Starting phenix.real_space_refine on Sun Apr 14 15:38:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uph_26666/04_2024/7uph_26666_updated.pdb" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.058 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 P 4556 5.49 5 S 139 5.16 5 C 70336 2.51 5 N 26201 2.21 5 O 39223 1.98 5 H 625 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 60": "NH1" <-> "NH2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 34": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 101": "NH1" <-> "NH2" Residue "K ASP 167": "OD1" <-> "OD2" Residue "K GLU 198": "OE1" <-> "OE2" Residue "K PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 108": "OD1" <-> "OD2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 14": "OD1" <-> "OD2" Residue "R TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 90": "OE1" <-> "OE2" Residue "R PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 129": "OE1" <-> "OE2" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 75": "OE1" <-> "OE2" Residue "W PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 164": "OD1" <-> "OD2" Residue "X GLU 27": "OE1" <-> "OE2" Residue "X TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 186": "OE1" <-> "OE2" Residue "Z PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 41": "OD1" <-> "OD2" Residue "a GLU 69": "OE1" <-> "OE2" Residue "b GLU 20": "OE1" <-> "OE2" Residue "b GLU 47": "OE1" <-> "OE2" Residue "b GLU 66": "OE1" <-> "OE2" Residue "c TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 50": "OE1" <-> "OE2" Residue "e TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 108": "OD1" <-> "OD2" Residue "j TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 45": "OE1" <-> "OE2" Residue "q GLU 46": "OE1" <-> "OE2" Residue "q GLU 62": "OE1" <-> "OE2" Residue "q PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 65": "OD1" <-> "OD2" Residue "t PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "y GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 141080 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "C" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "D" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "E" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 665 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "H" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "I" Number of atoms: 95909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4438, 95909 Classifications: {'RNA': 4438} Modifications used: {'rna2p': 8, 'rna2p_pur': 394, 'rna2p_pyr': 234, 'rna3p': 25, 'rna3p_pur': 2142, 'rna3p_pyr': 1635} Link IDs: {'rna2p': 635, 'rna3p': 3802} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 16 Chain: "J" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "M" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "O" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "R" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "S" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "T" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "W" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "X" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "Y" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "Z" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "a" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "b" Number of atoms: 1182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1182 Classifications: {'peptide': 151} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "c" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "d" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "e" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 787 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "f" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "g" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "h" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 884 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "i" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "j" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "k" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "l" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "m" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 569 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Time building chain proxies: 52.14, per 1000 atoms: 0.37 Number of scatterers: 141080 At special positions: 0 Unit cell: (264.88, 264.88, 248.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 139 16.00 P 4556 15.00 O 39223 8.00 N 26201 7.00 C 70336 6.00 H 625 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 81.67 Conformation dependent library (CDL) restraints added in 6.2 seconds 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9994 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 161 helices and 59 sheets defined 37.1% alpha, 13.8% beta 1436 base pairs and 1801 stacking pairs defined. Time for finding SS restraints: 67.12 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.636A pdb=" N LEU A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ASN A 34 " --> pdb=" O ILE A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 removed outlier: 4.545A pdb=" N LEU A 45 " --> pdb=" O TRP A 41 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.604A pdb=" N GLN A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 55 through 60' Processing helix chain 'A' and resid 79 through 90 removed outlier: 3.558A pdb=" N VAL A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.679A pdb=" N ILE B 10 " --> pdb=" O ALA B 6 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 11 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B 13 " --> pdb=" O LYS B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 46 removed outlier: 3.507A pdb=" N GLN B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS B 45 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 73 removed outlier: 3.958A pdb=" N ARG B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 85 removed outlier: 3.977A pdb=" N GLN B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLU B 82 " --> pdb=" O THR B 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 64 removed outlier: 3.909A pdb=" N GLY C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN C 63 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLY C 64 " --> pdb=" O TRP C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 79 removed outlier: 4.155A pdb=" N ALA C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 15 removed outlier: 4.332A pdb=" N ASN E 12 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR E 13 " --> pdb=" O THR E 9 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N THR E 15 " --> pdb=" O LYS E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 27 Processing helix chain 'E' and resid 29 through 47 removed outlier: 4.042A pdb=" N ARG E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG E 42 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU E 46 " --> pdb=" O ARG E 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 23 removed outlier: 4.035A pdb=" N LYS F 16 " --> pdb=" O HIS F 12 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 74 removed outlier: 4.191A pdb=" N PHE F 72 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA F 73 " --> pdb=" O LEU F 69 " (cutoff:3.500A) Proline residue: F 74 - end of helix No H-bonds generated for 'chain 'F' and resid 68 through 74' Processing helix chain 'G' and resid 5 through 40 removed outlier: 3.664A pdb=" N ALA G 9 " --> pdb=" O ALA G 5 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE G 10 " --> pdb=" O LYS G 6 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER G 21 " --> pdb=" O LYS G 17 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ARG G 22 " --> pdb=" O HIS G 18 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE G 29 " --> pdb=" O MET G 25 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS G 32 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 34 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY G 40 " --> pdb=" O ALA G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 61 Proline residue: G 54 - end of helix removed outlier: 4.007A pdb=" N ARG G 58 " --> pdb=" O PRO G 54 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN G 59 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA G 60 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 85 removed outlier: 4.085A pdb=" N ALA G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU G 77 " --> pdb=" O HIS G 73 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN G 82 " --> pdb=" O THR G 78 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G 84 " --> pdb=" O GLN G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 24 removed outlier: 4.042A pdb=" N ARG H 16 " --> pdb=" O ASP H 12 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG H 17 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS H 19 " --> pdb=" O LEU H 15 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N CYS H 22 " --> pdb=" O PHE H 18 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 35 removed outlier: 3.982A pdb=" N ARG H 33 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG H 34 " --> pdb=" O GLU H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 55 removed outlier: 3.740A pdb=" N GLU H 43 " --> pdb=" O LYS H 39 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS H 55 " --> pdb=" O ALA H 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 196 through 202 removed outlier: 3.947A pdb=" N MET K 200 " --> pdb=" O ASN K 196 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU K 201 " --> pdb=" O ALA K 197 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG K 202 " --> pdb=" O GLU K 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 196 through 202' Processing helix chain 'K' and resid 206 through 214 removed outlier: 4.391A pdb=" N ALA K 210 " --> pdb=" O LYS K 206 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG K 211 " --> pdb=" O ALA K 207 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ARG K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 264 removed outlier: 5.892A pdb=" N ASP K 263 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS K 264 " --> pdb=" O LYS K 260 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 259 through 264' Processing helix chain 'L' and resid 61 through 70 Processing helix chain 'L' and resid 120 through 126 Processing helix chain 'M' and resid 15 through 20 Processing helix chain 'M' and resid 24 through 39 removed outlier: 3.751A pdb=" N GLY M 38 " --> pdb=" O ALA M 34 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA M 39 " --> pdb=" O TYR M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 removed outlier: 3.613A pdb=" N TYR M 101 " --> pdb=" O ASN M 97 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU M 111 " --> pdb=" O SER M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 142 removed outlier: 3.911A pdb=" N ALA M 135 " --> pdb=" O THR M 131 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN M 136 " --> pdb=" O LYS M 132 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS M 137 " --> pdb=" O LEU M 133 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU M 138 " --> pdb=" O LEU M 134 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP M 140 " --> pdb=" O GLN M 136 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N MET M 141 " --> pdb=" O LYS M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 165 removed outlier: 3.905A pdb=" N PHE M 158 " --> pdb=" O ASP M 154 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA M 160 " --> pdb=" O ASN M 156 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA M 161 " --> pdb=" O LEU M 157 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU M 164 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N HIS M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.761A pdb=" N PHE M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 190 through 200 removed outlier: 4.763A pdb=" N LYS M 194 " --> pdb=" O ALA M 190 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN M 195 " --> pdb=" O ASP M 191 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL M 196 " --> pdb=" O ALA M 192 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU M 198 " --> pdb=" O LYS M 194 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU M 200 " --> pdb=" O VAL M 196 " (cutoff:3.500A) Processing helix chain 'N' and resid 1 through 11 removed outlier: 4.509A pdb=" N TYR N 6 " --> pdb=" O LYS N 2 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LYS N 8 " --> pdb=" O HIS N 4 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP N 9 " --> pdb=" O ASP N 5 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU N 10 " --> pdb=" O TYR N 6 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL N 11 " --> pdb=" O TYR N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 19 removed outlier: 3.838A pdb=" N GLU N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 Processing helix chain 'N' and resid 47 through 61 Processing helix chain 'N' and resid 92 through 105 removed outlier: 4.077A pdb=" N ARG N 101 " --> pdb=" O GLU N 97 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU N 102 " --> pdb=" O PHE N 98 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE N 103 " --> pdb=" O PHE N 99 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE N 105 " --> pdb=" O ARG N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 173 removed outlier: 3.694A pdb=" N GLY N 165 " --> pdb=" O SER N 161 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE N 172 " --> pdb=" O LEU N 168 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) Processing helix chain 'O' and resid 1 through 6 Processing helix chain 'O' and resid 59 through 80 removed outlier: 6.690A pdb=" N GLN O 63 " --> pdb=" O ASP O 59 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA O 64 " --> pdb=" O GLY O 60 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA O 67 " --> pdb=" O GLN O 63 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER O 73 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL O 78 " --> pdb=" O MET O 74 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N THR O 79 " --> pdb=" O VAL O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 136 through 152 removed outlier: 3.982A pdb=" N GLY O 141 " --> pdb=" O LYS O 137 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASP O 146 " --> pdb=" O GLN O 142 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU O 147 " --> pdb=" O VAL O 143 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ARG O 151 " --> pdb=" O LEU O 147 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG O 152 " --> pdb=" O ARG O 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 38 removed outlier: 3.525A pdb=" N LEU R 28 " --> pdb=" O THR R 24 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ALA R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N THR R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 72 removed outlier: 4.342A pdb=" N ASP R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS R 72 " --> pdb=" O LYS R 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 67 through 72' Processing helix chain 'R' and resid 88 through 96 removed outlier: 3.976A pdb=" N MET R 92 " --> pdb=" O THR R 88 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE R 93 " --> pdb=" O PHE R 89 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ALA R 94 " --> pdb=" O GLU R 90 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG R 95 " --> pdb=" O GLU R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 110 removed outlier: 4.468A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU R 109 " --> pdb=" O VAL R 105 " (cutoff:3.500A) Proline residue: R 110 - end of helix Processing helix chain 'R' and resid 112 through 123 removed outlier: 3.717A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 109 removed outlier: 4.050A pdb=" N ARG S 108 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER S 109 " --> pdb=" O ARG S 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 104 through 109' Processing helix chain 'S' and resid 112 through 119 removed outlier: 3.558A pdb=" N SER S 117 " --> pdb=" O MET S 113 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LEU S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA S 119 " --> pdb=" O ILE S 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 62 Proline residue: T 62 - end of helix Processing helix chain 'T' and resid 70 through 75 removed outlier: 4.159A pdb=" N THR T 74 " --> pdb=" O LYS T 70 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 70 through 75' Processing helix chain 'T' and resid 78 through 85 removed outlier: 4.521A pdb=" N ALA T 83 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LYS T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 98 removed outlier: 4.179A pdb=" N LEU T 95 " --> pdb=" O ASP T 91 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS T 96 " --> pdb=" O LEU T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 128 through 139 removed outlier: 3.665A pdb=" N ALA T 133 " --> pdb=" O LYS T 129 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA T 134 " --> pdb=" O GLY T 130 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA T 138 " --> pdb=" O ALA T 134 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY T 139 " --> pdb=" O ILE T 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 58 Processing helix chain 'U' and resid 109 through 124 removed outlier: 4.396A pdb=" N ALA U 113 " --> pdb=" O PRO U 109 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU U 115 " --> pdb=" O GLU U 111 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA U 116 " --> pdb=" O LEU U 112 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 32 removed outlier: 3.628A pdb=" N PHE V 21 " --> pdb=" O ARG V 17 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG V 22 " --> pdb=" O GLN V 18 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN V 23 " --> pdb=" O ALA V 19 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N MET V 24 " --> pdb=" O MET V 20 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY V 26 " --> pdb=" O ARG V 22 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N VAL V 29 " --> pdb=" O ALA V 25 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG V 30 " --> pdb=" O GLY V 26 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS V 31 " --> pdb=" O SER V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 57 Proline residue: V 50 - end of helix removed outlier: 3.869A pdb=" N LEU V 54 " --> pdb=" O PRO V 50 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA V 55 " --> pdb=" O LEU V 51 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS V 56 " --> pdb=" O ILE V 52 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N THR V 57 " --> pdb=" O THR V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 71 removed outlier: 5.049A pdb=" N THR V 70 " --> pdb=" O ALA V 66 " (cutoff:3.500A) Processing helix chain 'V' and resid 72 through 82 removed outlier: 4.843A pdb=" N VAL V 76 " --> pdb=" O ASP V 72 " (cutoff:3.500A) Processing helix chain 'V' and resid 83 through 88 removed outlier: 4.030A pdb=" N PHE V 87 " --> pdb=" O LEU V 83 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA V 88 " --> pdb=" O GLY V 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 83 through 88' Processing helix chain 'W' and resid 2 through 10 removed outlier: 3.863A pdb=" N MET W 6 " --> pdb=" O SER W 2 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU W 7 " --> pdb=" O MET W 3 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS W 8 " --> pdb=" O ARG W 4 " (cutoff:3.500A) Processing helix chain 'W' and resid 21 through 26 removed outlier: 3.951A pdb=" N LYS W 25 " --> pdb=" O ASN W 21 " (cutoff:3.500A) Proline residue: W 26 - end of helix No H-bonds generated for 'chain 'W' and resid 21 through 26' Processing helix chain 'W' and resid 40 through 61 Proline residue: W 45 - end of helix removed outlier: 3.511A pdb=" N ILE W 57 " --> pdb=" O GLU W 53 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS W 61 " --> pdb=" O ILE W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 73 through 85 removed outlier: 3.890A pdb=" N VAL W 77 " --> pdb=" O ALA W 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS W 78 " --> pdb=" O SER W 74 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP W 79 " --> pdb=" O GLU W 75 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS W 84 " --> pdb=" O ALA W 80 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP W 85 " --> pdb=" O ALA W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 120 removed outlier: 3.796A pdb=" N GLN W 106 " --> pdb=" O LYS W 102 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER W 107 " --> pdb=" O THR W 103 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 145 removed outlier: 7.074A pdb=" N ALA W 131 " --> pdb=" O THR W 127 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N LEU W 132 " --> pdb=" O LYS W 128 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS W 140 " --> pdb=" O ARG W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 167 Processing helix chain 'W' and resid 168 through 177 removed outlier: 3.534A pdb=" N LEU W 176 " --> pdb=" O GLU W 172 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY W 177 " --> pdb=" O ALA W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 203 through 224 Processing helix chain 'X' and resid 5 through 14 removed outlier: 4.578A pdb=" N GLY X 12 " --> pdb=" O GLY X 8 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE X 13 " --> pdb=" O ILE X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 47 removed outlier: 4.294A pdb=" N ALA X 29 " --> pdb=" O THR X 25 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ASP X 30 " --> pdb=" O LYS X 26 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE X 36 " --> pdb=" O LEU X 32 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS X 37 " --> pdb=" O ASP X 33 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL X 38 " --> pdb=" O SER X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 71 through 76 Processing helix chain 'X' and resid 81 through 95 Processing helix chain 'X' and resid 107 through 112 removed outlier: 3.641A pdb=" N ASP X 111 " --> pdb=" O LYS X 107 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ALA X 112 " --> pdb=" O PRO X 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 107 through 112' Processing helix chain 'X' and resid 113 through 126 removed outlier: 3.578A pdb=" N ARG X 125 " --> pdb=" O SER X 121 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG X 126 " --> pdb=" O GLN X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 144 removed outlier: 3.980A pdb=" N ARG X 142 " --> pdb=" O GLN X 138 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU X 143 " --> pdb=" O ASN X 139 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY X 144 " --> pdb=" O ALA X 140 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 15 removed outlier: 4.489A pdb=" N LEU Y 10 " --> pdb=" O PRO Y 6 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER Y 11 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 removed outlier: 3.523A pdb=" N LYS Y 30 " --> pdb=" O ALA Y 26 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 65 removed outlier: 3.779A pdb=" N GLU Y 56 " --> pdb=" O VAL Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 67 through 82 removed outlier: 3.514A pdb=" N TYR Y 75 " --> pdb=" O PHE Y 71 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS Y 76 " --> pdb=" O ARG Y 72 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS Y 82 " --> pdb=" O ALA Y 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 84 through 96 removed outlier: 3.884A pdb=" N ARG Y 96 " --> pdb=" O LEU Y 92 " (cutoff:3.500A) Processing helix chain 'Y' and resid 97 through 105 removed outlier: 3.543A pdb=" N GLY Y 105 " --> pdb=" O VAL Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 109 through 120 removed outlier: 4.037A pdb=" N LYS Y 120 " --> pdb=" O LEU Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 145 through 150 removed outlier: 4.160A pdb=" N LYS Y 150 " --> pdb=" O GLU Y 146 " (cutoff:3.500A) Processing helix chain 'Y' and resid 151 through 165 removed outlier: 3.734A pdb=" N LYS Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU Y 160 " --> pdb=" O ALA Y 156 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN Y 163 " --> pdb=" O GLU Y 159 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU Y 165 " --> pdb=" O ALA Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 186 through 191 removed outlier: 3.681A pdb=" N LEU Y 190 " --> pdb=" O GLU Y 186 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N SER Y 191 " --> pdb=" O ARG Y 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 186 through 191' Processing helix chain 'Y' and resid 195 through 205 removed outlier: 3.572A pdb=" N ILE Y 199 " --> pdb=" O ASN Y 195 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU Y 201 " --> pdb=" O HIS Y 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 46 through 62 removed outlier: 3.652A pdb=" N GLN Z 52 " --> pdb=" O PRO Z 48 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG Z 60 " --> pdb=" O GLU Z 56 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ASN Z 61 " --> pdb=" O LYS Z 57 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N MET Z 62 " --> pdb=" O ALA Z 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 110 removed outlier: 3.700A pdb=" N LEU Z 106 " --> pdb=" O MET Z 102 " (cutoff:3.500A) Processing helix chain 'Z' and resid 124 through 138 removed outlier: 3.591A pdb=" N VAL Z 128 " --> pdb=" O PRO Z 124 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ARG Z 129 " --> pdb=" O ILE Z 125 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA Z 130 " --> pdb=" O ASN Z 126 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR Z 131 " --> pdb=" O VAL Z 127 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ILE Z 132 " --> pdb=" O VAL Z 128 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU Z 136 " --> pdb=" O ILE Z 132 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN Z 137 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 140 through 149 removed outlier: 4.534A pdb=" N LYS Z 147 " --> pdb=" O MET Z 143 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG Z 148 " --> pdb=" O VAL Z 144 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY Z 149 " --> pdb=" O ALA Z 145 " (cutoff:3.500A) Processing helix chain 'a' and resid 16 through 33 removed outlier: 4.308A pdb=" N GLY a 20 " --> pdb=" O GLU a 16 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU a 23 " --> pdb=" O PRO a 19 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG a 24 " --> pdb=" O GLY a 20 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR a 25 " --> pdb=" O MET a 21 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA a 32 " --> pdb=" O ALA a 28 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU a 33 " --> pdb=" O ILE a 29 " (cutoff:3.500A) Processing helix chain 'a' and resid 67 through 82 removed outlier: 4.566A pdb=" N ASP a 82 " --> pdb=" O PHE a 78 " (cutoff:3.500A) Processing helix chain 'b' and resid 19 through 30 removed outlier: 3.992A pdb=" N PHE b 25 " --> pdb=" O LEU b 21 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL b 26 " --> pdb=" O LEU b 22 " (cutoff:3.500A) Processing helix chain 'b' and resid 34 through 54 removed outlier: 3.809A pdb=" N GLU b 39 " --> pdb=" O LYS b 35 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER b 40 " --> pdb=" O SER b 36 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA b 45 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU b 46 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU b 47 " --> pdb=" O TYR b 43 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN b 51 " --> pdb=" O GLU b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 69 removed outlier: 3.954A pdb=" N GLU b 62 " --> pdb=" O LEU b 58 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN b 67 " --> pdb=" O VAL b 63 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL b 68 " --> pdb=" O ALA b 64 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 110 removed outlier: 3.848A pdb=" N ALA b 97 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA b 107 " --> pdb=" O ILE b 103 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG b 108 " --> pdb=" O VAL b 104 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS b 109 " --> pdb=" O GLU b 105 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG b 110 " --> pdb=" O ALA b 106 " (cutoff:3.500A) Processing helix chain 'b' and resid 114 through 129 removed outlier: 3.751A pdb=" N GLU b 128 " --> pdb=" O SER b 124 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 148 removed outlier: 4.019A pdb=" N LYS b 135 " --> pdb=" O GLY b 131 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS b 136 " --> pdb=" O THR b 132 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET b 143 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA b 144 " --> pdb=" O VAL b 140 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU b 145 " --> pdb=" O HIS b 141 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN b 147 " --> pdb=" O MET b 143 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS b 148 " --> pdb=" O ALA b 144 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 20 removed outlier: 3.704A pdb=" N ASP c 8 " --> pdb=" O ASP c 4 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET c 9 " --> pdb=" O PRO c 5 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU c 10 " --> pdb=" O ILE c 6 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR c 11 " --> pdb=" O ALA c 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA c 19 " --> pdb=" O ASN c 15 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN c 20 " --> pdb=" O GLY c 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 29 through 43 removed outlier: 3.648A pdb=" N VAL c 38 " --> pdb=" O ALA c 34 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU c 39 " --> pdb=" O ILE c 35 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS c 40 " --> pdb=" O ALA c 36 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU c 41 " --> pdb=" O ASN c 37 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU c 42 " --> pdb=" O VAL c 38 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY c 43 " --> pdb=" O LEU c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 119 Processing helix chain 'd' and resid 31 through 36 Processing helix chain 'd' and resid 38 through 53 removed outlier: 3.563A pdb=" N VAL d 44 " --> pdb=" O THR d 40 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL d 45 " --> pdb=" O ALA d 41 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG d 46 " --> pdb=" O ARG d 42 " (cutoff:3.500A) Proline residue: d 48 - end of helix removed outlier: 4.642A pdb=" N LEU d 51 " --> pdb=" O GLN d 47 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP d 53 " --> pdb=" O LEU d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 88 Processing helix chain 'd' and resid 91 through 99 Processing helix chain 'e' and resid 10 through 29 removed outlier: 3.667A pdb=" N ILE e 14 " --> pdb=" O ASP e 10 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ASP e 15 " --> pdb=" O HIS e 11 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLN e 16 " --> pdb=" O ARG e 12 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR e 18 " --> pdb=" O ILE e 14 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA e 19 " --> pdb=" O ASP e 15 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N GLU e 20 " --> pdb=" O GLN e 16 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE e 21 " --> pdb=" O ALA e 17 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA e 25 " --> pdb=" O ILE e 21 " (cutoff:3.500A) Processing helix chain 'e' and resid 76 through 85 removed outlier: 3.912A pdb=" N ALA e 82 " --> pdb=" O LYS e 78 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU e 83 " --> pdb=" O THR e 79 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET e 84 " --> pdb=" O VAL e 80 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ARG e 85 " --> pdb=" O ASP e 81 " (cutoff:3.500A) Processing helix chain 'f' and resid 34 through 39 removed outlier: 3.561A pdb=" N SER f 38 " --> pdb=" O THR f 34 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY f 39 " --> pdb=" O ALA f 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 34 through 39' Processing helix chain 'f' and resid 42 through 47 removed outlier: 4.398A pdb=" N SER f 46 " --> pdb=" O GLY f 42 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N THR f 47 " --> pdb=" O SER f 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 42 through 47' Processing helix chain 'f' and resid 48 through 64 removed outlier: 5.302A pdb=" N ALA f 61 " --> pdb=" O ARG f 57 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL f 62 " --> pdb=" O CYS f 58 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS f 63 " --> pdb=" O ALA f 59 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU f 64 " --> pdb=" O ASP f 60 " (cutoff:3.500A) Processing helix chain 'f' and resid 79 through 92 removed outlier: 4.394A pdb=" N SER f 83 " --> pdb=" O PRO f 79 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR f 84 " --> pdb=" O GLY f 80 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE f 85 " --> pdb=" O ARG f 81 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA f 91 " --> pdb=" O ALA f 87 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY f 92 " --> pdb=" O LEU f 88 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 10 Proline residue: g 10 - end of helix Processing helix chain 'g' and resid 112 through 117 Processing helix chain 'h' and resid 13 through 21 removed outlier: 3.756A pdb=" N SER h 20 " --> pdb=" O ILE h 16 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE h 21 " --> pdb=" O ALA h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 37 Processing helix chain 'h' and resid 50 through 63 removed outlier: 3.996A pdb=" N THR h 54 " --> pdb=" O GLY h 50 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU h 55 " --> pdb=" O GLN h 51 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS h 61 " --> pdb=" O ASP h 57 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE h 62 " --> pdb=" O GLU h 58 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL h 63 " --> pdb=" O VAL h 59 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 83 removed outlier: 3.928A pdb=" N ARG h 69 " --> pdb=" O GLU h 65 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG h 70 " --> pdb=" O GLY h 66 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER h 75 " --> pdb=" O GLU h 71 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU h 79 " --> pdb=" O SER h 75 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET h 80 " --> pdb=" O ILE h 76 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP h 81 " --> pdb=" O LYS h 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 93 removed outlier: 3.646A pdb=" N GLY h 93 " --> pdb=" O ARG h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 105 through 110 Processing helix chain 'i' and resid 8 through 18 removed outlier: 4.047A pdb=" N ARG i 12 " --> pdb=" O THR i 8 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY i 13 " --> pdb=" O ARG i 9 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET i 14 " --> pdb=" O SER i 10 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS i 18 " --> pdb=" O MET i 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 23 through 28 Proline residue: j 28 - end of helix No H-bonds generated for 'chain 'j' and resid 23 through 28' Processing helix chain 'k' and resid 8 through 17 removed outlier: 3.519A pdb=" N ARG k 12 " --> pdb=" O SER k 8 " (cutoff:3.500A) Processing helix chain 'k' and resid 18 through 24 removed outlier: 4.439A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 25 through 38 removed outlier: 3.639A pdb=" N ARG k 34 " --> pdb=" O VAL k 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 14 removed outlier: 3.612A pdb=" N ALA l 10 " --> pdb=" O VAL l 6 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS l 11 " --> pdb=" O ARG l 7 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG l 12 " --> pdb=" O GLY l 8 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LYS l 14 " --> pdb=" O ALA l 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 6 through 14' Processing helix chain 'l' and resid 36 through 44 removed outlier: 4.354A pdb=" N LYS l 40 " --> pdb=" O ALA l 36 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LEU l 43 " --> pdb=" O ARG l 39 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARG l 44 " --> pdb=" O LYS l 40 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 62 removed outlier: 3.620A pdb=" N CYS l 60 " --> pdb=" O LEU l 56 " (cutoff:3.500A) Proline residue: l 62 - end of helix Processing helix chain 'n' and resid 1 through 21 removed outlier: 3.785A pdb=" N ALA n 5 " --> pdb=" O ASP n 1 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ARG n 6 " --> pdb=" O LYS n 2 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG n 8 " --> pdb=" O SER n 4 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG n 9 " --> pdb=" O ALA n 5 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA n 10 " --> pdb=" O ARG n 6 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG n 12 " --> pdb=" O ARG n 8 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG n 14 " --> pdb=" O ALA n 10 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG n 15 " --> pdb=" O THR n 11 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS n 16 " --> pdb=" O ARG n 12 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU n 17 " --> pdb=" O ALA n 13 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN n 18 " --> pdb=" O ARG n 14 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU n 19 " --> pdb=" O ARG n 15 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 82 removed outlier: 3.964A pdb=" N GLY n 74 " --> pdb=" O ALA n 70 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N LYS n 75 " --> pdb=" O ALA n 71 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA n 76 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N VAL n 77 " --> pdb=" O VAL n 73 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA n 78 " --> pdb=" O GLY n 74 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU n 79 " --> pdb=" O LYS n 75 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ARG n 80 " --> pdb=" O ALA n 76 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA n 81 " --> pdb=" O VAL n 77 " (cutoff:3.500A) Processing helix chain 'n' and resid 100 through 113 removed outlier: 4.180A pdb=" N ALA n 104 " --> pdb=" O GLY n 100 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU n 105 " --> pdb=" O ARG n 101 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG n 110 " --> pdb=" O ALA n 106 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU n 111 " --> pdb=" O ASP n 107 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA n 112 " --> pdb=" O ALA n 108 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY n 113 " --> pdb=" O ALA n 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 54 through 59 removed outlier: 5.101A pdb=" N GLU n 59 " --> pdb=" O GLU n 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 54 through 59' Processing helix chain 'o' and resid 1 through 12 removed outlier: 4.337A pdb=" N GLN o 6 " --> pdb=" O ASN o 2 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU o 7 " --> pdb=" O ILE o 3 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLU o 10 " --> pdb=" O GLN o 6 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN o 11 " --> pdb=" O LEU o 7 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET o 12 " --> pdb=" O GLU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 98 through 103 removed outlier: 3.670A pdb=" N ARG o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N THR o 103 " --> pdb=" O LEU o 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 98 through 103' Processing helix chain 'p' and resid 5 through 21 removed outlier: 3.899A pdb=" N ALA p 9 " --> pdb=" O ARG p 5 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG p 10 " --> pdb=" O GLY p 6 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LYS p 14 " --> pdb=" O ARG p 10 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS p 15 " --> pdb=" O ALA p 11 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE p 16 " --> pdb=" O ARG p 12 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN p 19 " --> pdb=" O LYS p 15 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA p 20 " --> pdb=" O ILE p 16 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS p 21 " --> pdb=" O LEU p 17 " (cutoff:3.500A) Processing helix chain 'p' and resid 24 through 30 removed outlier: 4.155A pdb=" N SER p 28 " --> pdb=" O TYR p 24 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG p 29 " --> pdb=" O GLY p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 31 through 36 removed outlier: 4.777A pdb=" N GLN p 36 " --> pdb=" O ARG p 32 " (cutoff:3.500A) Processing helix chain 'p' and resid 38 through 63 removed outlier: 3.519A pdb=" N ARG p 47 " --> pdb=" O GLN p 43 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG p 50 " --> pdb=" O TYR p 46 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE p 56 " --> pdb=" O ARG p 52 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ARG p 57 " --> pdb=" O LYS p 53 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU p 59 " --> pdb=" O GLN p 55 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 72 removed outlier: 3.881A pdb=" N GLN p 70 " --> pdb=" O ALA p 66 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN p 71 " --> pdb=" O ALA p 67 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY p 72 " --> pdb=" O ALA p 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 66 through 72' Processing helix chain 'p' and resid 74 through 86 removed outlier: 4.040A pdb=" N SER p 86 " --> pdb=" O LEU p 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 91 through 101 removed outlier: 3.984A pdb=" N ILE p 97 " --> pdb=" O ILE p 93 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA p 98 " --> pdb=" O LEU p 94 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL p 99 " --> pdb=" O ALA p 95 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE p 100 " --> pdb=" O ASP p 96 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP p 101 " --> pdb=" O ILE p 97 " (cutoff:3.500A) Processing helix chain 'p' and resid 102 through 117 removed outlier: 4.016A pdb=" N THR p 106 " --> pdb=" O LYS p 102 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA p 107 " --> pdb=" O VAL p 103 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU p 108 " --> pdb=" O ALA p 104 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL p 109 " --> pdb=" O PHE p 105 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU p 110 " --> pdb=" O THR p 106 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA p 115 " --> pdb=" O LYS p 111 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU p 116 " --> pdb=" O ALA p 112 " (cutoff:3.500A) Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.748A pdb=" N LEU r 19 " --> pdb=" O GLN r 15 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA r 21 " --> pdb=" O VAL r 17 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASP r 22 " --> pdb=" O ARG r 18 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG r 25 " --> pdb=" O ALA r 21 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 39 removed outlier: 4.126A pdb=" N ALA r 32 " --> pdb=" O LYS r 28 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU r 33 " --> pdb=" O VAL r 29 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP r 34 " --> pdb=" O SER r 30 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR r 39 " --> pdb=" O ILE r 35 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.762A pdb=" N LEU r 46 " --> pdb=" O LYS r 42 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS r 48 " --> pdb=" O ALA r 44 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL r 50 " --> pdb=" O LEU r 46 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU r 51 " --> pdb=" O VAL r 47 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA r 56 " --> pdb=" O GLU r 52 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA r 58 " --> pdb=" O ALA r 54 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN r 61 " --> pdb=" O ASN r 57 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 11 removed outlier: 3.735A pdb=" N LEU s 7 " --> pdb=" O ARG s 3 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 removed outlier: 5.335A pdb=" N SER s 21 " --> pdb=" O SER s 17 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR s 22 " --> pdb=" O GLU s 18 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N GLU s 25 " --> pdb=" O SER s 21 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS s 26 " --> pdb=" O THR s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 39 through 51 removed outlier: 3.891A pdb=" N LYS s 44 " --> pdb=" O LYS s 40 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE s 51 " --> pdb=" O VAL s 47 " (cutoff:3.500A) Processing helix chain 't' and resid 65 through 70 removed outlier: 4.136A pdb=" N ALA t 70 " --> pdb=" O VAL t 66 " (cutoff:3.500A) Processing helix chain 'u' and resid 14 through 24 removed outlier: 3.860A pdb=" N ASN u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 52 removed outlier: 3.756A pdb=" N MET u 50 " --> pdb=" O LYS u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 59 removed outlier: 4.294A pdb=" N TYR u 57 " --> pdb=" O LYS u 53 " (cutoff:3.500A) Processing helix chain 'w' and resid 51 through 62 removed outlier: 4.140A pdb=" N LYS w 61 " --> pdb=" O VAL w 57 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY w 62 " --> pdb=" O ILE w 58 " (cutoff:3.500A) Processing helix chain 'w' and resid 63 through 74 removed outlier: 3.966A pdb=" N LEU w 67 " --> pdb=" O ILE w 63 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA w 68 " --> pdb=" O ASP w 64 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLU w 69 " --> pdb=" O THR w 65 " (cutoff:3.500A) Processing helix chain 'x' and resid 3 through 9 removed outlier: 4.460A pdb=" N GLU x 7 " --> pdb=" O LYS x 3 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS x 8 " --> pdb=" O GLU x 4 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER x 9 " --> pdb=" O LEU x 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 3 through 9' Processing helix chain 'x' and resid 11 through 31 removed outlier: 3.757A pdb=" N ASN x 19 " --> pdb=" O THR x 15 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU x 23 " --> pdb=" O ASN x 19 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 60 removed outlier: 4.295A pdb=" N VAL x 45 " --> pdb=" O LEU x 41 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ARG x 46 " --> pdb=" O LEU x 42 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ARG x 47 " --> pdb=" O LYS x 43 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ASP x 48 " --> pdb=" O GLN x 44 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA x 50 " --> pdb=" O ARG x 46 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG x 51 " --> pdb=" O ARG x 47 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL x 52 " --> pdb=" O ASP x 48 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN x 57 " --> pdb=" O LYS x 53 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU x 58 " --> pdb=" O THR x 54 " (cutoff:3.500A) Processing helix chain 'y' and resid 16 through 25 removed outlier: 4.555A pdb=" N ALA y 21 " --> pdb=" O PRO y 17 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY y 25 " --> pdb=" O ALA y 21 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 51 Processing sheet with id= 1, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.899A pdb=" N ARG C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY C 49 " --> pdb=" O ASN C 40 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 3 through 9 removed outlier: 5.917A pdb=" N ARG D 3 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASP D 54 " --> pdb=" O VAL D 9 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 19 through 23 Processing sheet with id= 4, first strand: chain 'F' and resid 28 through 32 removed outlier: 3.525A pdb=" N LEU F 29 " --> pdb=" O THR F 46 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'K' and resid 1 through 5 removed outlier: 4.011A pdb=" N VAL K 19 " --> pdb=" O ALA K 1 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL K 15 " --> pdb=" O CYS K 5 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'K' and resid 74 through 77 removed outlier: 5.226A pdb=" N VAL K 93 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU K 99 " --> pdb=" O TYR K 95 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'K' and resid 169 through 174 removed outlier: 7.971A pdb=" N ALA K 169 " --> pdb=" O ALA K 185 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L' and resid 10 through 16 removed outlier: 5.624A pdb=" N VAL L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP L 181 " --> pdb=" O LEU L 186 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'L' and resid 78 through 84 removed outlier: 5.636A pdb=" N ARG L 46 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN L 49 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN L 36 " --> pdb=" O GLN L 49 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N THR L 51 " --> pdb=" O VAL L 34 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL L 34 " --> pdb=" O THR L 51 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'L' and resid 168 through 173 removed outlier: 4.752A pdb=" N GLU L 168 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR L 112 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL L 170 " --> pdb=" O THR L 110 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N VAL L 172 " --> pdb=" O ASP L 108 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP L 108 " --> pdb=" O VAL L 172 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'M' and resid 118 through 121 Processing sheet with id= 12, first strand: chain 'N' and resid 64 through 68 removed outlier: 3.687A pdb=" N CYS N 86 " --> pdb=" O MET N 37 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N VAL N 88 " --> pdb=" O LEU N 35 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU N 35 " --> pdb=" O VAL N 88 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS N 32 " --> pdb=" O THR N 156 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N THR N 157 " --> pdb=" O GLY N 125 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLY N 125 " --> pdb=" O THR N 157 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'O' and resid 14 through 18 removed outlier: 3.504A pdb=" N ASP O 15 " --> pdb=" O LYS O 26 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR O 24 " --> pdb=" O LYS O 17 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N GLY O 30 " --> pdb=" O GLY O 27 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'O' and resid 81 through 88 removed outlier: 3.774A pdb=" N LEU O 132 " --> pdb=" O LYS O 84 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU O 86 " --> pdb=" O ILE O 130 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU O 88 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR O 128 " --> pdb=" O LEU O 88 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'O' and resid 93 through 97 Processing sheet with id= 16, first strand: chain 'R' and resid 14 through 19 Processing sheet with id= 17, first strand: chain 'R' and resid 74 through 78 removed outlier: 3.746A pdb=" N ALA R 87 " --> pdb=" O TYR R 74 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N HIS R 76 " --> pdb=" O LYS R 85 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS R 85 " --> pdb=" O HIS R 76 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N GLY R 83 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'S' and resid 17 through 21 removed outlier: 5.419A pdb=" N ASN S 82 " --> pdb=" O MET S 7 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'S' and resid 66 through 71 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'U' and resid 30 through 35 removed outlier: 8.111A pdb=" N SER U 30 " --> pdb=" O LYS U 133 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'U' and resid 71 through 74 removed outlier: 3.608A pdb=" N LYS U 71 " --> pdb=" O VAL U 93 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR U 91 " --> pdb=" O ILE U 73 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'V' and resid 95 through 101 removed outlier: 3.709A pdb=" N CYS V 100 " --> pdb=" O MET V 110 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N MET V 110 " --> pdb=" O CYS V 100 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'W' and resid 12 through 15 removed outlier: 5.891A pdb=" N HIS W 12 " --> pdb=" O ILE W 38 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N HIS W 36 " --> pdb=" O GLY W 14 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'W' and resid 63 through 68 removed outlier: 3.562A pdb=" N ALA W 182 " --> pdb=" O PHE W 195 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'X' and resid 53 through 58 removed outlier: 3.694A pdb=" N ARG X 53 " --> pdb=" O HIS X 68 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU X 57 " --> pdb=" O ARG X 64 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL X 65 " --> pdb=" O GLN X 99 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'X' and resid 163 through 170 removed outlier: 4.892A pdb=" N ARG X 163 " --> pdb=" O GLY X 154 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE X 201 " --> pdb=" O ASP X 182 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP X 180 " --> pdb=" O LYS X 203 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Y' and resid 140 through 144 removed outlier: 3.966A pdb=" N ASP Y 140 " --> pdb=" O PHE Y 181 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N MET Y 177 " --> pdb=" O ILE Y 144 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Z' and resid 2 through 7 removed outlier: 3.662A pdb=" N GLN Z 3 " --> pdb=" O GLY Z 31 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY Z 31 " --> pdb=" O GLN Z 3 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS Z 5 " --> pdb=" O VAL Z 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL Z 29 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU Z 27 " --> pdb=" O ILE Z 7 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA Z 8 " --> pdb=" O LEU Z 27 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Z' and resid 74 through 79 removed outlier: 7.535A pdb=" N HIS Z 74 " --> pdb=" O PRO Z 89 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Z 76 " --> pdb=" O MET Z 87 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'a' and resid 34 through 37 removed outlier: 6.311A pdb=" N ASN a 63 " --> pdb=" O HIS a 37 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N HIS a 3 " --> pdb=" O THR a 92 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR a 92 " --> pdb=" O HIS a 3 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL a 7 " --> pdb=" O MET a 88 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET a 88 " --> pdb=" O VAL a 7 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'a' and resid 38 through 42 removed outlier: 4.035A pdb=" N ARG a 38 " --> pdb=" O ASN a 63 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N TYR a 59 " --> pdb=" O TRP a 42 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'a' and resid 43 through 46 removed outlier: 3.579A pdb=" N GLY a 43 " --> pdb=" O TYR a 59 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'c' and resid 48 through 51 Processing sheet with id= 34, first strand: chain 'c' and resid 73 through 76 removed outlier: 3.614A pdb=" N CYS c 126 " --> pdb=" O VAL c 102 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'd' and resid 2 through 5 removed outlier: 3.760A pdb=" N VAL d 16 " --> pdb=" O GLY d 5 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS d 65 " --> pdb=" O ALA d 13 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'e' and resid 1 through 9 removed outlier: 3.531A pdb=" N ILE e 2 " --> pdb=" O ILE e 72 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE e 4 " --> pdb=" O VAL e 70 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA e 8 " --> pdb=" O HIS e 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS e 66 " --> pdb=" O ALA e 8 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'f' and resid 18 through 23 removed outlier: 3.732A pdb=" N LYS f 75 " --> pdb=" O ILE f 11 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA f 13 " --> pdb=" O LYS f 75 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'g' and resid 28 through 31 Processing sheet with id= 39, first strand: chain 'g' and resid 35 through 40 removed outlier: 3.659A pdb=" N THR g 39 " --> pdb=" O ARG g 49 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LYS g 50 " --> pdb=" O ILE g 66 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'j' and resid 17 through 22 removed outlier: 3.735A pdb=" N GLU j 4 " --> pdb=" O LYS j 22 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'm' and resid 13 through 18 removed outlier: 5.315A pdb=" N ILE m 23 " --> pdb=" O GLN m 37 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N HIS m 33 " --> pdb=" O CYS m 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'n' and resid 23 through 26 removed outlier: 4.603A pdb=" N ASP n 92 " --> pdb=" O LEU n 25 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'n' and resid 35 through 38 removed outlier: 4.296A pdb=" N VAL n 38 " --> pdb=" O VAL n 48 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'o' and resid 25 through 28 removed outlier: 4.629A pdb=" N PHE o 42 " --> pdb=" O VAL o 27 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'o' and resid 48 through 51 removed outlier: 5.927A pdb=" N ALA o 48 " --> pdb=" O THR o 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR o 59 " --> pdb=" O ALA o 48 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'q' and resid 11 through 15 removed outlier: 4.007A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N LEU q 39 " --> pdb=" O ILE q 49 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE q 49 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'q' and resid 30 through 33 removed outlier: 4.183A pdb=" N VAL q 58 " --> pdb=" O SER q 102 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER q 102 " --> pdb=" O VAL q 58 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS q 60 " --> pdb=" O GLY q 100 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'q' and resid 71 through 77 removed outlier: 3.502A pdb=" N HIS q 89 " --> pdb=" O VAL q 72 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN q 87 " --> pdb=" O ILE q 74 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS q 85 " --> pdb=" O LYS q 76 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'r' and resid 2 through 8 removed outlier: 3.508A pdb=" N VAL r 107 " --> pdb=" O THR r 3 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA r 5 " --> pdb=" O VAL r 105 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL r 105 " --> pdb=" O ALA r 5 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N HIS r 7 " --> pdb=" O ILE r 103 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE r 103 " --> pdb=" O HIS r 7 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N THR r 100 " --> pdb=" O GLY r 79 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY r 79 " --> pdb=" O THR r 100 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE r 75 " --> pdb=" O THR r 104 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS r 73 " --> pdb=" O VAL r 106 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'r' and resid 81 through 85 removed outlier: 3.559A pdb=" N ILE r 96 " --> pdb=" O ARG r 84 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 's' and resid 12 through 15 removed outlier: 4.626A pdb=" N VAL s 31 " --> pdb=" O HIS s 15 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 's' and resid 60 through 69 removed outlier: 7.043A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG s 77 " --> pdb=" O LYS s 66 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 't' and resid 93 through 96 removed outlier: 5.355A pdb=" N ARG t 93 " --> pdb=" O ILE t 102 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'u' and resid 6 through 9 removed outlier: 3.644A pdb=" N GLU u 7 " --> pdb=" O GLU u 41 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU u 41 " --> pdb=" O GLU u 7 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE u 29 " --> pdb=" O ILE u 89 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP u 90 " --> pdb=" O ASP u 76 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP u 76 " --> pdb=" O ASP u 90 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'v' and resid 18 through 22 removed outlier: 3.857A pdb=" N GLU v 19 " --> pdb=" O VAL v 57 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'v' and resid 35 through 38 Processing sheet with id= 57, first strand: chain 'w' and resid 11 through 18 removed outlier: 3.873A pdb=" N VAL w 12 " --> pdb=" O PHE w 28 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN w 22 " --> pdb=" O SER w 18 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'w' and resid 36 through 39 Processing sheet with id= 59, first strand: chain 'y' and resid 4 through 9 removed outlier: 7.824A pdb=" N MET y 53 " --> pdb=" O THR y 9 " (cutoff:3.500A) 1206 hydrogen bonds defined for protein. 3570 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3621 hydrogen bonds 5704 hydrogen bond angles 0 basepair planarities 1436 basepair parallelities 1801 stacking parallelities Total time for adding SS restraints: 333.58 Time building geometry restraints manager: 86.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 625 1.04 - 1.24: 8682 1.24 - 1.44: 72633 1.44 - 1.64: 71200 1.64 - 1.84: 258 Bond restraints: 153398 Sorted by residual: bond pdb=" C2 G I 226 " pdb=" N3 G I 226 " ideal model delta sigma weight residual 1.323 1.790 -0.467 2.00e-02 2.50e+03 5.46e+02 bond pdb=" N3 G I 226 " pdb=" C4 G I 226 " ideal model delta sigma weight residual 1.350 1.811 -0.461 2.00e-02 2.50e+03 5.31e+02 bond pdb=" C GLY K 26 " pdb=" N LYS K 27 " ideal model delta sigma weight residual 1.327 1.591 -0.264 1.32e-02 5.74e+03 4.00e+02 bond pdb=" N1 G I 226 " pdb=" C2 G I 226 " ideal model delta sigma weight residual 1.373 1.733 -0.360 2.00e-02 2.50e+03 3.23e+02 bond pdb=" C6 G I 226 " pdb=" N1 G I 226 " ideal model delta sigma weight residual 1.391 1.740 -0.349 2.00e-02 2.50e+03 3.04e+02 ... (remaining 153393 not shown) Histogram of bond angle deviations from ideal: 94.48 - 105.46: 22643 105.46 - 116.43: 114590 116.43 - 127.41: 83195 127.41 - 138.38: 9847 138.38 - 149.36: 9 Bond angle restraints: 230284 Sorted by residual: angle pdb=" C GLY C 62 " pdb=" N GLN C 63 " pdb=" CA GLN C 63 " ideal model delta sigma weight residual 122.41 149.36 -26.95 1.47e+00 4.63e-01 3.36e+02 angle pdb=" C ASN H 8 " pdb=" N GLU H 9 " pdb=" CA GLU H 9 " ideal model delta sigma weight residual 121.83 106.15 15.68 1.56e+00 4.11e-01 1.01e+02 angle pdb=" N GLY K 26 " pdb=" CA GLY K 26 " pdb=" C GLY K 26 " ideal model delta sigma weight residual 111.67 120.76 -9.09 9.20e-01 1.18e+00 9.76e+01 angle pdb=" CB GLU T 115 " pdb=" CG GLU T 115 " pdb=" CD GLU T 115 " ideal model delta sigma weight residual 112.60 127.77 -15.17 1.70e+00 3.46e-01 7.96e+01 angle pdb=" C GLU M 127 " pdb=" N ALA M 128 " pdb=" CA ALA M 128 " ideal model delta sigma weight residual 123.65 139.03 -15.38 1.88e+00 2.83e-01 6.69e+01 ... (remaining 230279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 84396 35.98 - 71.95: 12015 71.95 - 107.93: 1407 107.93 - 143.90: 70 143.90 - 179.88: 23 Dihedral angle restraints: 97911 sinusoidal: 82415 harmonic: 15496 Sorted by residual: dihedral pdb=" CA ARG K 100 " pdb=" C ARG K 100 " pdb=" N ARG K 101 " pdb=" CA ARG K 101 " ideal model delta harmonic sigma weight residual 180.00 124.26 55.74 0 5.00e+00 4.00e-02 1.24e+02 dihedral pdb=" C4' C I3640 " pdb=" C3' C I3640 " pdb=" C2' C I3640 " pdb=" C1' C I3640 " ideal model delta sinusoidal sigma weight residual -35.00 34.75 -69.75 1 8.00e+00 1.56e-02 9.81e+01 dihedral pdb=" C4' A I1820 " pdb=" C3' A I1820 " pdb=" C2' A I1820 " pdb=" C1' A I1820 " ideal model delta sinusoidal sigma weight residual -35.00 33.66 -68.66 1 8.00e+00 1.56e-02 9.54e+01 ... (remaining 97908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 28843 0.150 - 0.301: 325 0.301 - 0.451: 12 0.451 - 0.602: 1 0.602 - 0.752: 1 Chirality restraints: 29182 Sorted by residual: chirality pdb=" CG LEU s 11 " pdb=" CB LEU s 11 " pdb=" CD1 LEU s 11 " pdb=" CD2 LEU s 11 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" CB ILE U 46 " pdb=" CA ILE U 46 " pdb=" CG1 ILE U 46 " pdb=" CG2 ILE U 46 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" C3' C I 271 " pdb=" C4' C I 271 " pdb=" O3' C I 271 " pdb=" C2' C I 271 " both_signs ideal model delta sigma weight residual False -2.48 -2.11 -0.36 2.00e-01 2.50e+01 3.29e+00 ... (remaining 29179 not shown) Planarity restraints: 12109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MC I1406 " 0.048 2.00e-02 2.50e+03 6.18e-01 8.59e+03 pdb=" C4' 5MC I1406 " 0.469 2.00e-02 2.50e+03 pdb=" O4' 5MC I1406 " 0.808 2.00e-02 2.50e+03 pdb=" C3' 5MC I1406 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 5MC I1406 " -0.592 2.00e-02 2.50e+03 pdb=" C2' 5MC I1406 " -0.233 2.00e-02 2.50e+03 pdb=" O2' 5MC I1406 " 0.894 2.00e-02 2.50e+03 pdb=" C1' 5MC I1406 " 0.181 2.00e-02 2.50e+03 pdb=" N1 5MC I1406 " -0.990 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU I2247 " 0.056 2.00e-02 2.50e+03 6.15e-01 8.50e+03 pdb=" C4' 5MU I2247 " 0.456 2.00e-02 2.50e+03 pdb=" O4' 5MU I2247 " 0.759 2.00e-02 2.50e+03 pdb=" C3' 5MU I2247 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 5MU I2247 " -0.611 2.00e-02 2.50e+03 pdb=" C2' 5MU I2247 " -0.218 2.00e-02 2.50e+03 pdb=" O2' 5MU I2247 " 0.931 2.00e-02 2.50e+03 pdb=" C1' 5MU I2247 " 0.190 2.00e-02 2.50e+03 pdb=" N1 5MU I2247 " -0.968 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I3329 " -0.032 2.00e-02 2.50e+03 6.06e-01 8.27e+03 pdb=" C4' 2MG I3329 " -0.465 2.00e-02 2.50e+03 pdb=" O4' 2MG I3329 " -0.838 2.00e-02 2.50e+03 pdb=" C3' 2MG I3329 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG I3329 " 0.543 2.00e-02 2.50e+03 pdb=" C2' 2MG I3329 " 0.264 2.00e-02 2.50e+03 pdb=" O2' 2MG I3329 " -0.848 2.00e-02 2.50e+03 pdb=" C1' 2MG I3329 " -0.177 2.00e-02 2.50e+03 pdb=" N9 2MG I3329 " 0.962 2.00e-02 2.50e+03 ... (remaining 12106 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 92 1.87 - 2.56: 5672 2.56 - 3.24: 182182 3.24 - 3.92: 392834 3.92 - 4.60: 510332 Nonbonded interactions: 1091112 Sorted by model distance: nonbonded pdb=" N GLN C 63 " pdb=" N3 G I 226 " model vdw 1.193 2.500 nonbonded pdb=" H1 G I1463 " pdb=" O2' G I4342 " model vdw 1.283 1.850 nonbonded pdb=" N GLN C 63 " pdb=" C2 G I 226 " model vdw 1.630 3.300 nonbonded pdb=" O4 U I1462 " pdb=" H62 A I4345 " model vdw 1.646 1.850 nonbonded pdb=" O6 G I3783 " pdb=" O2 U I3837 " model vdw 1.658 2.240 ... (remaining 1091107 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.730 Extract box with map and model: 29.410 Check model and map are aligned: 1.500 Set scattering table: 0.950 Process input model: 633.130 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.340 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 681.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3429 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.467 152773 Z= 0.420 Angle : 0.997 26.946 228847 Z= 0.517 Chirality : 0.047 0.752 29182 Planarity : 0.019 0.618 12064 Dihedral : 25.160 179.876 87789 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 122.79 Ramachandran Plot: Outliers : 0.99 % Allowed : 12.50 % Favored : 86.50 % Rotamer: Outliers : 0.02 % Allowed : 0.63 % Favored : 99.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.10), residues: 5342 helix: -1.71 (0.14), residues: 1191 sheet: -1.92 (0.19), residues: 618 loop : -2.11 (0.10), residues: 3533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP R 15 HIS 0.029 0.003 HIS v 47 PHE 0.049 0.004 PHE N 121 TYR 0.044 0.003 TYR R 125 ARG 0.071 0.002 ARG x 28 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 414 time to evaluate : 5.734 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: K 145 MET cc_start: 0.2079 (ttm) cc_final: 0.1417 (ttm) REVERT: K 180 MET cc_start: 0.3072 (tpt) cc_final: 0.2688 (tpt) REVERT: K 228 ASP cc_start: 0.7902 (p0) cc_final: 0.7490 (p0) REVERT: O 148 ARG cc_start: 0.1524 (ptt180) cc_final: 0.1192 (ptt-90) REVERT: S 44 LYS cc_start: 0.5515 (mppt) cc_final: 0.4158 (mmtt) REVERT: S 67 LYS cc_start: 0.2164 (mmpt) cc_final: 0.1415 (mmtt) REVERT: U 46 ILE cc_start: 0.7593 (mt) cc_final: 0.7290 (mt) REVERT: U 90 GLU cc_start: 0.6812 (mp0) cc_final: 0.6508 (mp0) REVERT: V 75 ILE cc_start: 0.4640 (mm) cc_final: 0.4108 (tp) REVERT: V 106 ASP cc_start: 0.7753 (p0) cc_final: 0.7383 (p0) REVERT: W 23 LYS cc_start: 0.2391 (mmtp) cc_final: 0.1823 (mmtp) REVERT: W 67 VAL cc_start: -0.1576 (t) cc_final: -0.1843 (t) REVERT: h 74 MET cc_start: -0.3657 (ptp) cc_final: -0.4736 (ttt) REVERT: o 12 MET cc_start: 0.0716 (ttt) cc_final: -0.0101 (ttt) REVERT: q 14 VAL cc_start: 0.5702 (m) cc_final: 0.5022 (m) REVERT: u 48 MET cc_start: 0.4096 (mmm) cc_final: 0.3818 (mtp) REVERT: u 50 MET cc_start: 0.3342 (mmt) cc_final: 0.2527 (mmt) REVERT: y 20 LYS cc_start: 0.7770 (mmtm) cc_final: 0.7533 (mmtp) outliers start: 1 outliers final: 1 residues processed: 415 average time/residue: 1.3561 time to fit residues: 991.0652 Evaluate side-chains 305 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 304 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 825 optimal weight: 20.0000 chunk 741 optimal weight: 50.0000 chunk 411 optimal weight: 10.0000 chunk 253 optimal weight: 10.0000 chunk 500 optimal weight: 50.0000 chunk 396 optimal weight: 20.0000 chunk 766 optimal weight: 0.7980 chunk 296 optimal weight: 20.0000 chunk 466 optimal weight: 20.0000 chunk 570 optimal weight: 0.9990 chunk 888 optimal weight: 2.9990 overall best weight: 4.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 26 ASN G 19 ASN ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 23 ASN V 62 ASN ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 48 ASN ** X 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 11 HIS ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 8 GLN ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 78 HIS ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 111 GLN h 51 GLN ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 29 GLN ** l 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3300 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.461 152773 Z= 0.251 Angle : 0.715 24.257 228847 Z= 0.380 Chirality : 0.036 0.317 29182 Planarity : 0.007 0.132 12064 Dihedral : 25.228 179.619 77037 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 83.75 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.84 % Favored : 90.53 % Rotamer: Outliers : 0.20 % Allowed : 4.49 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -2.68 (0.11), residues: 5342 helix: -1.19 (0.13), residues: 1462 sheet: -1.89 (0.18), residues: 711 loop : -2.10 (0.10), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP K 212 HIS 0.029 0.002 HIS U 13 PHE 0.024 0.002 PHE O 51 TYR 0.023 0.002 TYR X 167 ARG 0.011 0.001 ARG V 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 391 time to evaluate : 5.747 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: K 145 MET cc_start: 0.1541 (ttm) cc_final: 0.0663 (ttm) REVERT: K 228 ASP cc_start: 0.8073 (p0) cc_final: 0.7430 (p0) REVERT: S 40 LYS cc_start: 0.5297 (tptt) cc_final: 0.4572 (tttt) REVERT: S 67 LYS cc_start: 0.2431 (mmpt) cc_final: 0.1109 (mmpt) REVERT: V 20 MET cc_start: 0.7311 (ptm) cc_final: 0.6866 (ptp) REVERT: V 24 MET cc_start: 0.5890 (mmt) cc_final: 0.5526 (tpp) REVERT: V 106 ASP cc_start: 0.7313 (p0) cc_final: 0.7006 (p0) REVERT: Z 2 LEU cc_start: 0.7594 (mm) cc_final: 0.7305 (mm) REVERT: a 88 MET cc_start: -0.0634 (tpt) cc_final: -0.1331 (tpt) REVERT: b 30 MET cc_start: -0.1299 (tmm) cc_final: -0.1795 (ttp) REVERT: h 74 MET cc_start: -0.3663 (ptp) cc_final: -0.4882 (ttt) REVERT: o 12 MET cc_start: -0.0067 (ttt) cc_final: -0.0673 (ttt) REVERT: y 20 LYS cc_start: 0.7751 (mmtm) cc_final: 0.7326 (mmtp) outliers start: 9 outliers final: 2 residues processed: 400 average time/residue: 1.3009 time to fit residues: 923.9109 Evaluate side-chains 311 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 309 time to evaluate : 5.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 493 optimal weight: 20.0000 chunk 275 optimal weight: 20.0000 chunk 739 optimal weight: 10.0000 chunk 604 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 889 optimal weight: 30.0000 chunk 961 optimal weight: 3.9990 chunk 792 optimal weight: 30.0000 chunk 882 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 713 optimal weight: 50.0000 overall best weight: 7.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 HIS ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS ** R 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 HIS ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 ASN ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 139 ASN a 52 ASN ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 6 GLN ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3409 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.462 152773 Z= 0.296 Angle : 0.717 24.309 228847 Z= 0.377 Chirality : 0.036 0.461 29182 Planarity : 0.007 0.128 12064 Dihedral : 25.131 178.951 77037 Min Nonbonded Distance : 1.182 Molprobity Statistics. All-atom Clashscore : 92.96 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.85 % Favored : 87.59 % Rotamer: Outliers : 0.11 % Allowed : 5.23 % Favored : 94.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -2.48 (0.11), residues: 5342 helix: -0.59 (0.13), residues: 1426 sheet: -1.77 (0.19), residues: 689 loop : -2.20 (0.10), residues: 3227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 212 HIS 0.009 0.002 HIS R 130 PHE 0.035 0.003 PHE H 11 TYR 0.033 0.002 TYR R 125 ARG 0.042 0.001 ARG x 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 388 time to evaluate : 5.838 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: K 180 MET cc_start: 0.3351 (tpt) cc_final: 0.2980 (tpt) REVERT: K 228 ASP cc_start: 0.7902 (p0) cc_final: 0.7417 (p0) REVERT: L 11 MET cc_start: 0.4263 (mtt) cc_final: 0.3826 (mtt) REVERT: R 81 ILE cc_start: 0.8535 (tp) cc_final: 0.8179 (tt) REVERT: S 40 LYS cc_start: 0.5712 (tptt) cc_final: 0.4884 (tttt) REVERT: U 53 MET cc_start: 0.4507 (ptp) cc_final: 0.2776 (mtp) REVERT: W 67 VAL cc_start: -0.1168 (t) cc_final: -0.1462 (t) REVERT: Z 2 LEU cc_start: 0.7600 (mm) cc_final: 0.7325 (mm) REVERT: Z 138 MET cc_start: 0.3109 (tpt) cc_final: 0.2877 (tpt) REVERT: b 30 MET cc_start: -0.1083 (tmm) cc_final: -0.1730 (ttp) REVERT: b 115 MET cc_start: 0.0113 (mtt) cc_final: -0.0338 (mtm) REVERT: d 43 MET cc_start: 0.0723 (mmp) cc_final: 0.0242 (ttp) REVERT: h 74 MET cc_start: -0.4384 (ptp) cc_final: -0.5656 (ttt) REVERT: o 12 MET cc_start: -0.0179 (ttt) cc_final: -0.0699 (ttt) REVERT: p 43 GLN cc_start: 0.6946 (mm-40) cc_final: 0.6600 (tp-100) REVERT: y 20 LYS cc_start: 0.7753 (mmtm) cc_final: 0.7385 (mmtp) outliers start: 5 outliers final: 1 residues processed: 393 average time/residue: 1.3030 time to fit residues: 921.7580 Evaluate side-chains 307 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 879 optimal weight: 20.0000 chunk 668 optimal weight: 4.9990 chunk 461 optimal weight: 20.0000 chunk 98 optimal weight: 50.0000 chunk 424 optimal weight: 50.0000 chunk 597 optimal weight: 2.9990 chunk 892 optimal weight: 20.0000 chunk 945 optimal weight: 8.9990 chunk 466 optimal weight: 20.0000 chunk 846 optimal weight: 8.9990 chunk 254 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 HIS ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS R 130 HIS ** R 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 43 GLN ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 19 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3411 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.465 152773 Z= 0.276 Angle : 0.670 22.750 228847 Z= 0.357 Chirality : 0.034 0.294 29182 Planarity : 0.006 0.125 12064 Dihedral : 24.995 179.627 77037 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 85.88 Ramachandran Plot: Outliers : 0.56 % Allowed : 10.24 % Favored : 89.20 % Rotamer: Outliers : 0.09 % Allowed : 3.64 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.02 % 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: -2.46 (0.11), residues: 5342 helix: -0.51 (0.13), residues: 1466 sheet: -1.92 (0.18), residues: 720 loop : -2.19 (0.10), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O 61 HIS 0.026 0.002 HIS R 132 PHE 0.039 0.002 PHE U 68 TYR 0.029 0.002 TYR j 46 ARG 0.031 0.001 ARG o 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 5.900 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: K 145 MET cc_start: 0.3142 (mtp) cc_final: 0.2780 (mtp) REVERT: K 228 ASP cc_start: 0.8012 (p0) cc_final: 0.7076 (p0) REVERT: L 11 MET cc_start: 0.4155 (mtt) cc_final: 0.3777 (mtt) REVERT: R 81 ILE cc_start: 0.8641 (tp) cc_final: 0.8334 (tt) REVERT: V 20 MET cc_start: 0.7037 (ptm) cc_final: 0.6697 (ptm) REVERT: W 23 LYS cc_start: 0.2395 (mmtp) cc_final: 0.2130 (mptt) REVERT: Z 62 MET cc_start: 0.0721 (tmm) cc_final: -0.0295 (mtp) REVERT: b 30 MET cc_start: -0.1424 (tmm) cc_final: -0.1994 (ttp) REVERT: d 54 MET cc_start: 0.0104 (mtm) cc_final: -0.0665 (mtm) REVERT: h 74 MET cc_start: -0.4492 (ptp) cc_final: -0.5750 (ttt) REVERT: o 12 MET cc_start: -0.0292 (ttt) cc_final: -0.0653 (ttt) REVERT: p 43 GLN cc_start: 0.6953 (tp40) cc_final: 0.6709 (tp-100) REVERT: r 94 ASP cc_start: 0.6388 (p0) cc_final: 0.5830 (p0) REVERT: u 45 ASP cc_start: 0.4872 (p0) cc_final: 0.4620 (p0) REVERT: v 31 ARG cc_start: 0.3999 (tpp80) cc_final: 0.3203 (tpp80) REVERT: y 20 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7220 (mmtp) REVERT: y 26 LEU cc_start: 0.7131 (mt) cc_final: 0.6859 (mt) outliers start: 4 outliers final: 1 residues processed: 397 average time/residue: 1.3132 time to fit residues: 931.3816 Evaluate side-chains 314 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 313 time to evaluate : 5.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 787 optimal weight: 50.0000 chunk 536 optimal weight: 0.3980 chunk 13 optimal weight: 6.9990 chunk 703 optimal weight: 0.0010 chunk 390 optimal weight: 20.0000 chunk 806 optimal weight: 9.9990 chunk 653 optimal weight: 1.9990 chunk 1 optimal weight: 50.0000 chunk 482 optimal weight: 20.0000 chunk 848 optimal weight: 1.9990 chunk 238 optimal weight: 20.0000 overall best weight: 2.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 HIS ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 HIS ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS ** R 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 13 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 95 HIS ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3308 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.463 152773 Z= 0.200 Angle : 0.551 23.211 228847 Z= 0.302 Chirality : 0.030 0.303 29182 Planarity : 0.005 0.121 12064 Dihedral : 24.714 179.316 77037 Min Nonbonded Distance : 1.181 Molprobity Statistics. All-atom Clashscore : 71.42 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.93 % Favored : 90.51 % Rotamer: Outliers : 0.02 % Allowed : 1.73 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.02 % 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: -2.04 (0.11), residues: 5342 helix: -0.04 (0.14), residues: 1496 sheet: -1.82 (0.19), residues: 697 loop : -1.98 (0.11), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 212 HIS 0.013 0.001 HIS U 13 PHE 0.028 0.001 PHE N 172 TYR 0.016 0.001 TYR n 98 ARG 0.007 0.000 ARG O 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 408 time to evaluate : 5.781 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: K 228 ASP cc_start: 0.7689 (p0) cc_final: 0.7396 (p0) REVERT: L 11 MET cc_start: 0.3909 (mtt) cc_final: 0.3645 (mtt) REVERT: O 93 TYR cc_start: 0.4983 (m-10) cc_final: 0.4622 (m-80) REVERT: R 81 ILE cc_start: 0.8557 (tp) cc_final: 0.8203 (tt) REVERT: R 122 LEU cc_start: 0.5693 (mp) cc_final: 0.5357 (tp) REVERT: S 112 PHE cc_start: 0.5900 (m-80) cc_final: 0.5603 (m-80) REVERT: U 1 MET cc_start: 0.5337 (pmm) cc_final: 0.4918 (pmm) REVERT: V 1 MET cc_start: 0.6513 (tpp) cc_final: 0.5905 (tpp) REVERT: Z 62 MET cc_start: 0.0480 (tmm) cc_final: -0.0517 (mtt) REVERT: b 30 MET cc_start: -0.1777 (tmm) cc_final: -0.2305 (ttp) REVERT: b 115 MET cc_start: 0.0539 (mtt) cc_final: -0.0026 (mtm) REVERT: d 54 MET cc_start: -0.0199 (mtm) cc_final: -0.1251 (mtm) REVERT: h 74 MET cc_start: -0.4440 (ptp) cc_final: -0.5501 (ttt) REVERT: m 18 LYS cc_start: 0.4025 (tttt) cc_final: 0.3768 (tttt) REVERT: o 12 MET cc_start: -0.0309 (ttt) cc_final: -0.0634 (ttt) REVERT: p 43 GLN cc_start: 0.6869 (tp40) cc_final: 0.6483 (tp-100) REVERT: r 66 ILE cc_start: 0.3438 (mm) cc_final: 0.3223 (mm) REVERT: r 94 ASP cc_start: 0.6189 (p0) cc_final: 0.5615 (p0) REVERT: s 1 MET cc_start: 0.0424 (mpp) cc_final: -0.1075 (mmm) REVERT: v 19 GLU cc_start: 0.2600 (tp30) cc_final: 0.2360 (mm-30) REVERT: y 20 LYS cc_start: 0.7525 (mmtm) cc_final: 0.7017 (mmtp) outliers start: 1 outliers final: 0 residues processed: 409 average time/residue: 1.2695 time to fit residues: 922.7521 Evaluate side-chains 325 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 5.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 318 optimal weight: 50.0000 chunk 851 optimal weight: 2.9990 chunk 186 optimal weight: 70.0000 chunk 555 optimal weight: 9.9990 chunk 233 optimal weight: 20.0000 chunk 946 optimal weight: 20.0000 chunk 785 optimal weight: 30.0000 chunk 438 optimal weight: 30.0000 chunk 78 optimal weight: 50.0000 chunk 313 optimal weight: 40.0000 chunk 496 optimal weight: 50.0000 overall best weight: 16.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 HIS K 225 ASN ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN N 4 HIS ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 138 GLN Y 119 HIS ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 75 GLN ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 72 GLN ** t 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3653 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.465 152773 Z= 0.478 Angle : 1.019 23.720 228847 Z= 0.509 Chirality : 0.047 0.662 29182 Planarity : 0.009 0.164 12064 Dihedral : 25.694 179.981 77037 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 125.17 Ramachandran Plot: Outliers : 0.77 % Allowed : 15.56 % Favored : 83.68 % Rotamer: Outliers : 0.04 % Allowed : 4.31 % Favored : 95.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % 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: -3.04 (0.11), residues: 5342 helix: -0.91 (0.13), residues: 1455 sheet: -1.95 (0.20), residues: 614 loop : -2.69 (0.10), residues: 3273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP O 61 HIS 0.021 0.003 HIS K 141 PHE 0.036 0.004 PHE n 116 TYR 0.052 0.003 TYR o 98 ARG 0.039 0.002 ARG U 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 5.850 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: F 42 MET cc_start: 0.4836 (mmm) cc_final: 0.4429 (mtt) REVERT: K 228 ASP cc_start: 0.8065 (p0) cc_final: 0.7651 (p0) REVERT: O 140 ILE cc_start: 0.0496 (pt) cc_final: 0.0207 (pt) REVERT: R 122 LEU cc_start: 0.7057 (mp) cc_final: 0.6712 (tp) REVERT: Z 62 MET cc_start: 0.2054 (tmm) cc_final: 0.1795 (tmm) REVERT: Z 64 ASN cc_start: 0.4001 (m110) cc_final: 0.3680 (m110) REVERT: b 30 MET cc_start: -0.1423 (tmm) cc_final: -0.1919 (ttp) REVERT: d 54 MET cc_start: -0.0190 (mtm) cc_final: -0.2037 (ttt) REVERT: h 74 MET cc_start: -0.4399 (ptp) cc_final: -0.5737 (ttt) REVERT: s 1 MET cc_start: 0.4392 (mpp) cc_final: 0.3610 (mpp) REVERT: s 11 LEU cc_start: 0.6955 (mp) cc_final: 0.6707 (mt) REVERT: y 43 ILE cc_start: 0.6099 (mm) cc_final: 0.4659 (mm) outliers start: 2 outliers final: 1 residues processed: 360 average time/residue: 1.2755 time to fit residues: 817.6534 Evaluate side-chains 284 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 5.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 912 optimal weight: 5.9990 chunk 106 optimal weight: 50.0000 chunk 539 optimal weight: 2.9990 chunk 691 optimal weight: 0.9980 chunk 535 optimal weight: 0.6980 chunk 796 optimal weight: 6.9990 chunk 528 optimal weight: 5.9990 chunk 942 optimal weight: 6.9990 chunk 589 optimal weight: 9.9990 chunk 574 optimal weight: 0.8980 chunk 435 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 GLN ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 HIS ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS ** R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 138 GLN ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 2 ASN ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 48 GLN ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 72 GLN ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 19 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3390 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.464 152773 Z= 0.214 Angle : 0.601 23.165 228847 Z= 0.328 Chirality : 0.032 0.280 29182 Planarity : 0.006 0.117 12064 Dihedral : 24.871 179.414 77037 Min Nonbonded Distance : 1.182 Molprobity Statistics. All-atom Clashscore : 72.64 Ramachandran Plot: Outliers : 0.56 % Allowed : 9.12 % Favored : 90.32 % Rotamer: Outliers : 0.02 % Allowed : 0.99 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -2.47 (0.11), residues: 5342 helix: -0.37 (0.13), residues: 1504 sheet: -1.87 (0.19), residues: 709 loop : -2.33 (0.10), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP W 101 HIS 0.018 0.001 HIS r 102 PHE 0.023 0.002 PHE t 86 TYR 0.030 0.001 TYR O 93 ARG 0.025 0.001 ARG r 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 5.752 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: F 42 MET cc_start: 0.4748 (mmm) cc_final: 0.4357 (mtt) REVERT: K 228 ASP cc_start: 0.7996 (p0) cc_final: 0.7321 (p0) REVERT: U 12 MET cc_start: 0.6368 (tpp) cc_final: 0.6156 (tpp) REVERT: W 67 VAL cc_start: -0.1021 (t) cc_final: -0.1286 (t) REVERT: X 128 MET cc_start: 0.1978 (pmm) cc_final: 0.1742 (pmm) REVERT: Z 64 ASN cc_start: 0.4409 (m110) cc_final: 0.3839 (m110) REVERT: b 30 MET cc_start: -0.1506 (tmm) cc_final: -0.1837 (ttp) REVERT: d 54 MET cc_start: -0.0167 (mtm) cc_final: -0.1131 (mtm) REVERT: h 74 MET cc_start: -0.3954 (ptp) cc_final: -0.5245 (ttt) REVERT: p 43 GLN cc_start: 0.6742 (tp40) cc_final: 0.6388 (tp-100) REVERT: r 66 ILE cc_start: 0.4170 (mm) cc_final: 0.3904 (mm) REVERT: u 45 ASP cc_start: 0.4663 (p0) cc_final: 0.4445 (p0) REVERT: u 48 MET cc_start: 0.3669 (mmm) cc_final: 0.3223 (mtt) REVERT: v 22 LEU cc_start: 0.4681 (tt) cc_final: 0.4046 (mt) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 1.1761 time to fit residues: 816.0301 Evaluate side-chains 305 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 5.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 583 optimal weight: 0.3980 chunk 376 optimal weight: 10.0000 chunk 562 optimal weight: 0.9980 chunk 283 optimal weight: 20.0000 chunk 185 optimal weight: 50.0000 chunk 182 optimal weight: 60.0000 chunk 599 optimal weight: 3.9990 chunk 642 optimal weight: 20.0000 chunk 466 optimal weight: 20.0000 chunk 87 optimal weight: 60.0000 chunk 740 optimal weight: 40.0000 overall best weight: 7.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 HIS ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS ** R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 38 GLN ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 138 GLN ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 197 HIS ** Z 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 126 ASN ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 37 HIS ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3519 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.465 152773 Z= 0.274 Angle : 0.655 23.442 228847 Z= 0.348 Chirality : 0.034 0.276 29182 Planarity : 0.006 0.122 12064 Dihedral : 24.938 179.819 77037 Min Nonbonded Distance : 1.177 Molprobity Statistics. All-atom Clashscore : 88.32 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.99 % Favored : 86.43 % Rotamer: Outliers : 0.02 % Allowed : 1.08 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -2.51 (0.11), residues: 5342 helix: -0.39 (0.13), residues: 1536 sheet: -1.95 (0.19), residues: 687 loop : -2.36 (0.10), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP R 15 HIS 0.013 0.001 HIS o 76 PHE 0.032 0.002 PHE K 66 TYR 0.023 0.002 TYR O 57 ARG 0.008 0.001 ARG W 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 361 time to evaluate : 5.743 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: F 42 MET cc_start: 0.4780 (mmm) cc_final: 0.4327 (mtt) REVERT: K 228 ASP cc_start: 0.7996 (p0) cc_final: 0.7448 (p0) REVERT: V 20 MET cc_start: 0.6942 (ptm) cc_final: 0.6203 (ptp) REVERT: W 67 VAL cc_start: -0.0885 (t) cc_final: -0.1115 (t) REVERT: Z 64 ASN cc_start: 0.4177 (m110) cc_final: 0.3860 (m110) REVERT: b 30 MET cc_start: -0.1636 (tmm) cc_final: -0.1888 (ttp) REVERT: d 54 MET cc_start: -0.0270 (mtm) cc_final: -0.1220 (mtm) REVERT: h 74 MET cc_start: -0.3883 (ptp) cc_final: -0.5459 (ttt) REVERT: p 43 GLN cc_start: 0.6824 (tp40) cc_final: 0.6521 (tp-100) REVERT: r 66 ILE cc_start: 0.4251 (mm) cc_final: 0.3879 (mm) REVERT: u 45 ASP cc_start: 0.4775 (p0) cc_final: 0.4520 (p0) REVERT: v 31 ARG cc_start: 0.5250 (tpp80) cc_final: 0.4791 (ttm170) outliers start: 1 outliers final: 0 residues processed: 362 average time/residue: 1.1444 time to fit residues: 740.4315 Evaluate side-chains 293 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 5.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 857 optimal weight: 3.9990 chunk 903 optimal weight: 5.9990 chunk 823 optimal weight: 40.0000 chunk 878 optimal weight: 9.9990 chunk 902 optimal weight: 8.9990 chunk 528 optimal weight: 9.9990 chunk 382 optimal weight: 20.0000 chunk 689 optimal weight: 50.0000 chunk 269 optimal weight: 20.0000 chunk 793 optimal weight: 50.0000 chunk 830 optimal weight: 50.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 HIS ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS ** R 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 64 ASN ** Z 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 141 HIS ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3540 moved from start: 0.7237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.466 152773 Z= 0.283 Angle : 0.659 23.332 228847 Z= 0.352 Chirality : 0.034 0.551 29182 Planarity : 0.007 0.218 12064 Dihedral : 25.009 179.973 77037 Min Nonbonded Distance : 1.177 Molprobity Statistics. All-atom Clashscore : 87.51 Ramachandran Plot: Outliers : 0.60 % Allowed : 12.07 % Favored : 87.33 % Rotamer: Outliers : 0.02 % Allowed : 0.70 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -2.57 (0.11), residues: 5342 helix: -0.37 (0.13), residues: 1532 sheet: -1.87 (0.19), residues: 688 loop : -2.48 (0.10), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP K 212 HIS 0.019 0.002 HIS o 76 PHE 0.027 0.002 PHE V 21 TYR 0.033 0.002 TYR K 160 ARG 0.025 0.001 ARG u 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 5.689 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: B 31 LEU cc_start: 0.4901 (mp) cc_final: 0.4603 (mt) REVERT: F 42 MET cc_start: 0.4756 (mmm) cc_final: 0.4430 (mtt) REVERT: K 145 MET cc_start: 0.5142 (mtp) cc_final: 0.4851 (mtp) REVERT: K 228 ASP cc_start: 0.7906 (p0) cc_final: 0.7436 (p0) REVERT: N 72 SER cc_start: 0.6009 (m) cc_final: 0.5284 (p) REVERT: U 136 MET cc_start: 0.6870 (pmm) cc_final: 0.6601 (pmm) REVERT: V 20 MET cc_start: 0.6837 (ptm) cc_final: 0.6570 (ptp) REVERT: Z 64 ASN cc_start: 0.4498 (m-40) cc_final: 0.4066 (m-40) REVERT: d 54 MET cc_start: -0.0323 (mtm) cc_final: -0.2168 (ttt) REVERT: h 74 MET cc_start: -0.3576 (ptp) cc_final: -0.5316 (ttt) REVERT: o 103 THR cc_start: 0.7183 (p) cc_final: 0.6409 (p) REVERT: p 43 GLN cc_start: 0.6855 (tp40) cc_final: 0.6576 (tp-100) REVERT: p 61 ILE cc_start: 0.7586 (mp) cc_final: 0.7361 (mp) REVERT: r 66 ILE cc_start: 0.4436 (mm) cc_final: 0.4174 (mm) outliers start: 1 outliers final: 0 residues processed: 369 average time/residue: 1.2616 time to fit residues: 835.7995 Evaluate side-chains 299 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 5.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 875 optimal weight: 20.0000 chunk 576 optimal weight: 7.9990 chunk 928 optimal weight: 9.9990 chunk 566 optimal weight: 10.0000 chunk 440 optimal weight: 20.0000 chunk 645 optimal weight: 0.1980 chunk 974 optimal weight: 0.7980 chunk 896 optimal weight: 7.9990 chunk 775 optimal weight: 7.9990 chunk 80 optimal weight: 50.0000 chunk 599 optimal weight: 5.9990 overall best weight: 4.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 HIS ** K 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 HIS ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 95 HIS ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3490 moved from start: 0.7627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.465 152773 Z= 0.225 Angle : 0.574 23.352 228847 Z= 0.312 Chirality : 0.031 0.284 29182 Planarity : 0.006 0.120 12064 Dihedral : 24.789 179.533 77037 Min Nonbonded Distance : 1.181 Molprobity Statistics. All-atom Clashscore : 77.40 Ramachandran Plot: Outliers : 0.60 % Allowed : 11.18 % Favored : 88.23 % Rotamer: Outliers : 0.02 % Allowed : 0.22 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -2.31 (0.11), residues: 5342 helix: -0.09 (0.13), residues: 1551 sheet: -1.81 (0.19), residues: 707 loop : -2.33 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP K 212 HIS 0.015 0.001 HIS o 76 PHE 0.021 0.001 PHE O 51 TYR 0.019 0.001 TYR Y 74 ARG 0.040 0.001 ARG u 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10684 Ramachandran restraints generated. 5342 Oldfield, 0 Emsley, 5342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 363 time to evaluate : 5.992 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: B 31 LEU cc_start: 0.5078 (mp) cc_final: 0.4792 (mt) REVERT: F 42 MET cc_start: 0.4736 (mmm) cc_final: 0.4321 (mtt) REVERT: K 228 ASP cc_start: 0.7833 (p0) cc_final: 0.7350 (p0) REVERT: N 25 MET cc_start: 0.0662 (ptp) cc_final: 0.0386 (ptp) REVERT: O 104 LEU cc_start: 0.4507 (mp) cc_final: 0.4146 (mt) REVERT: W 67 VAL cc_start: -0.0781 (t) cc_final: -0.0994 (t) REVERT: Z 64 ASN cc_start: 0.4592 (m-40) cc_final: 0.4224 (m-40) REVERT: d 54 MET cc_start: -0.0193 (mtm) cc_final: -0.2081 (ttt) REVERT: h 74 MET cc_start: -0.3528 (ptp) cc_final: -0.5260 (ttt) REVERT: v 26 ILE cc_start: 0.7061 (mp) cc_final: 0.6758 (mm) outliers start: 1 outliers final: 0 residues processed: 364 average time/residue: 1.2465 time to fit residues: 808.1956 Evaluate side-chains 284 residues out of total 4453 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 5.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 475 optimal weight: 20.0000 chunk 616 optimal weight: 1.9990 chunk 826 optimal weight: 9.9990 chunk 237 optimal weight: 20.0000 chunk 715 optimal weight: 30.0000 chunk 114 optimal weight: 60.0000 chunk 215 optimal weight: 20.0000 chunk 777 optimal weight: 40.0000 chunk 325 optimal weight: 30.0000 chunk 797 optimal weight: 0.0060 chunk 98 optimal weight: 50.0000 overall best weight: 10.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** D 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 HIS ** K 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 HIS ** N 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 GLN ** T 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 70 HIS ** t 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.110305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064334 restraints weight = 1043404.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.060634 restraints weight = 742555.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.060936 restraints weight = 621453.841| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.8245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.466 152773 Z= 0.337 Angle : 0.747 23.563 228847 Z= 0.390 Chirality : 0.037 0.358 29182 Planarity : 0.007 0.173 12064 Dihedral : 25.183 179.953 77037 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 98.60 Ramachandran Plot: Outliers : 0.58 % Allowed : 14.86 % Favored : 84.56 % Rotamer: Outliers : 0.02 % Allowed : 0.31 % Favored : 99.66 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % 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: -2.71 (0.11), residues: 5342 helix: -0.39 (0.13), residues: 1554 sheet: -1.95 (0.19), residues: 705 loop : -2.64 (0.10), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP K 212 HIS 0.018 0.002 HIS o 76 PHE 0.031 0.002 PHE M 19 TYR 0.051 0.003 TYR R 53 ARG 0.055 0.001 ARG E 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22666.19 seconds wall clock time: 408 minutes 40.65 seconds (24520.65 seconds total)