chain '4' and resid 6 through 11 Processing helix chain '4' and resid 14 through 32 removed outlier: 3.775A pdb=" N ARG 4 18 " --> pdb=" O ASN 4 14 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN 4 20 " --> pdb=" O LYS 4 16 " (cutoff:3.500A) Processing helix chain '4' and resid 38 through 55 removed outlier: 3.627A pdb=" N TYR 4 51 " --> pdb=" O LYS 4 47 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA 4 52 " --> pdb=" O GLY 4 48 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET 4 53 " --> pdb=" O LEU 4 49 " (cutoff:3.500A) Processing helix chain '4' and resid 61 through 71 removed outlier: 4.485A pdb=" N ASN 4 67 " --> pdb=" O GLN 4 63 " (cutoff:3.500A) Processing helix chain '4' and resid 71 through 76 Processing helix chain '4' and resid 91 through 109 removed outlier: 3.530A pdb=" N LYS 4 97 " --> pdb=" O LYS 4 93 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG 4 100 " --> pdb=" O ILE 4 96 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE 4 102 " --> pdb=" O PHE 4 98 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS 4 107 " --> pdb=" O TRP 4 103 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 135 removed outlier: 3.600A pdb=" N TYR 4 121 " --> pdb=" O ARG 4 117 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU 4 129 " --> pdb=" O ILE 4 125 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU 4 133 " --> pdb=" O LEU 4 129 " (cutoff:3.500A) Processing helix chain '4' and resid 142 through 150 removed outlier: 4.084A pdb=" N ASP 4 147 " --> pdb=" O LYS 4 143 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU 4 148 " --> pdb=" O LYS 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 182 removed outlier: 3.882A pdb=" N ILE 4 171 " --> pdb=" O THR 4 167 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU 4 178 " --> pdb=" O VAL 4 174 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ASP 4 179 " --> pdb=" O ASP 4 175 " (cutoff:3.500A) Processing helix chain '4' and resid 218 through 218 No H-bonds generated for 'chain '4' and resid 218 through 218' Processing helix chain '4' and resid 221 through 226 removed outlier: 4.241A pdb=" N ALA 4 226 " --> pdb=" O GLN 4 222 " (cutoff:3.500A) Processing helix chain '4' and resid 231 through 242 removed outlier: 3.680A pdb=" N LYS 4 239 " --> pdb=" O ARG 4 235 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU 4 240 " --> pdb=" O GLU 4 236 " (cutoff:3.500A) Processing helix chain '5' and resid 119 through 127 removed outlier: 4.029A pdb=" N LEU 5 123 " --> pdb=" O ASP 5 119 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU 5 126 " --> pdb=" O LYS 5 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.929A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.795A pdb=" N ALA A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 81 " --> pdb=" O ILE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.538A pdb=" N PHE A 143 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 removed outlier: 4.634A pdb=" N ILE A 152 " --> pdb=" O HIS A 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N HIS A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 28 removed outlier: 3.650A pdb=" N VAL b 21 " --> pdb=" O LEU b 17 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASN b 23 " --> pdb=" O ASP b 19 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N GLN b 26 " --> pdb=" O LEU b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 66 removed outlier: 3.544A pdb=" N TYR b 52 " --> pdb=" O ARG b 48 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL b 58 " --> pdb=" O GLY b 54 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE b 64 " --> pdb=" O LYS b 60 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS b 66 " --> pdb=" O GLU b 62 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 84 removed outlier: 3.796A pdb=" N ASP b 80 " --> pdb=" O PRO b 76 " (cutoff:3.500A) Processing helix chain 'b' and resid 87 through 117 removed outlier: 4.206A pdb=" N ILE b 98 " --> pdb=" O SER b 94 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER b 103 " --> pdb=" O SER b 99 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU b 106 " --> pdb=" O LYS b 102 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG b 114 " --> pdb=" O ARG b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 142 removed outlier: 3.550A pdb=" N LYS b 129 " --> pdb=" O CYS b 125 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE b 139 " --> pdb=" O ARG b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 160 removed outlier: 3.956A pdb=" N TYR b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY b 158 " --> pdb=" O ARG b 154 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 removed outlier: 4.336A pdb=" N CYS b 186 " --> pdb=" O SER b 182 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE b 187 " --> pdb=" O PHE b 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR b 188 " --> pdb=" O LEU b 184 " (cutoff:3.500A) Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.777A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE b 243 " --> pdb=" O SER b 239 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA b 244 " --> pdb=" O ILE b 240 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS b 245 " --> pdb=" O TYR b 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU b 246 " --> pdb=" O ALA b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 274 removed outlier: 3.646A pdb=" N GLN b 267 " --> pdb=" O THR b 263 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS b 269 " --> pdb=" O GLU b 265 " (cutoff:3.500A) Processing helix chain 'b' and resid 274 through 279 removed outlier: 4.308A pdb=" N PHE b 278 " --> pdb=" O ILE b 274 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA b 279 " --> pdb=" O LYS b 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 274 through 279' Processing helix chain 'b' and resid 280 through 282 No H-bonds generated for 'chain 'b' and resid 280 through 282' Processing helix chain 'b' and resid 308 through 312 removed outlier: 3.714A pdb=" N GLU b 311 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 342 removed outlier: 4.276A pdb=" N VAL b 328 " --> pdb=" O LEU b 324 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL b 331 " --> pdb=" O ASN b 327 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG b 332 " --> pdb=" O VAL b 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU b 337 " --> pdb=" O ASN b 333 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU b 340 " --> pdb=" O CYS b 336 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA b 341 " --> pdb=" O GLU b 337 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER b 342 " --> pdb=" O LYS b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 385 removed outlier: 3.976A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU b 385 " --> pdb=" O SER b 381 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 407 removed outlier: 3.621A pdb=" N ALA b 404 " --> pdb=" O ARG b 400 " (cutoff:3.500A) Processing helix chain 'b' and resid 424 through 429 removed outlier: 3.943A pdb=" N TRP b 427 " --> pdb=" O ASP b 424 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS b 428 " --> pdb=" O ASP b 425 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASN b 429 " --> pdb=" O GLU b 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 424 through 429' Processing helix chain 'b' and resid 442 through 444 No H-bonds generated for 'chain 'b' and resid 442 through 444' Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.621A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU b 461 " --> pdb=" O GLU b 457 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS b 462 " --> pdb=" O GLU b 458 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN b 465 " --> pdb=" O GLU b 461 " (cutoff:3.500A) Processing helix chain 'J' and resid 198 through 208 removed outlier: 3.699A pdb=" N HIS J 203 " --> pdb=" O LYS J 199 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU J 206 " --> pdb=" O LYS J 202 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG J 207 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 216 through 221 removed outlier: 3.685A pdb=" N HIS J 220 " --> pdb=" O SER J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 259 removed outlier: 3.967A pdb=" N LEU J 244 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE J 246 " --> pdb=" O ARG J 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA J 253 " --> pdb=" O GLN J 249 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J 254 " --> pdb=" O SER J 250 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU J 255 " --> pdb=" O LEU J 251 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL J 256 " --> pdb=" O ASP J 252 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP J 259 " --> pdb=" O LEU J 255 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 removed outlier: 3.614A pdb=" N HIS r 10 " --> pdb=" O TYR r 6 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 41 removed outlier: 4.506A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 43 through 70 removed outlier: 3.734A pdb=" N GLY r 47 " --> pdb=" O THR r 43 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS r 52 " --> pdb=" O LYS r 48 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA r 56 " --> pdb=" O LYS r 52 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS r 68 " --> pdb=" O LYS r 64 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 17 Processing helix chain 's' and resid 19 through 32 removed outlier: 4.141A pdb=" N ALA s 25 " --> pdb=" O LYS s 21 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU s 30 " --> pdb=" O HIS s 26 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS s 31 " --> pdb=" O ARG s 27 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS s 32 " --> pdb=" O LYS s 28 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 removed outlier: 3.796A pdb=" N GLN u 42 " --> pdb=" O LYS u 38 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 57 removed outlier: 4.128A pdb=" N ARG u 56 " --> pdb=" O THR u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 88 through 113 removed outlier: 3.643A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU u 98 " --> pdb=" O ALA u 94 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU u 104 " --> pdb=" O ARG u 100 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 12 removed outlier: 3.517A pdb=" N LYS v 8 " --> pdb=" O VAL v 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET v 9 " --> pdb=" O ARG v 5 " (cutoff:3.500A) Processing helix chain 'v' and resid 33 through 39 removed outlier: 3.745A pdb=" N ALA v 38 " --> pdb=" O PRO v 34 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN v 39 " --> pdb=" O ILE v 35 " (cutoff:3.500A) Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 158 through 163 Processing helix chain 'v' and resid 164 through 166 No H-bonds generated for 'chain 'v' and resid 164 through 166' Processing helix chain 'v' and resid 178 through 193 removed outlier: 3.562A pdb=" N GLU v 183 " --> pdb=" O GLU v 179 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS v 191 " --> pdb=" O LYS v 187 " (cutoff:3.500A) Processing helix chain 'v' and resid 195 through 201 Processing helix chain 'v' and resid 211 through 226 removed outlier: 3.534A pdb=" N ARG v 225 " --> pdb=" O ARG v 221 " (cutoff:3.500A) Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.918A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG W 25 " --> pdb=" O GLU W 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG W 31 " --> pdb=" O PHE W 27 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ASP W 35 " --> pdb=" O ARG W 31 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR W 36 " --> pdb=" O GLU W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 removed outlier: 4.060A pdb=" N TRP W 60 " --> pdb=" O ILE W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 69 through 78 removed outlier: 3.945A pdb=" N LEU W 77 " --> pdb=" O LEU W 73 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 96 removed outlier: 4.033A pdb=" N SER W 93 " --> pdb=" O LEU W 89 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU W 95 " --> pdb=" O GLN W 91 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N CYS W 96 " --> pdb=" O LEU W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 removed outlier: 3.642A pdb=" N VAL W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR W 115 " --> pdb=" O THR W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 161 through 168 removed outlier: 3.538A pdb=" N ASN W 167 " --> pdb=" O PRO W 163 " (cutoff:3.500A) Processing helix chain 'W' and resid 196 through 206 removed outlier: 4.011A pdb=" N LEU W 203 " --> pdb=" O GLN W 199 " (cutoff:3.500A) Processing helix chain 'y' and resid 32 through 42 removed outlier: 3.941A pdb=" N PHE y 38 " --> pdb=" O PHE y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 59 through 63 removed outlier: 3.808A pdb=" N THR y 63 " --> pdb=" O GLY y 60 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 88 removed outlier: 3.686A pdb=" N ARG y 85 " --> pdb=" O LEU y 81 " (cutoff:3.500A) Processing helix chain 'y' and resid 103 through 108 Processing helix chain 'y' and resid 122 through 133 removed outlier: 3.911A pdb=" N GLU y 126 " --> pdb=" O ASP y 122 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER y 130 " --> pdb=" O GLU y 126 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP y 131 " --> pdb=" O GLU y 127 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 175 removed outlier: 3.674A pdb=" N LEU y 173 " --> pdb=" O ASP y 169 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER y 175 " --> pdb=" O GLU y 171 " (cutoff:3.500A) Processing helix chain 'y' and resid 211 through 222 removed outlier: 3.619A pdb=" N VAL y 217 " --> pdb=" O PRO y 213 " (cutoff:3.500A) Processing helix chain 'z' and resid 7 through 17 removed outlier: 3.805A pdb=" N LEU z 11 " --> pdb=" O ALA z 7 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN z 12 " --> pdb=" O SER z 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER z 15 " --> pdb=" O LEU z 11 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL z 16 " --> pdb=" O ASN z 12 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS z 17 " --> pdb=" O ALA z 13 " (cutoff:3.500A) Processing helix chain 'z' and resid 18 through 22 removed outlier: 5.833A pdb=" N VAL z 21 " --> pdb=" O ARG z 18 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE z 22 " --> pdb=" O ARG z 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 18 through 22' Processing helix chain 'z' and resid 23 through 34 removed outlier: 3.773A pdb=" N ASP z 27 " --> pdb=" O GLN z 23 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN z 31 " --> pdb=" O ASP z 27 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG z 32 " --> pdb=" O ALA z 28 " (cutoff:3.500A) Processing helix chain 'z' and resid 35 through 56 removed outlier: 3.541A pdb=" N LEU z 41 " --> pdb=" O LEU z 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU z 53 " --> pdb=" O LEU z 49 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLU z 54 " --> pdb=" O LYS z 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN z 55 " --> pdb=" O LYS z 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 117 removed outlier: 3.525A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 Processing helix chain 'B' and resid 187 through 196 Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.830A pdb=" N GLU B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'C' and resid 31 through 44 removed outlier: 4.564A pdb=" N SER C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.585A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 138 Processing helix chain 'C' and resid 154 through 157 Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.710A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 169 " --> pdb=" O ALA C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 184 removed outlier: 3.563A pdb=" N LEU C 179 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU C 182 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 183 " --> pdb=" O LEU C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.616A pdb=" N ARG C 195 " --> pdb=" O GLY C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 221 removed outlier: 4.343A pdb=" N ASN C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.510A pdb=" N LEU C 238 " --> pdb=" O ASN C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 263 removed outlier: 3.989A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 294 through 298 Processing helix chain 'C' and resid 322 through 327 removed outlier: 3.596A pdb=" N ARG C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 337 removed outlier: 3.544A pdb=" N GLU C 337 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'e' and resid 41 through 45 Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 removed outlier: 3.638A pdb=" N GLU e 83 " --> pdb=" O VAL e 79 " (cutoff:3.500A) Processing helix chain 'e' and resid 84 through 88 removed outlier: 4.306A pdb=" N MET e 87 " --> pdb=" O THR e 84 " (cutoff:3.500A) Processing helix chain 'e' and resid 101 through 116 removed outlier: 4.449A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG e 111 " --> pdb=" O VAL e 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 103 through 107 removed outlier: 3.663A pdb=" N ALA E 107 " --> pdb=" O GLU E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 152 removed outlier: 3.616A pdb=" N GLU E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS E 151 " --> pdb=" O ALA E 147 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR E 152 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 removed outlier: 3.534A pdb=" N SER E 160 " --> pdb=" O LYS E 156 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 43 removed outlier: 3.654A pdb=" N ALA f 41 " --> pdb=" O THR f 37 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE f 43 " --> pdb=" O GLN f 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 95 Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 101 through 117 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.770A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 173 Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.987A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 222 Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.993A pdb=" N THR h 11 " --> pdb=" O TYR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 34 removed outlier: 3.659A pdb=" N GLU h 27 " --> pdb=" O ASP h 23 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 70 removed outlier: 4.012A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG h 63 " --> pdb=" O ASN h 59 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU h 69 " --> pdb=" O ALA h 65 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 90 Processing helix chain 'h' and resid 93 through 99 removed outlier: 3.729A pdb=" N SER h 98 " --> pdb=" O LYS h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.600A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N MET H 78 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL H 82 " --> pdb=" O MET H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 150 through 164 removed outlier: 3.545A pdb=" N VAL H 154 " --> pdb=" O SER H 150 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE H 164 " --> pdb=" O ASP H 160 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.729A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 63 removed outlier: 4.101A pdb=" N ASP i 59 " --> pdb=" O ARG i 55 " (cutoff:3.500A) Processing helix chain 'i' and resid 64 through 77 removed outlier: 4.244A pdb=" N ARG i 68 " --> pdb=" O SER i 64 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS i 71 " --> pdb=" O LYS i 67 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL i 72 " --> pdb=" O ARG i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 99 removed outlier: 3.586A pdb=" N ASN i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG i 98 " --> pdb=" O ILE i 94 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 55 removed outlier: 3.775A pdb=" N ARG j 55 " --> pdb=" O ALA j 51 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 75 Processing helix chain 'L' and resid 27 through 46 removed outlier: 3.693A pdb=" N ASN L 37 " --> pdb=" O VAL L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 92 Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 95 removed outlier: 3.662A pdb=" N LYS M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 111 removed outlier: 3.618A pdb=" N ARG M 109 " --> pdb=" O GLN M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 135 removed outlier: 3.625A pdb=" N TYR M 129 " --> pdb=" O LYS M 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.621A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.668A pdb=" N LEU N 22 " --> pdb=" O VAL N 18 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG N 24 " --> pdb=" O ARG N 20 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP N 28 " --> pdb=" O ARG N 24 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 50 Processing helix chain 'N' and resid 97 through 110 removed outlier: 3.940A pdb=" N THR N 101 " --> pdb=" O SER N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 145 removed outlier: 3.918A pdb=" N ASP N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.643A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 163 removed outlier: 3.635A pdb=" N GLY N 163 " --> pdb=" O GLU N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 172 Processing helix chain 'N' and resid 188 through 195 Processing helix chain 'O' and resid 15 through 29 removed outlier: 4.244A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU O 27 " --> pdb=" O VAL O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 51 removed outlier: 4.408A pdb=" N ASN O 50 " --> pdb=" O GLU O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 60 Processing helix chain 'O' and resid 65 through 69 Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'O' and resid 138 through 144 Processing helix chain 'O' and resid 149 through 159 Processing helix chain 'O' and resid 160 through 185 removed outlier: 4.114A pdb=" N GLU O 166 " --> pdb=" O VAL O 162 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR O 167 " --> pdb=" O SER O 163 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS O 177 " --> pdb=" O ALA O 173 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL O 178 " --> pdb=" O PHE O 174 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA O 183 " --> pdb=" O ALA O 179 " (cutoff:3.500A) Processing helix chain 'O' and resid 190 through 198 Processing helix chain 'P' and resid 25 through 37 removed outlier: 3.504A pdb=" N THR P 29 " --> pdb=" O SER P 25 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU P 31 " --> pdb=" O LYS P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 76 Processing helix chain 'P' and resid 84 through 105 removed outlier: 3.924A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 23 through 41 removed outlier: 3.879A pdb=" N PHE Q 35 " --> pdb=" O LYS Q 31 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG Q 38 " --> pdb=" O THR Q 34 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP Q 41 " --> pdb=" O ALA Q 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 54 removed outlier: 4.114A pdb=" N LYS Q 50 " --> pdb=" O LYS Q 46 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 removed outlier: 3.503A pdb=" N ALA Q 70 " --> pdb=" O ARG Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 116 Processing helix chain 'Q' and resid 124 through 131 Processing helix chain 'S' and resid 33 through 49 removed outlier: 3.618A pdb=" N TYR S 43 " --> pdb=" O SER S 39 " (cutoff:3.500A) Processing helix chain 'S' and resid 98 through 113 Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'V' and resid 119 through 124 removed outlier: 3.537A pdb=" N ASP V 124 " --> pdb=" O LYS V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 128 through 132 Processing helix chain 'Y' and resid 11 through 20 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.759A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 38 through 43 Processing helix chain 'Y' and resid 75 through 78 Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'K' and resid 33 through 49 removed outlier: 3.697A pdb=" N VAL K 37 " --> pdb=" O PRO K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 77 Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 130 through 135 Processing helix chain 'K' and resid 136 through 145 removed outlier: 3.957A pdb=" N LEU K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 175 Processing helix chain 'K' and resid 184 through 188 removed outlier: 4.550A pdb=" N THR K 188 " --> pdb=" O ASP K 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 188' Processing helix chain 'K' and resid 189 through 194 removed outlier: 3.793A pdb=" N LEU K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 232 removed outlier: 3.822A pdb=" N LEU K 222 " --> pdb=" O SER K 218 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN K 225 " --> pdb=" O THR K 221 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS K 227 " --> pdb=" O THR K 223 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 274 removed outlier: 3.825A pdb=" N ASP K 261 " --> pdb=" O GLU K 257 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS K 272 " --> pdb=" O GLU K 268 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA K 273 " --> pdb=" O GLN K 269 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR K 274 " --> pdb=" O LEU K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 297 through 301 removed outlier: 3.548A pdb=" N GLU K 300 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 266 Processing helix chain 'm' and resid 269 through 285 removed outlier: 4.061A pdb=" N ARG m 281 " --> pdb=" O MET m 277 " (cutoff:3.500A) Processing helix chain 'm' and resid 290 through 300 removed outlier: 3.962A pdb=" N LYS m 295 " --> pdb=" O PRO m 291 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU m 296 " --> pdb=" O LYS m 292 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS m 298 " --> pdb=" O LEU m 294 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS m 300 " --> pdb=" O GLU m 296 " (cutoff:3.500A) Processing helix chain 'm' and resid 349 through 357 removed outlier: 3.749A pdb=" N GLU m 355 " --> pdb=" O LYS m 351 " (cutoff:3.500A) Processing helix chain 'm' and resid 383 through 396 removed outlier: 3.708A pdb=" N TYR m 395 " --> pdb=" O SER m 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 287 removed outlier: 4.394A pdb=" N LEU D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D 285 " --> pdb=" O PHE D 281 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG D 286 " --> pdb=" O SER D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 312 removed outlier: 4.507A pdb=" N GLU D 307 " --> pdb=" O LYS D 303 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N ASN D 310 " --> pdb=" O ALA D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 removed outlier: 3.688A pdb=" N PHE D 332 " --> pdb=" O ARG D 328 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 334 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 378 removed outlier: 4.319A pdb=" N HIS D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY D 378 " --> pdb=" O ILE D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 434 removed outlier: 3.815A pdb=" N LYS D 434 " --> pdb=" O GLU D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 456 removed outlier: 3.899A pdb=" N SER D 449 " --> pdb=" O ASP D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 475 removed outlier: 3.594A pdb=" N ALA D 471 " --> pdb=" O LYS D 467 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS D 475 " --> pdb=" O ALA D 471 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 111 Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 212 removed outlier: 3.755A pdb=" N LEU o 211 " --> pdb=" O ARG o 207 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA o 212 " --> pdb=" O ILE o 208 " (cutoff:3.500A) Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 64 through 72 Processing helix chain 'n' and resid 74 through 97 removed outlier: 3.726A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA n 93 " --> pdb=" O LYS n 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 108 Processing helix chain 'n' and resid 115 through 120 removed outlier: 3.886A pdb=" N LYS n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU n 120 " --> pdb=" O HIS n 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 115 through 120' Processing helix chain 'n' and resid 124 through 144 removed outlier: 4.345A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ASN n 137 " --> pdb=" O ASP n 133 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET n 138 " --> pdb=" O ASP n 134 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU n 139 " --> pdb=" O ALA n 135 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASN n 144 " --> pdb=" O PHE n 140 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 173 removed outlier: 3.508A pdb=" N ILE n 156 " --> pdb=" O SER n 152 " (cutoff:3.500A) Processing helix chain 'n' and resid 216 through 241 removed outlier: 3.682A pdb=" N THR n 220 " --> pdb=" O ARG n 216 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR n 227 " --> pdb=" O GLU n 223 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 254 Processing helix chain 'n' and resid 354 through 359 Processing helix chain 'n' and resid 376 through 384 Processing helix chain 'n' and resid 391 through 394 Processing helix chain 'n' and resid 428 through 430 No H-bonds generated for 'chain 'n' and resid 428 through 430' Processing helix chain 'n' and resid 431 through 439 removed outlier: 4.386A pdb=" N ASN n 437 " --> pdb=" O PHE n 433 " (cutoff:3.500A) Processing helix chain 'n' and resid 443 through 447 removed outlier: 4.009A pdb=" N LYS n 446 " --> pdb=" O PRO n 443 " (cutoff:3.500A) Processing helix chain 't' and resid 57 through 87 removed outlier: 3.983A pdb=" N THR t 65 " --> pdb=" O ILE t 61 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 156 through 166 removed outlier: 3.747A pdb=" N ILE t 162 " --> pdb=" O LYS t 158 " (cutoff:3.500A) Processing helix chain 't' and resid 182 through 191 removed outlier: 4.246A pdb=" N LEU t 186 " --> pdb=" O ASN t 182 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS t 188 " --> pdb=" O TYR t 184 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL t 189 " --> pdb=" O PRO t 185 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE t 190 " --> pdb=" O LEU t 186 " (cutoff:3.500A) Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 232 through 239 Processing helix chain 't' and resid 246 through 256 Processing helix chain 't' and resid 260 through 265 Processing helix chain 't' and resid 281 through 299 removed outlier: 3.657A pdb=" N ARG t 285 " --> pdb=" O GLY t 281 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU t 286 " --> pdb=" O SER t 282 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER t 296 " --> pdb=" O ARG t 292 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG t 297 " --> pdb=" O GLU t 293 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'x' and resid 120 through 123 removed outlier: 6.528A pdb=" N ILE x 95 " --> pdb=" O THR x 122 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP x 146 " --> pdb=" O LYS x 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY x 159 " --> pdb=" O ASN x 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'x' and resid 196 through 198 removed outlier: 3.900A pdb=" N ARG x 253 " --> pdb=" O LYS x 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 83 through 87 Processing sheet with id=AA4, first strand: chain 'F' and resid 135 through 136 Processing sheet with id=AA5, first strand: chain 'F' and resid 153 through 155 Processing sheet with id=AA6, first strand: chain '3' and resid 50 through 55 Processing sheet with id=AA7, first strand: chain '3' and resid 135 through 136 Processing sheet with id=AA8, first strand: chain '5' and resid 34 through 38 removed outlier: 6.770A pdb=" N ARG 5 2 " --> pdb=" O LEU 5 410 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE 5 406 " --> pdb=" O SER 5 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '5' and resid 51 through 52 removed outlier: 6.159A pdb=" N VAL 5 67 " --> pdb=" O SER 5 113 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N SER 5 113 " --> pdb=" O VAL 5 67 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU 5 69 " --> pdb=" O THR 5 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '5' and resid 140 through 145 removed outlier: 6.668A pdb=" N ALA 5 158 " --> pdb=" O VAL 5 141 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU 5 143 " --> pdb=" O VAL 5 156 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N VAL 5 156 " --> pdb=" O LEU 5 143 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR 5 154 " --> pdb=" O PRO 5 145 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU 5 163 " --> pdb=" O THR 5 159 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA 5 179 " --> pdb=" O ILE 5 166 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS 5 168 " --> pdb=" O LYS 5 177 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS 5 177 " --> pdb=" O LYS 5 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '5' and resid 189 through 192 removed outlier: 4.805A pdb=" N GLY 5 209 " --> pdb=" O LEU 5 213 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LEU 5 213 " --> pdb=" O GLY 5 209 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP 5 230 " --> pdb=" O LEU 5 216 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU 5 218 " --> pdb=" O GLN 5 228 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLN 5 228 " --> pdb=" O GLU 5 218 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '5' and resid 248 through 251 removed outlier: 4.667A pdb=" N HIS 5 278 " --> pdb=" O THR 5 274 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA 5 292 " --> pdb=" O LYS 5 281 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '5' and resid 303 through 308 removed outlier: 5.288A pdb=" N GLN 5 305 " --> pdb=" O THR 5 336 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR 5 336 " --> pdb=" O GLN 5 305 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '5' and resid 369 through 370 removed outlier: 6.420A pdb=" N VAL 5 384 " --> pdb=" O LYS 5 397 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS 5 397 " --> pdb=" O VAL 5 384 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE 5 386 " --> pdb=" O LEU 5 395 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS 5 393 " --> pdb=" O ASP 5 388 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 35 through 37 removed outlier: 4.214A pdb=" N TYR A 98 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 137 through 138 removed outlier: 5.867A pdb=" N LEU A 137 " --> pdb=" O VAL J 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 176 through 177 removed outlier: 3.605A pdb=" N VAL A 176 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 191 " --> pdb=" O VAL A 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 180 through 182 removed outlier: 4.258A pdb=" N SER A 180 " --> pdb=" O TRP A 187 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL A 182 " --> pdb=" O LYS A 185 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 185 " --> pdb=" O VAL A 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'b' and resid 168 through 172 removed outlier: 4.174A pdb=" N ARG b 168 " --> pdb=" O ARG b 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 251 through 255 removed outlier: 6.356A pdb=" N TYR b 252 " --> pdb=" O VAL b 286 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASN b 288 " --> pdb=" O TYR b 252 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N MET b 254 " --> pdb=" O ASN b 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'b' and resid 435 through 436 removed outlier: 3.806A pdb=" N LYS b 439 " --> pdb=" O LEU b 436 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.732A pdb=" N TYR u 4 " --> pdb=" O CYS u 13 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'u' and resid 28 through 30 removed outlier: 3.634A pdb=" N TYR V 94 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL u 22 " --> pdb=" O TYR V 94 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU V 93 " --> pdb=" O TRP V 85 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 64 through 66 removed outlier: 3.552A pdb=" N VAL W 42 " --> pdb=" O ALA W 219 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS W 44 " --> pdb=" O VAL W 217 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL W 217 " --> pdb=" O HIS W 44 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 120 through 123 Processing sheet with id=AC8, first strand: chain 'W' and resid 174 through 176 Processing sheet with id=AC9, first strand: chain 'y' and resid 2 through 4 Processing sheet with id=AD1, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.859A pdb=" N CYS y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'y' and resid 64 through 65 removed outlier: 6.438A pdb=" N LEU y 70 " --> pdb=" O GLN y 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'y' and resid 109 through 110 Processing sheet with id=AD4, first strand: chain 'y' and resid 152 through 154 removed outlier: 6.563A pdb=" N GLY y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 355 through 359 removed outlier: 4.859A pdb=" N SER B 355 " --> pdb=" O ASP B 59 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP B 59 " --> pdb=" O SER B 355 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL B 72 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 57 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU B 74 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N THR B 55 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 76 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N MET B 53 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.213A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 157 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 162 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 98 through 106 removed outlier: 7.213A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 15 through 21 removed outlier: 6.009A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 8 " --> pdb=" O ASN C 18 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU C 150 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU C 206 " --> pdb=" O ILE C 249 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR C 251 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL C 208 " --> pdb=" O THR C 251 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 62 through 64 Processing sheet with id=AE1, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AE2, first strand: chain 'e' and resid 72 through 76 removed outlier: 6.390A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 77 through 80 removed outlier: 6.506A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'f' and resid 8 through 16 removed outlier: 6.540A pdb=" N LEU f 29 " --> pdb=" O LEU f 14 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG f 73 " --> pdb=" O ARG f 82 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA f 96 " --> pdb=" O HIS f 13 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.233A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'h' and resid 115 through 118 removed outlier: 4.734A pdb=" N LYS h 115 " --> pdb=" O PHE L 126 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 33 through 37 Processing sheet with id=AF1, first strand: chain 'H' and resid 133 through 136 removed outlier: 3.560A pdb=" N LYS H 87 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG H 91 " --> pdb=" O VAL H 181 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL H 181 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL H 93 " --> pdb=" O ILE H 179 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE H 179 " --> pdb=" O VAL H 93 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 102 through 104 removed outlier: 3.501A pdb=" N ASN H 102 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'j' and resid 16 through 17 removed outlier: 3.558A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 23 through 24 removed outlier: 7.121A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 58 through 59 Processing sheet with id=AF6, first strand: chain 'M' and resid 32 through 34 removed outlier: 5.758A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 37 through 38 removed outlier: 5.315A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.400A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.400A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN N 122 " --> pdb=" O TYR N 129 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.527A pdb=" N LEU P 148 " --> pdb=" O ALA P 17 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL P 149 " --> pdb=" O SER P 115 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 14 through 22 removed outlier: 3.527A pdb=" N LEU P 148 " --> pdb=" O ALA P 17 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Q' and resid 62 through 63 removed outlier: 4.484A pdb=" N VAL Q 101 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL Q 83 " --> pdb=" O VAL Q 101 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA Q 103 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY Q 85 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Q' and resid 62 through 63 removed outlier: 3.760A pdb=" N LEU Q 138 " --> pdb=" O THR Q 80 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 27 through 31 removed outlier: 7.325A pdb=" N GLU S 6 " --> pdb=" O GLN S 63 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLN S 63 " --> pdb=" O GLU S 6 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N GLN S 8 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE S 61 " --> pdb=" O GLN S 8 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE S 10 " --> pdb=" O VAL S 59 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 88 through 96 removed outlier: 7.050A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'V' and resid 22 through 24 removed outlier: 7.146A pdb=" N ASN V 33 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS V 63 " --> pdb=" O ASN V 33 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET V 74 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 114 through 118 removed outlier: 6.025A pdb=" N SER V 133 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N GLY V 116 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL V 135 " --> pdb=" O GLY V 116 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AH1, first strand: chain 'Y' and resid 94 through 99 removed outlier: 3.509A pdb=" N ILE Y 97 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL Y 85 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N LEU Y 99 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 10.313A pdb=" N ASP Y 83 " --> pdb=" O LEU Y 99 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP Y 83 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS Y 69 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL Y 85 " --> pdb=" O GLU Y 67 " (cutoff:3.500A) removed outlier: 9.668A pdb=" N GLU Y 67 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU Y 55 " --> pdb=" O THR Y 107 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 243 through 250 removed outlier: 3.554A pdb=" N LEU K 248 " --> pdb=" O GLN K 79 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN K 79 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AH4, first strand: chain 'K' and resid 151 through 155 removed outlier: 6.779A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE K 180 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE K 209 " --> pdb=" O ILE K 180 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA K 182 " --> pdb=" O ILE K 209 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 212 through 213 Processing sheet with id=AH6, first strand: chain 'D' and resid 317 through 318 removed outlier: 6.317A pdb=" N LEU D 317 " --> pdb=" O ILE D 344 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N THR D 346 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE D 292 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N CYS D 345 " --> pdb=" O ILE D 292 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N VAL D 294 " --> pdb=" O CYS D 345 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 391 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLN D 363 " --> pdb=" O LEU D 391 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'o' and resid 117 through 124 removed outlier: 3.547A pdb=" N GLU o 119 " --> pdb=" O GLU o 138 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N TYR o 134 " --> pdb=" O ALA o 123 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLY o 91 " --> pdb=" O PHE o 139 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE o 92 " --> pdb=" O LEU o 167 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS o 160 " --> pdb=" O LEU o 157 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU o 157 " --> pdb=" O HIS o 160 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR o 155 " --> pdb=" O LEU o 162 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'n' and resid 178 through 181 removed outlier: 3.706A pdb=" N LYS n 178 " --> pdb=" O GLN n 189 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 386 through 389 Processing sheet with id=AI1, first strand: chain 't' and resid 129 through 130 removed outlier: 3.628A pdb=" N ILE t 129 " --> pdb=" O THR t 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR t 104 " --> pdb=" O ILE t 129 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 't' and resid 129 through 130 removed outlier: 3.628A pdb=" N ILE t 129 " --> pdb=" O THR t 104 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR t 104 " --> pdb=" O ILE t 129 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N PHE t 99 " --> pdb=" O VAL t 309 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N GLU t 311 " --> pdb=" O PHE t 99 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU t 101 " --> pdb=" O GLU t 311 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 't' and resid 174 through 179 1977 hydrogen bonds defined for protein. 5649 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1475 hydrogen bonds 2384 hydrogen bond angles 0 basepair planarities 600 basepair parallelities 1018 stacking parallelities Total time for adding SS restraints: 79.48 Time building geometry restraints manager: 37.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.52: 77271 1.52 - 1.83: 28847 1.83 - 2.13: 6 2.13 - 2.44: 0 2.44 - 2.75: 1 Bond restraints: 106125 Sorted by residual: bond pdb=" C GLU x 285 " pdb=" N MET x 286 " ideal model delta sigma weight residual 1.332 2.748 -1.415 1.40e-02 5.10e+03 1.02e+04 bond pdb=" C LEU Y 126 " pdb=" O LEU Y 126 " ideal model delta sigma weight residual 1.231 1.443 -0.212 2.00e-02 2.50e+03 1.12e+02 bond pdb=" CZ ARG N 105 " pdb=" NH1 ARG N 105 " ideal model delta sigma weight residual 1.323 1.418 -0.095 1.40e-02 5.10e+03 4.58e+01 bond pdb=" NE ARG N 105 " pdb=" CZ ARG N 105 " ideal model delta sigma weight residual 1.326 1.391 -0.065 1.10e-02 8.26e+03 3.49e+01 bond pdb=" O5' A 11159 " pdb=" C5' A 11159 " ideal model delta sigma weight residual 1.424 1.512 -0.088 1.50e-02 4.44e+03 3.47e+01 ... (remaining 106120 not shown) Histogram of bond angle deviations from ideal: 95.58 - 103.63: 6789 103.63 - 111.68: 49969 111.68 - 119.72: 48198 119.72 - 127.77: 44452 127.77 - 135.81: 3530 Bond angle restraints: 152938 Sorted by residual: angle pdb=" O GLU x 285 " pdb=" C GLU x 285 " pdb=" N MET x 286 " ideal model delta sigma weight residual 122.09 103.98 18.11 1.23e+00 6.61e-01 2.17e+02 angle pdb=" O3' A 1 649 " pdb=" C3' A 1 649 " pdb=" C2' A 1 649 " ideal model delta sigma weight residual 113.70 129.27 -15.57 1.50e+00 4.44e-01 1.08e+02 angle pdb=" C4' U 11347 " pdb=" C3' U 11347 " pdb=" O3' U 11347 " ideal model delta sigma weight residual 113.00 128.28 -15.28 1.50e+00 4.44e-01 1.04e+02 angle pdb=" O3' C 1 480 " pdb=" C3' C 1 480 " pdb=" C2' C 1 480 " ideal model delta sigma weight residual 109.50 124.50 -15.00 1.50e+00 4.44e-01 1.00e+02 angle pdb=" CA GLU x 285 " pdb=" C GLU x 285 " pdb=" N MET x 286 " ideal model delta sigma weight residual 118.04 105.04 13.00 1.32e+00 5.74e-01 9.71e+01 ... (remaining 152933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 56737 35.86 - 71.73: 2862 71.73 - 107.59: 199 107.59 - 143.46: 10 143.46 - 179.32: 64 Dihedral angle restraints: 59872 sinusoidal: 39202 harmonic: 20670 Sorted by residual: dihedral pdb=" CA VAL 4 225 " pdb=" C VAL 4 225 " pdb=" N ALA 4 226 " pdb=" CA ALA 4 226 " ideal model delta harmonic sigma weight residual 180.00 90.00 90.00 0 5.00e+00 4.00e-02 3.24e+02 dihedral pdb=" CA GLU x 285 " pdb=" C GLU x 285 " pdb=" N MET x 286 " pdb=" CA MET x 286 " ideal model delta harmonic sigma weight residual 180.00 102.34 77.66 0 5.00e+00 4.00e-02 2.41e+02 dihedral pdb=" O4' U 13214 " pdb=" C1' U 13214 " pdb=" N1 U 13214 " pdb=" C2 U 13214 " ideal model delta sinusoidal sigma weight residual 200.00 22.80 177.20 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 59869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 17559 0.208 - 0.417: 1080 0.417 - 0.625: 36 0.625 - 0.834: 14 0.834 - 1.042: 2 Chirality restraints: 18691 Sorted by residual: chirality pdb=" C3' A 1 649 " pdb=" C4' A 1 649 " pdb=" O3' A 1 649 " pdb=" C2' A 1 649 " both_signs ideal model delta sigma weight residual False -2.48 -1.44 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" C3' U 11347 " pdb=" C4' U 11347 " pdb=" O3' U 11347 " pdb=" C2' U 11347 " both_signs ideal model delta sigma weight residual False -2.48 -1.55 -0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" C3' C 1 480 " pdb=" C4' C 1 480 " pdb=" O3' C 1 480 " pdb=" C2' C 1 480 " both_signs ideal model delta sigma weight residual False -2.74 -1.99 -0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 18688 not shown) Planarity restraints: 11918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU x 285 " 0.134 2.00e-02 2.50e+03 2.10e-01 4.40e+02 pdb=" C GLU x 285 " -0.355 2.00e-02 2.50e+03 pdb=" O GLU x 285 " 0.173 2.00e-02 2.50e+03 pdb=" N MET x 286 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 4 136 " -0.038 2.00e-02 2.50e+03 8.01e-02 6.42e+01 pdb=" C LEU 4 136 " 0.138 2.00e-02 2.50e+03 pdb=" O LEU 4 136 " -0.054 2.00e-02 2.50e+03 pdb=" N GLN 4 137 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 11389 " 0.069 2.00e-02 2.50e+03 2.94e-02 2.60e+01 pdb=" N9 G 11389 " -0.069 2.00e-02 2.50e+03 pdb=" C8 G 11389 " -0.015 2.00e-02 2.50e+03 pdb=" N7 G 11389 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G 11389 " 0.005 2.00e-02 2.50e+03 pdb=" C6 G 11389 " 0.012 2.00e-02 2.50e+03 pdb=" O6 G 11389 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G 11389 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G 11389 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G 11389 " -0.010 2.00e-02 2.50e+03 pdb=" N3 G 11389 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 11389 " -0.007 2.00e-02 2.50e+03 ... (remaining 11915 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.77: 44 1.77 - 2.55: 663 2.55 - 3.34: 109814 3.34 - 4.12: 294218 4.12 - 4.90: 448124 Warning: very small nonbonded interaction distances. Nonbonded interactions: 852863 Sorted by model distance: nonbonded pdb=" NH2 ARG G 84 " pdb=" NH1 ARG t 57 " model vdw 0.990 3.200 nonbonded pdb=" NE1 TRP 4 54 " pdb=" NE ARG 4 117 " model vdw 0.996 3.200 nonbonded pdb=" NH1 ARG G 84 " pdb=" NH2 ARG t 57 " model vdw 1.135 3.200 nonbonded pdb=" C5' U 2 127 " pdb=" OH TYR n 64 " model vdw 1.281 3.440 nonbonded pdb=" O LEU O 52 " pdb=" N TYR O 54 " model vdw 1.331 2.520 ... (remaining 852858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.750 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: 0.080 Extract box with map and model: 21.440 Check model and map are aligned: 1.130 Set scattering table: 0.660 Process input model: 265.520 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.270 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:2.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 298.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.009 1.415 106125 Z= 0.573 Angle : 1.366 20.715 152938 Z= 0.878 Chirality : 0.106 1.042 18691 Planarity : 0.006 0.210 11918 Dihedral : 18.645 179.321 46450 Min Nonbonded Distance : 0.990 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 3.11 % Allowed : 9.40 % Favored : 87.49 % Rotamer Outliers : 9.41 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -4.15 (0.08), residues: 6936 helix: -3.24 (0.07), residues: 2562 sheet: -2.02 (0.15), residues: 914 loop : -2.51 (0.09), residues: 3460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13872 Ramachandran restraints generated. 6936 Oldfield, 0 Emsley, 6936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13872 Ramachandran restraints generated. 6936 Oldfield, 0 Emsley, 6936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2342 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 581 poor density : 1761 time to evaluate : 6.379 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: 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: 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: 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: 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 outliers start: 581 outliers final: 157 residues processed: 2200 average time/residue: 1.0745 time to fit residues: 3922.8881 Evaluate side-chains 1078 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 921 time to evaluate : 6.225 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 157 outliers final: 2 residues processed: 157 average time/residue: 0.8399 time to fit residues: 251.6159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 750 optimal weight: 30.0000 chunk 673 optimal weight: 5.9990 chunk 373 optimal weight: 0.7980 chunk 230 optimal weight: 6.9990 chunk 454 optimal weight: 10.0000 chunk 359 optimal weight: 0.9990 chunk 696 optimal weight: 30.0000 chunk 269 optimal weight: 8.9990 chunk 423 optimal weight: 6.9990 chunk 518 optimal weight: 0.9990 chunk 807 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 102 ASN x 164 HIS x 187 HIS x 228 GLN F 19 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 186 HIS ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 23 ASN ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 41 GLN 4 14 ASN 4 63 GLN 5 34 HIS 5 63 ASN 5 191 GLN 5 237 ASN 5 269 GLN 5 285 GLN 5 286 HIS 5 299 ASN 5 305 GLN ** A 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN b 23 ASN b 26 GLN b 70 ASN b 89 ASN b 90 HIS b 208 HIS b 217 GLN b 238 GLN ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 228 ASN ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 10 HIS ** r 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 7 HIS u 101 GLN v 10 ASN ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 33 ASN W 167 ASN W 205 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 232 ASN y 21 ASN y 33 ASN y 86 ASN y 157 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN C 58 HIS C 87 GLN C 114 ASN C 260 GLN ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN E 138 GLN f 42 GLN G 95 ASN G 137 ASN h 20 GLN h 59 ASN h 68 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN L 37 ASN L 114 GLN L 120 GLN ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 178 HIS O 31 GLN O 42 ASN O 50 ASN ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN P 121 GLN Q 58 ASN Q 73 GLN Q 126 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 49 HIS S 62 ASN S 74 ASN S 142 GLN K 42 ASN K 262 ASN D 397 ASN D 428 GLN D 441 GLN o 163 GLN n 150 GLN n 164 ASN n 191 ASN n 437 ASN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 154 ASN t 238 GLN Total number of N/Q/H flips: 85 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 106125 Z= 0.272 Angle : 0.762 14.133 152938 Z= 0.392 Chirality : 0.043 0.251 18691 Planarity : 0.006 0.065 11918 Dihedral : 16.362 179.659 31822 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.56 % Allowed : 6.69 % Favored : 92.75 % Rotamer Outliers : 4.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.83 (0.09), residues: 6938 helix: -1.68 (0.09), residues: 2639 sheet: -1.60 (0.15), residues: 989 loop : -2.06 (0.10), residues: 3310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1329 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 291 poor density : 1038 time to evaluate : 6.254 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 291 outliers final: 124 residues processed: 1261 average time/residue: 0.9606 time to fit residues: 2053.9219 Evaluate side-chains 939 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 815 time to evaluate : 6.348 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 0 residues processed: 124 average time/residue: 0.7262 time to fit residues: 178.2656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 448 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 671 optimal weight: 7.9990 chunk 549 optimal weight: 0.9990 chunk 222 optimal weight: 7.9990 chunk 808 optimal weight: 30.0000 chunk 873 optimal weight: 5.9990 chunk 720 optimal weight: 10.0000 chunk 802 optimal weight: 3.9990 chunk 275 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 193 HIS F 19 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 23 ASN ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 HIS b 156 HIS ** b 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 GLN ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 206 ASN W 22 ASN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 21 ASN y 164 GLN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 291 ASN G 192 GLN h 20 GLN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN L 105 ASN L 112 ASN M 41 GLN ** N 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 46 GLN ** K 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 284 ASN K 295 GLN D 428 GLN D 436 ASN o 100 HIS o 204 HIS n 108 ASN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.104 106125 Z= 0.351 Angle : 0.733 13.254 152938 Z= 0.376 Chirality : 0.042 0.249 18691 Planarity : 0.006 0.135 11918 Dihedral : 16.392 179.866 31822 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.43 % Allowed : 7.99 % Favored : 91.58 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.20 (0.09), residues: 6938 helix: -0.92 (0.09), residues: 2645 sheet: -1.47 (0.15), residues: 981 loop : -1.86 (0.10), residues: 3312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 890 time to evaluate : 6.206 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 250 outliers final: 113 residues processed: 1075 average time/residue: 0.9675 time to fit residues: 1792.9972 Evaluate side-chains 864 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 751 time to evaluate : 6.248 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 0 residues processed: 113 average time/residue: 0.7683 time to fit residues: 170.4612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 799 optimal weight: 0.0000 chunk 608 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 385 optimal weight: 5.9990 chunk 543 optimal weight: 9.9990 chunk 811 optimal weight: 4.9990 chunk 859 optimal weight: 3.9990 chunk 424 optimal weight: 8.9990 chunk 769 optimal weight: 20.0000 chunk 231 optimal weight: 8.9990 overall best weight: 4.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 208 GLN x 262 GLN ** F 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 23 ASN ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN A 45 HIS ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 208 HIS ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 331 ASN C 48 GLN ** E 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 116 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS Y 26 GLN D 375 HIS ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 100 HIS n 83 HIS n 137 ASN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 106125 Z= 0.291 Angle : 0.674 10.401 152938 Z= 0.345 Chirality : 0.040 0.242 18691 Planarity : 0.005 0.113 11918 Dihedral : 16.348 179.989 31822 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.76 % Favored : 92.82 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.84 (0.10), residues: 6938 helix: -0.50 (0.10), residues: 2656 sheet: -1.24 (0.16), residues: 959 loop : -1.78 (0.10), residues: 3323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 850 time to evaluate : 6.288 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 208 outliers final: 96 residues processed: 999 average time/residue: 0.9338 time to fit residues: 1607.0249 Evaluate side-chains 848 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 752 time to evaluate : 6.209 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 96 outliers final: 1 residues processed: 96 average time/residue: 0.7588 time to fit residues: 143.9072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 715 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 639 optimal weight: 10.0000 chunk 354 optimal weight: 6.9990 chunk 733 optimal weight: 50.0000 chunk 593 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 438 optimal weight: 5.9990 chunk 771 optimal weight: 4.9990 chunk 216 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 262 GLN F 12 GLN F 19 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 146 GLN ** 4 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN A 45 HIS ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 HIS b 233 ASN ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** W 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 ASN H 125 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 163 GLN L 114 GLN N 182 ASN ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN n 150 GLN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 106125 Z= 0.330 Angle : 0.695 10.607 152938 Z= 0.355 Chirality : 0.041 0.300 18691 Planarity : 0.005 0.070 11918 Dihedral : 16.447 179.781 31822 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.03 % Favored : 91.57 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.74 (0.10), residues: 6938 helix: -0.35 (0.10), residues: 2653 sheet: -1.21 (0.16), residues: 979 loop : -1.78 (0.10), residues: 3306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 800 time to evaluate : 6.189 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: 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: symmetry clash outliers start: 191 outliers final: 82 residues processed: 940 average time/residue: 0.9362 time to fit residues: 1520.5522 Evaluate side-chains 803 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 721 time to evaluate : 6.305 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 82 outliers final: 1 residues processed: 82 average time/residue: 0.7320 time to fit residues: 121.9343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 289 optimal weight: 8.9990 chunk 773 optimal weight: 8.9990 chunk 169 optimal weight: 0.0020 chunk 504 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 860 optimal weight: 30.0000 chunk 714 optimal weight: 10.0000 chunk 398 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 451 optimal weight: 7.9990 overall best weight: 1.8394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 73 HIS 5 63 ASN 5 152 ASN 5 299 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 HIS ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 HIS J 218 GLN ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 ASN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 ASN L 114 GLN ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN ** t 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 106125 Z= 0.181 Angle : 0.617 11.909 152938 Z= 0.315 Chirality : 0.037 0.290 18691 Planarity : 0.004 0.060 11918 Dihedral : 16.265 179.875 31822 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.15 % Favored : 93.50 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.44 (0.10), residues: 6938 helix: -0.08 (0.10), residues: 2651 sheet: -1.05 (0.17), residues: 934 loop : -1.62 (0.10), residues: 3353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 817 time to evaluate : 7.293 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: 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 outliers start: 107 outliers final: 44 residues processed: 890 average time/residue: 0.9462 time to fit residues: 1452.7803 Evaluate side-chains 770 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 726 time to evaluate : 6.225 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 0.7640 time to fit residues: 70.5348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 829 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 490 optimal weight: 0.9980 chunk 628 optimal weight: 8.9990 chunk 486 optimal weight: 2.9990 chunk 724 optimal weight: 10.0000 chunk 480 optimal weight: 3.9990 chunk 856 optimal weight: 5.9990 chunk 536 optimal weight: 20.0000 chunk 522 optimal weight: 7.9990 chunk 395 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 228 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 HIS E 167 ASN ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 436 ASN D 441 GLN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.084 106125 Z= 0.255 Angle : 0.642 12.608 152938 Z= 0.328 Chirality : 0.038 0.286 18691 Planarity : 0.005 0.061 11918 Dihedral : 16.282 179.959 31822 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.62 % Favored : 92.01 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.38 (0.10), residues: 6938 helix: -0.01 (0.10), residues: 2640 sheet: -1.02 (0.17), residues: 944 loop : -1.60 (0.10), residues: 3354 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 879 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 779 time to evaluate : 6.345 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: 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 outliers start: 100 outliers final: 49 residues processed: 843 average time/residue: 0.9441 time to fit residues: 1374.3186 Evaluate side-chains 783 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 734 time to evaluate : 6.244 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 49 outliers final: 1 residues processed: 49 average time/residue: 0.7637 time to fit residues: 77.7507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 530 optimal weight: 4.9990 chunk 342 optimal weight: 8.9990 chunk 511 optimal weight: 0.8980 chunk 258 optimal weight: 0.2980 chunk 168 optimal weight: 0.7980 chunk 166 optimal weight: 20.0000 chunk 544 optimal weight: 10.0000 chunk 583 optimal weight: 10.0000 chunk 423 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 673 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 152 ASN 5 299 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 GLN ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 HIS ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 3 GLN s 7 GLN ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** y 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 83 HIS n 108 ASN ** t 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 291 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 106125 Z= 0.193 Angle : 0.617 14.461 152938 Z= 0.315 Chirality : 0.037 0.316 18691 Planarity : 0.004 0.059 11918 Dihedral : 16.214 179.559 31822 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.26 % Favored : 93.44 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.27 (0.10), residues: 6938 helix: 0.08 (0.10), residues: 2656 sheet: -1.00 (0.16), residues: 969 loop : -1.54 (0.11), residues: 3313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 785 time to evaluate : 6.262 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: 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: symmetry clash outliers start: 54 outliers final: 22 residues processed: 812 average time/residue: 0.9551 time to fit residues: 1333.7698 Evaluate side-chains 759 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 737 time to evaluate : 6.076 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.7394 time to fit residues: 39.1281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 779 optimal weight: 20.0000 chunk 820 optimal weight: 4.9990 chunk 748 optimal weight: 10.0000 chunk 798 optimal weight: 20.0000 chunk 480 optimal weight: 0.9990 chunk 347 optimal weight: 0.2980 chunk 626 optimal weight: 10.0000 chunk 245 optimal weight: 8.9990 chunk 721 optimal weight: 10.0000 chunk 755 optimal weight: 20.0000 chunk 795 optimal weight: 4.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** x 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN 5 370 HIS ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN y 6 GLN y 79 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 HIS ** f 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 59 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 122 GLN ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** P 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 106125 Z= 0.286 Angle : 0.661 17.164 152938 Z= 0.337 Chirality : 0.039 0.392 18691 Planarity : 0.005 0.061 11918 Dihedral : 16.306 179.869 31822 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.68 % Favored : 92.03 % Rotamer Outliers : 1.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.33 (0.10), residues: 6938 helix: 0.03 (0.10), residues: 2659 sheet: -1.03 (0.16), residues: 961 loop : -1.57 (0.11), residues: 3318 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 748 time to evaluate : 6.368 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: 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 outliers start: 63 outliers final: 34 residues processed: 784 average time/residue: 0.9602 time to fit residues: 1298.0045 Evaluate side-chains 754 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 720 time to evaluate : 6.295 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 34 outliers final: 1 residues processed: 34 average time/residue: 0.7722 time to fit residues: 56.8219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 524 optimal weight: 3.9990 chunk 844 optimal weight: 7.9990 chunk 515 optimal weight: 3.9990 chunk 400 optimal weight: 0.7980 chunk 586 optimal weight: 10.0000 chunk 885 optimal weight: 20.0000 chunk 815 optimal weight: 10.0000 chunk 705 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 544 optimal weight: 20.0000 chunk 432 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: x 44 ASN ** 3 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 299 ASN 5 368 HIS ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 48 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 8 GLN H 59 ASN ** H 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 GLN N 178 HIS ** P 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 116 HIS ** S 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 26 GLN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 GLN ** o 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 108 ASN t 291 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.074 106125 Z= 0.269 Angle : 0.658 16.369 152938 Z= 0.336 Chirality : 0.039 0.236 18691 Planarity : 0.005 0.060 11918 Dihedral : 16.357 179.988 31822 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.19 % Favored : 92.51 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.34 (0.10), residues: 6938 helix: 0.01 (0.10), residues: 2659 sheet: -1.01 (0.16), residues: 982 loop : -1.58 (0.11), residues: 3297 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13876 Ramachandran restraints generated. 6938 Oldfield, 0 Emsley, 6938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 735 time to evaluate : 6.428 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: 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 outliers start: 32 outliers final: 18 residues processed: 748 average time/residue: 0.9544 time to fit residues: 1239.3633 Evaluate side-chains 729 residues out of total 6174 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 711 time to evaluate : 5.575 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 18 outliers final: 1 residues processed: 18 average time/residue: 0.7309 time to fit residues: 31.9834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 889 random chunks: chunk 560 optimal weight: 9.9990 chunk 751 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 650 optimal weight: 20.0000 chunk 104 optimal weight: 0.1980 chunk 195 optimal weight: 9.9990 chunk 706 optimal weight: 30.0000 chunk 295 optimal weight: 7.9990 chunk 725 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 overall best weight: 6.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in