Starting phenix.real_space_refine on Tue Mar 19 17:45:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2u_29681/03_2024/8g2u_29681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2u_29681/03_2024/8g2u_29681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2u_29681/03_2024/8g2u_29681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2u_29681/03_2024/8g2u_29681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2u_29681/03_2024/8g2u_29681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g2u_29681/03_2024/8g2u_29681.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.012 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4556 5.49 5 S 137 5.16 5 C 70575 2.51 5 N 26272 2.21 5 O 39315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "1 GLU 34": "OE1" <-> "OE2" Residue "1 GLU 50": "OE1" <-> "OE2" Residue "3 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C ASP 65": "OD1" <-> "OD2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 99": "OE1" <-> "OE2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E ASP 191": "OD1" <-> "OD2" Residue "F ASP 152": "OD1" <-> "OD2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 11": "OD1" <-> "OD2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 115": "OE1" <-> "OE2" Residue "M ASP 70": "OD1" <-> "OD2" Residue "M GLU 90": "OE1" <-> "OE2" Residue "N GLU 32": "OE1" <-> "OE2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "Q ASP 101": "OD1" <-> "OD2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 78": "OE1" <-> "OE2" Residue "T GLU 4": "OE1" <-> "OE2" Residue "T ASP 37": "OD1" <-> "OD2" Residue "T ASP 79": "OD1" <-> "OD2" Residue "U GLU 36": "OE1" <-> "OE2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 55": "OE1" <-> "OE2" Residue "V PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 28": "OE1" <-> "OE2" Residue "W PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 42": "OE1" <-> "OE2" Residue "X GLU 75": "OE1" <-> "OE2" Residue "a ASP 152": "OD1" <-> "OD2" Residue "a GLU 174": "OE1" <-> "OE2" Residue "a ASP 191": "OD1" <-> "OD2" Residue "b PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 27": "OE1" <-> "OE2" Residue "b PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 45": "OE1" <-> "OE2" Residue "b GLU 104": "OE1" <-> "OE2" Residue "b GLU 109": "OE1" <-> "OE2" Residue "b GLU 124": "OE1" <-> "OE2" Residue "b GLU 160": "OE1" <-> "OE2" Residue "b GLU 165": "OE1" <-> "OE2" Residue "b GLU 187": "OE1" <-> "OE2" Residue "b TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 159": "OE1" <-> "OE2" Residue "c GLU 178": "OE1" <-> "OE2" Residue "f GLU 59": "OE1" <-> "OE2" Residue "f GLU 73": "OE1" <-> "OE2" Residue "f GLU 145": "OE1" <-> "OE2" Residue "h PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 19": "OD1" <-> "OD2" Residue "j PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 140855 Number of models: 1 Model: "" Number of chains: 51 Chain: "0" 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: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "2" 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: "3" 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: "4" 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: "A" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 2504 Classifications: {'RNA': 117} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 57, 'rna3p_pyr': 50} Link IDs: {'rna2p': 10, 'rna3p': 106} Chain: "B" Number of atoms: 62317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62317 Classifications: {'RNA': 2903} Modifications used: {'5*END': 1, 'rna2p_pur': 264, 'rna2p_pyr': 143, 'rna3p_pur': 1410, 'rna3p_pyr': 1086} Link IDs: {'rna2p': 407, 'rna3p': 2495} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" 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: "E" 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: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1420 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 171} Chain: "G" 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: "J" 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: "K" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 931 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "O" 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: "P" 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: "Q" 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: "R" 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: "S" 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: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 739 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 780 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "V" 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: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" 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: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" 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} Chain: "a" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1705 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "b" 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: "c" 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: "d" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1106 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "e" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 818 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "f" 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: "g" 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: "h" 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: "i" 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: "j" 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: "k" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "l" 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: "m" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 774 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "n" 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: "o" 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: "p" 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: "q" 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: "r" 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: "s" 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: "t" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 426 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "u" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 468 Classifications: {'peptide': 59} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "v" Number of atoms: 33012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33012 Classifications: {'RNA': 1539} Modifications used: {'5*END': 1, 'rna2p_pur': 123, 'rna2p_pyr': 90, 'rna3p_pur': 751, 'rna3p_pyr': 575} Link IDs: {'rna2p': 212, 'rna3p': 1326} Time building chain proxies: 52.29, per 1000 atoms: 0.37 Number of scatterers: 140855 At special positions: 0 Unit cell: (248.23, 262.65, 268.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 137 16.00 P 4556 15.00 O 39315 8.00 N 26272 7.00 C 70575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 54.62 Conformation dependent library (CDL) restraints added in 6.1 seconds 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10078 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 65 sheets defined 33.8% alpha, 18.4% beta 1521 base pairs and 2384 stacking pairs defined. Time for finding SS restraints: 48.20 Creating SS restraints... Processing helix chain '0' and resid 8 through 16 Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.176A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 Processing helix chain '3' and resid 6 through 13 Processing helix chain '3' and resid 36 through 44 Processing helix chain '3' and resid 53 through 61 Processing helix chain '4' and resid 30 through 34 removed outlier: 3.844A pdb=" N LYS 4 34 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 198 through 202 removed outlier: 3.561A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.889A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.958A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.679A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'F' and resid 2 through 9 Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 91 through 107 Processing helix chain 'F' and resid 162 through 168 Processing helix chain 'G' and resid 2 through 6 Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 151 removed outlier: 4.105A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 95 Processing helix chain 'J' and resid 98 through 109 Processing helix chain 'J' and resid 112 through 121 Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.501A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 118 Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 80 through 85 removed outlier: 3.830A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 98 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'M' and resid 43 through 57 Processing helix chain 'M' and resid 109 through 122 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 56 Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 Processing helix chain 'N' and resid 72 through 82 Processing helix chain 'O' and resid 3 through 22 removed outlier: 4.589A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 5 through 12 Processing helix chain 'Q' and resid 5 through 20 removed outlier: 3.506A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 3.570A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 92 through 99 removed outlier: 3.810A pdb=" N ILE Q 97 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.623A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.626A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.501A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 18 through 28 Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'V' and resid 13 through 23 Processing helix chain 'V' and resid 44 through 53 Processing helix chain 'X' and resid 52 through 62 Processing helix chain 'X' and resid 62 through 74 Processing helix chain 'Y' and resid 12 through 22 Processing helix chain 'Y' and resid 23 through 35 Processing helix chain 'Y' and resid 38 through 60 removed outlier: 3.995A pdb=" N LEU Y 42 " --> pdb=" O GLN Y 38 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 Processing helix chain 'a' and resid 26 through 30 removed outlier: 3.756A pdb=" N ILE a 30 " --> pdb=" O LYS a 27 " (cutoff:3.500A) Processing helix chain 'a' and resid 32 through 37 removed outlier: 4.132A pdb=" N LYS a 36 " --> pdb=" O GLY a 32 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL a 37 " --> pdb=" O ALA a 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 32 through 37' Processing helix chain 'a' and resid 41 through 62 Proline residue: a 47 - end of helix Processing helix chain 'a' and resid 75 through 83 removed outlier: 4.027A pdb=" N ASP a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA a 83 " --> pdb=" O VAL a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 118 removed outlier: 4.058A pdb=" N GLN a 108 " --> pdb=" O LYS a 104 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER a 109 " --> pdb=" O THR a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 148 removed outlier: 4.619A pdb=" N MET a 135 " --> pdb=" O LYS a 131 " (cutoff:3.500A) Processing helix chain 'a' and resid 149 through 154 Processing helix chain 'a' and resid 168 through 179 Processing helix chain 'a' and resid 205 through 218 Processing helix chain 'b' and resid 5 through 11 Processing helix chain 'b' and resid 24 through 46 removed outlier: 4.655A pdb=" N ASP b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 71 through 77 removed outlier: 3.864A pdb=" N VAL b 75 " --> pdb=" O ARG b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 95 Processing helix chain 'b' and resid 111 through 125 removed outlier: 3.532A pdb=" N ALA b 116 " --> pdb=" O ALA b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 143 Processing helix chain 'c' and resid 6 through 15 removed outlier: 4.081A pdb=" N LEU c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 42 removed outlier: 3.509A pdb=" N GLY c 41 " --> pdb=" O GLY c 38 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA c 42 " --> pdb=" O GLN c 39 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 38 through 42' Processing helix chain 'c' and resid 48 through 65 Processing helix chain 'c' and resid 67 through 81 Processing helix chain 'c' and resid 84 through 96 Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 109 through 119 Processing helix chain 'c' and resid 151 through 163 Processing helix chain 'c' and resid 186 through 191 Processing helix chain 'c' and resid 196 through 204 Processing helix chain 'd' and resid 54 through 68 Processing helix chain 'd' and resid 110 through 118 Processing helix chain 'd' and resid 131 through 136 Processing helix chain 'd' and resid 137 through 146 Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'e' and resid 17 through 32 Processing helix chain 'e' and resid 67 through 81 Processing helix chain 'f' and resid 19 through 30 Processing helix chain 'f' and resid 34 through 54 Processing helix chain 'f' and resid 56 through 69 Processing helix chain 'f' and resid 91 through 110 Processing helix chain 'f' and resid 114 through 128 removed outlier: 3.526A pdb=" N ALA f 127 " --> pdb=" O LEU f 123 " (cutoff:3.500A) Processing helix chain 'f' and resid 131 through 148 Processing helix chain 'g' and resid 4 through 19 Processing helix chain 'g' and resid 29 through 42 Processing helix chain 'g' and resid 93 through 98 removed outlier: 4.183A pdb=" N ALA g 96 " --> pdb=" O LYS g 93 " (cutoff:3.500A) Processing helix chain 'g' and resid 112 through 119 Processing helix chain 'h' and resid 33 through 38 Processing helix chain 'h' and resid 44 through 47 removed outlier: 3.719A pdb=" N VAL h 47 " --> pdb=" O ARG h 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 44 through 47' Processing helix chain 'h' and resid 48 through 55 removed outlier: 3.738A pdb=" N VAL h 54 " --> pdb=" O PRO h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 70 through 90 Processing helix chain 'h' and resid 91 through 101 Processing helix chain 'i' and resid 14 through 30 Processing helix chain 'i' and resid 80 through 86 Processing helix chain 'j' and resid 46 through 50 Processing helix chain 'j' and resid 53 through 58 Processing helix chain 'j' and resid 58 through 74 removed outlier: 3.938A pdb=" N ALA j 62 " --> pdb=" O THR j 58 " (cutoff:3.500A) Processing helix chain 'j' and resid 91 through 103 removed outlier: 4.140A pdb=" N ARG j 97 " --> pdb=" O GLU j 93 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 9 Processing helix chain 'k' and resid 114 through 118 removed outlier: 3.818A pdb=" N GLY k 117 " --> pdb=" O SER k 114 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL k 118 " --> pdb=" O LYS k 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 114 through 118' Processing helix chain 'l' and resid 13 through 21 Processing helix chain 'l' and resid 25 through 37 Processing helix chain 'l' and resid 48 through 62 removed outlier: 3.849A pdb=" N PHE l 62 " --> pdb=" O GLU l 58 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 83 Processing helix chain 'l' and resid 84 through 93 Processing helix chain 'l' and resid 105 through 110 Processing helix chain 'm' and resid 2 through 19 Processing helix chain 'm' and resid 23 through 25 No H-bonds generated for 'chain 'm' and resid 23 through 25' Processing helix chain 'm' and resid 26 through 32 Processing helix chain 'm' and resid 42 through 49 Processing helix chain 'm' and resid 56 through 60 Processing helix chain 'm' and resid 80 through 91 Processing helix chain 'n' and resid 3 through 15 Processing helix chain 'n' and resid 23 through 45 removed outlier: 3.965A pdb=" N GLU n 44 " --> pdb=" O GLY n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 73 removed outlier: 3.805A pdb=" N GLY n 54 " --> pdb=" O HIS n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 73 through 85 Processing helix chain 'o' and resid 53 through 63 removed outlier: 3.672A pdb=" N ILE o 57 " --> pdb=" O ASP o 53 " (cutoff:3.500A) Processing helix chain 'o' and resid 68 through 78 Processing helix chain 'q' and resid 25 through 32 Processing helix chain 'q' and resid 40 through 45 Processing helix chain 'q' and resid 47 through 64 Processing helix chain 'r' and resid 11 through 25 Processing helix chain 's' and resid 5 through 41 removed outlier: 3.966A pdb=" N ARG s 9 " --> pdb=" O SER s 5 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 64 Proline residue: s 55 - end of helix Processing helix chain 's' and resid 68 through 86 Processing helix chain 't' and resid 23 through 32 removed outlier: 3.547A pdb=" N ALA t 29 " --> pdb=" O ALA t 25 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU t 30 " --> pdb=" O GLY t 26 " (cutoff:3.500A) Processing helix chain 't' and resid 39 through 52 Processing sheet with id=AA1, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AA3, first strand: chain '1' and resid 19 through 24 removed outlier: 5.001A pdb=" N VAL 1 11 " --> pdb=" O LYS 1 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 14 through 15 Processing sheet with id=AA5, first strand: chain '4' and resid 14 through 19 Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA7, first strand: chain 'C' and resid 33 through 36 removed outlier: 4.098A pdb=" N ASN C 36 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLN C 59 " --> pdb=" O ASN C 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 64 through 65 removed outlier: 4.739A pdb=" N LEU C 104 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 128 through 130 removed outlier: 6.598A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG C 166 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N TYR C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 143 through 144 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 14 removed outlier: 5.883A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 38 removed outlier: 5.521A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 117 through 119 Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.720A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.508A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 15 through 19 Processing sheet with id=AB9, first strand: chain 'G' and resid 40 through 44 removed outlier: 3.759A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 121 through 123 Processing sheet with id=AC2, first strand: chain 'G' and resid 94 through 98 Processing sheet with id=AC3, first strand: chain 'J' and resid 122 through 124 removed outlier: 5.843A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AC5, first strand: chain 'K' and resid 6 through 9 removed outlier: 5.408A pdb=" N CYS K 20 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR K 41 " --> pdb=" O CYS K 20 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS K 22 " --> pdb=" O LYS K 39 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA K 82 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N CYS K 83 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ASN K 8 " --> pdb=" O CYS K 83 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU K 85 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 68 through 69 removed outlier: 3.724A pdb=" N VAL K 75 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 74 through 77 Processing sheet with id=AC8, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AC9, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.637A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 39 through 42 removed outlier: 5.689A pdb=" N VAL M 89 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU M 75 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.660A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 47 through 52 removed outlier: 6.551A pdb=" N LEU O 26 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 89 through 90 removed outlier: 4.311A pdb=" N ARG P 108 " --> pdb=" O ALA P 90 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.811A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.457A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.552A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 70 through 78 removed outlier: 6.892A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR S 104 " --> pdb=" O ILE S 74 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AE1, first strand: chain 'T' and resid 11 through 13 removed outlier: 6.841A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.875A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE U 71 " --> pdb=" O ASP U 80 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 40 through 42 Processing sheet with id=AE4, first strand: chain 'U' and resid 82 through 84 Processing sheet with id=AE5, first strand: chain 'V' and resid 3 through 8 removed outlier: 7.829A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 26 through 27 removed outlier: 6.231A pdb=" N PHE W 44 " --> pdb=" O ILE W 79 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE W 81 " --> pdb=" O PHE W 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'W' and resid 32 through 34 Processing sheet with id=AE8, first strand: chain 'X' and resid 12 through 16 Processing sheet with id=AE9, first strand: chain 'X' and resid 32 through 39 Processing sheet with id=AF1, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AF2, first strand: chain 'a' and resid 90 through 91 removed outlier: 6.737A pdb=" N PHE a 68 " --> pdb=" O VAL a 91 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU a 160 " --> pdb=" O PHE a 183 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ILE a 185 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL a 162 " --> pdb=" O ILE a 185 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'b' and resid 51 through 57 removed outlier: 6.448A pdb=" N HIS b 68 " --> pdb=" O SER b 52 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE b 54 " --> pdb=" O THR b 66 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR b 66 " --> pdb=" O ILE b 54 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE b 56 " --> pdb=" O ARG b 64 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG b 64 " --> pdb=" O ILE b 56 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 165 through 170 removed outlier: 3.735A pdb=" N GLU b 165 " --> pdb=" O VAL b 152 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL b 150 " --> pdb=" O TYR b 167 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU b 169 " --> pdb=" O ILE b 148 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE b 148 " --> pdb=" O GLU b 169 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N GLY b 147 " --> pdb=" O PHE b 202 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'c' and resid 127 through 128 Processing sheet with id=AF6, first strand: chain 'd' and resid 11 through 23 removed outlier: 6.763A pdb=" N LEU d 35 " --> pdb=" O ILE d 15 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL d 17 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR d 33 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ARG d 19 " --> pdb=" O SER d 31 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N SER d 31 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N SER d 21 " --> pdb=" O ILE d 29 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE d 29 " --> pdb=" O SER d 21 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'd' and resid 84 through 87 removed outlier: 3.685A pdb=" N LEU d 123 " --> pdb=" O GLN d 96 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 35 through 45 removed outlier: 5.280A pdb=" N ILE e 36 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLU e 65 " --> pdb=" O ILE e 36 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TYR e 59 " --> pdb=" O TRP e 42 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG e 44 " --> pdb=" O ALA e 57 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ALA e 57 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG e 86 " --> pdb=" O MET e 9 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 23 through 27 removed outlier: 3.686A pdb=" N ASP g 47 " --> pdb=" O THR g 61 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'g' and resid 73 through 76 Processing sheet with id=AG2, first strand: chain 'g' and resid 73 through 76 removed outlier: 6.570A pdb=" N VAL g 102 " --> pdb=" O ILE g 125 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR g 127 " --> pdb=" O ILE g 100 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE g 100 " --> pdb=" O TYR g 127 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 5 through 7 Processing sheet with id=AG4, first strand: chain 'i' and resid 40 through 52 removed outlier: 7.831A pdb=" N LEU i 73 " --> pdb=" O PRO i 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU i 71 " --> pdb=" O PRO i 43 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'i' and resid 40 through 52 removed outlier: 7.831A pdb=" N LEU i 73 " --> pdb=" O PRO i 41 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LEU i 71 " --> pdb=" O PRO i 43 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'j' and resid 40 through 45 removed outlier: 6.749A pdb=" N ILE j 33 " --> pdb=" O LEU j 41 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TRP j 43 " --> pdb=" O VAL j 31 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL j 31 " --> pdb=" O TRP j 43 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N THR j 45 " --> pdb=" O THR j 29 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N THR j 29 " --> pdb=" O THR j 45 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY j 18 " --> pdb=" O GLU j 82 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N MET j 84 " --> pdb=" O GLY j 18 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA j 20 " --> pdb=" O MET j 84 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LYS j 86 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE j 22 " --> pdb=" O LYS j 86 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N LEU j 81 " --> pdb=" O ASN j 108 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR j 110 " --> pdb=" O LEU j 81 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL j 83 " --> pdb=" O THR j 110 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 61 through 65 removed outlier: 6.554A pdb=" N ARG k 55 " --> pdb=" O CYS k 33 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N CYS k 33 " --> pdb=" O ARG k 55 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU k 80 " --> pdb=" O VAL k 97 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'o' and resid 34 through 39 removed outlier: 3.774A pdb=" N GLU o 34 " --> pdb=" O VAL o 21 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL o 19 " --> pdb=" O VAL o 36 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N PHE o 38 " --> pdb=" O TYR o 17 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR o 17 " --> pdb=" O PHE o 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'p' and resid 6 through 13 removed outlier: 14.889A pdb=" N LEU p 7 " --> pdb=" O PHE p 27 " (cutoff:3.500A) removed outlier: 12.936A pdb=" N PHE p 27 " --> pdb=" O LEU p 7 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLY p 9 " --> pdb=" O GLU p 25 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLU p 25 " --> pdb=" O GLY p 9 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL p 11 " --> pdb=" O ALA p 23 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ALA p 23 " --> pdb=" O VAL p 11 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER p 13 " --> pdb=" O VAL p 21 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL p 28 " --> pdb=" O ILE p 37 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS p 30 " --> pdb=" O LYS p 35 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS p 35 " --> pdb=" O HIS p 30 " (cutoff:3.500A) removed outlier: 15.665A pdb=" N LYS p 70 " --> pdb=" O THR p 40 " (cutoff:3.500A) removed outlier: 14.159A pdb=" N LYS p 42 " --> pdb=" O LYS p 70 " (cutoff:3.500A) removed outlier: 10.664A pdb=" N TRP p 72 " --> pdb=" O LYS p 42 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N HIS p 44 " --> pdb=" O TRP p 72 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N LEU p 74 " --> pdb=" O HIS p 44 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N HIS p 46 " --> pdb=" O LEU p 74 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ARG p 76 " --> pdb=" O HIS p 46 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N SER p 71 " --> pdb=" O CYS p 63 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU p 59 " --> pdb=" O VAL p 75 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N VAL p 77 " --> pdb=" O VAL p 57 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL p 57 " --> pdb=" O VAL p 77 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'r' and resid 31 through 32 removed outlier: 3.709A pdb=" N VAL r 57 " --> pdb=" O VAL r 50 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN r 52 " --> pdb=" O GLN r 55 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN r 55 " --> pdb=" O ASN r 52 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'u' and resid 147 through 152 removed outlier: 3.868A pdb=" N VAL u 147 " --> pdb=" O SER u 161 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LYS u 159 " --> pdb=" O GLU u 149 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N VAL u 151 " --> pdb=" O ARG u 157 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ARG u 157 " --> pdb=" O VAL u 151 " (cutoff:3.500A) 1748 hydrogen bonds defined for protein. 4974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3835 hydrogen bonds 5972 hydrogen bond angles 0 basepair planarities 1521 basepair parallelities 2384 stacking parallelities Total time for adding SS restraints: 206.28 Time building geometry restraints manager: 59.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 17279 1.33 - 1.45: 67884 1.45 - 1.58: 58659 1.58 - 1.70: 9114 1.70 - 1.83: 247 Bond restraints: 153183 Sorted by residual: bond pdb=" C VAL a 46 " pdb=" N PRO a 47 " ideal model delta sigma weight residual 1.334 1.398 -0.064 2.34e-02 1.83e+03 7.54e+00 bond pdb=" C ILE l 8 " pdb=" N PRO l 9 " ideal model delta sigma weight residual 1.331 1.352 -0.020 7.90e-03 1.60e+04 6.64e+00 bond pdb=" CA THR f 83 " pdb=" CB THR f 83 " ideal model delta sigma weight residual 1.522 1.554 -0.032 1.27e-02 6.20e+03 6.42e+00 bond pdb=" CB ILE S 24 " pdb=" CG2 ILE S 24 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.29e+00 bond pdb=" CB MET f 30 " pdb=" CG MET f 30 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.19e+00 ... (remaining 153178 not shown) Histogram of bond angle deviations from ideal: 93.59 - 102.71: 7500 102.71 - 111.83: 93651 111.83 - 120.95: 83794 120.95 - 130.07: 41876 130.07 - 139.19: 2600 Bond angle restraints: 229421 Sorted by residual: angle pdb=" C ILE P 4 " pdb=" N LYS P 5 " pdb=" CA LYS P 5 " ideal model delta sigma weight residual 126.45 139.19 -12.74 1.77e+00 3.19e-01 5.18e+01 angle pdb=" C GLU K 91 " pdb=" N GLN K 92 " pdb=" CA GLN K 92 " ideal model delta sigma weight residual 120.68 131.17 -10.49 1.52e+00 4.33e-01 4.76e+01 angle pdb=" C HIS s 67 " pdb=" N LYS s 68 " pdb=" CA LYS s 68 " ideal model delta sigma weight residual 121.54 134.40 -12.86 1.91e+00 2.74e-01 4.54e+01 angle pdb=" CB MET M 53 " pdb=" CG MET M 53 " pdb=" SD MET M 53 " ideal model delta sigma weight residual 112.70 93.59 19.11 3.00e+00 1.11e-01 4.06e+01 angle pdb=" C ALA a 218 " pdb=" N THR a 219 " pdb=" CA THR a 219 " ideal model delta sigma weight residual 122.61 131.28 -8.67 1.56e+00 4.11e-01 3.09e+01 ... (remaining 229416 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 86104 35.98 - 71.97: 10822 71.97 - 107.95: 1178 107.95 - 143.94: 18 143.94 - 179.92: 57 Dihedral angle restraints: 98179 sinusoidal: 82552 harmonic: 15627 Sorted by residual: dihedral pdb=" CA LYS F 160 " pdb=" C LYS F 160 " pdb=" N SER F 161 " pdb=" CA SER F 161 " ideal model delta harmonic sigma weight residual -180.00 -123.71 -56.29 0 5.00e+00 4.00e-02 1.27e+02 dihedral pdb=" CA ALA F 171 " pdb=" C ALA F 171 " pdb=" N PHE F 172 " pdb=" CA PHE F 172 " ideal model delta harmonic sigma weight residual -180.00 -132.74 -47.26 0 5.00e+00 4.00e-02 8.93e+01 dihedral pdb=" CA PHE F 172 " pdb=" C PHE F 172 " pdb=" N ASP F 173 " pdb=" CA ASP F 173 " ideal model delta harmonic sigma weight residual 180.00 132.99 47.01 0 5.00e+00 4.00e-02 8.84e+01 ... (remaining 98176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 28765 0.123 - 0.245: 522 0.245 - 0.368: 36 0.368 - 0.490: 5 0.490 - 0.613: 1 Chirality restraints: 29329 Sorted by residual: chirality pdb=" CB VAL D 142 " pdb=" CA VAL D 142 " pdb=" CG1 VAL D 142 " pdb=" CG2 VAL D 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.40e+00 chirality pdb=" CB ILE Q 93 " pdb=" CA ILE Q 93 " pdb=" CG1 ILE Q 93 " pdb=" CG2 ILE Q 93 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CB ILE a 185 " pdb=" CA ILE a 185 " pdb=" CG1 ILE a 185 " pdb=" CG2 ILE a 185 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 29326 not shown) Planarity restraints: 12128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G v1272 " -0.021 2.00e-02 2.50e+03 2.48e-02 1.84e+01 pdb=" N9 G v1272 " 0.030 2.00e-02 2.50e+03 pdb=" C8 G v1272 " 0.008 2.00e-02 2.50e+03 pdb=" N7 G v1272 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G v1272 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G v1272 " -0.064 2.00e-02 2.50e+03 pdb=" O6 G v1272 " 0.039 2.00e-02 2.50e+03 pdb=" N1 G v1272 " -0.000 2.00e-02 2.50e+03 pdb=" C2 G v1272 " -0.007 2.00e-02 2.50e+03 pdb=" N2 G v1272 " 0.010 2.00e-02 2.50e+03 pdb=" N3 G v1272 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G v1272 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 155 " 0.348 9.50e-02 1.11e+02 1.56e-01 1.50e+01 pdb=" NE ARG C 155 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 155 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG C 155 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 155 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 27 " 0.056 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO F 28 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO F 28 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO F 28 " 0.046 5.00e-02 4.00e+02 ... (remaining 12125 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 8840 2.70 - 3.25: 114243 3.25 - 3.80: 291797 3.80 - 4.35: 376413 4.35 - 4.90: 497910 Nonbonded interactions: 1289203 Sorted by model distance: nonbonded pdb=" O2 U B1680 " pdb=" O2' G B1763 " model vdw 2.144 2.440 nonbonded pdb=" OP1 G v 126 " pdb=" O2' U v 605 " model vdw 2.243 2.440 nonbonded pdb=" O2' G v1268 " pdb=" O2' U v1326 " model vdw 2.247 2.440 nonbonded pdb=" O2' U B2202 " pdb=" OP1 G B2204 " model vdw 2.247 2.440 nonbonded pdb=" O2' G B1826 " pdb=" OP2 U B1971 " model vdw 2.261 2.440 ... (remaining 1289198 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.120 Extract box with map and model: 13.620 Check model and map are aligned: 1.510 Set scattering table: 0.950 Process input model: 452.590 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 485.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3105 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 : 0.004 0.076 153183 Z= 0.266 Angle : 0.846 19.330 229421 Z= 0.420 Chirality : 0.043 0.613 29329 Planarity : 0.007 0.156 12128 Dihedral : 23.510 179.923 88101 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.16 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.10), residues: 5392 helix: -0.97 (0.11), residues: 1763 sheet: -0.45 (0.17), residues: 920 loop : -1.80 (0.10), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 60 HIS 0.020 0.002 HIS T 15 PHE 0.027 0.003 PHE b 202 TYR 0.036 0.002 TYR t 37 ARG 0.019 0.001 ARG K 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1132 time to evaluate : 5.622 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: 2 43 THR cc_start: 0.2617 (p) cc_final: 0.2321 (p) REVERT: C 229 HIS cc_start: 0.4872 (t-90) cc_final: 0.4606 (t70) outliers start: 0 outliers final: 1 residues processed: 1132 average time/residue: 2.0639 time to fit residues: 3342.9620 Evaluate side-chains 666 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 665 time to evaluate : 5.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain i residue 100 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 828 optimal weight: 20.0000 chunk 743 optimal weight: 8.9990 chunk 412 optimal weight: 6.9990 chunk 253 optimal weight: 10.0000 chunk 501 optimal weight: 0.7980 chunk 397 optimal weight: 4.9990 chunk 768 optimal weight: 30.0000 chunk 297 optimal weight: 8.9990 chunk 467 optimal weight: 9.9990 chunk 572 optimal weight: 2.9990 chunk 890 optimal weight: 20.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 42 HIS 4 33 HIS ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS C 116 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 HIS ** F 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 67 ASN J 86 GLN J 136 GLN L 104 GLN M 13 HIS O 29 HIS R 12 HIS T 15 HIS U 39 ASN V 24 ASN W 45 HIS ** W 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS a 92 ASN a 93 HIS a 145 ASN ** c 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN f 27 ASN f 67 ASN f 129 ASN g 3 GLN ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 49 GLN ** i 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 99 GLN ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 36 ASN ** o 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 8 GLN r 68 HIS s 69 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.8731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.558 153183 Z= 0.511 Angle : 1.035 20.892 229421 Z= 0.514 Chirality : 0.054 2.633 29329 Planarity : 0.009 0.202 12128 Dihedral : 24.031 179.867 77252 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.07 % Rotamer: Outliers : 5.76 % Allowed : 16.20 % Favored : 78.04 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.10), residues: 5392 helix: -0.79 (0.11), residues: 1749 sheet: -0.65 (0.17), residues: 903 loop : -1.97 (0.10), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP M 64 HIS 0.021 0.003 HIS P 55 PHE 0.086 0.004 PHE h 38 TYR 0.055 0.004 TYR b 41 ARG 0.052 0.002 ARG n 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1151 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 892 time to evaluate : 5.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 7 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7673 (ptpt) REVERT: E 139 LYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5827 (tttp) REVERT: J 1 MET cc_start: 0.3361 (mmm) cc_final: 0.2477 (tpp) REVERT: K 36 ASP cc_start: 0.7061 (m-30) cc_final: 0.6848 (m-30) REVERT: K 76 ILE cc_start: 0.7740 (OUTLIER) cc_final: 0.7446 (mt) REVERT: K 115 ILE cc_start: 0.7650 (pt) cc_final: 0.7381 (pt) REVERT: M 38 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7699 (mtp85) REVERT: M 70 ASP cc_start: 0.7827 (p0) cc_final: 0.7488 (p0) REVERT: Q 18 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8513 (tttp) REVERT: Q 65 ASN cc_start: 0.7296 (t0) cc_final: 0.6924 (t0) REVERT: S 1 MET cc_start: 0.0608 (mtt) cc_final: 0.0221 (mmm) REVERT: S 74 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6629 (tt) REVERT: S 88 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7653 (mmm160) REVERT: T 22 THR cc_start: 0.8529 (m) cc_final: 0.8051 (m) REVERT: V 25 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7672 (mttt) REVERT: W 70 VAL cc_start: 0.8309 (m) cc_final: 0.8060 (t) REVERT: Y 7 ARG cc_start: 0.4259 (OUTLIER) cc_final: 0.3468 (mpp80) REVERT: Y 31 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: e 9 MET cc_start: 0.6733 (OUTLIER) cc_final: 0.6500 (ptp) outliers start: 259 outliers final: 60 residues processed: 1038 average time/residue: 2.1023 time to fit residues: 3113.7207 Evaluate side-chains 735 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 665 time to evaluate : 5.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 61 LEU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 65 ASP Chi-restraints excluded: chain D residue 7 LYS Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 114 LEU Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 38 ARG Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 88 ARG Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain V residue 25 LYS Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Y residue 31 GLN Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 199 ILE Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 24 VAL Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 22 ILE Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain f residue 44 SER Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain k residue 103 CYS Chi-restraints excluded: chain l residue 2 ARG Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain m residue 64 CYS Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain o residue 25 ARG Chi-restraints excluded: chain o residue 53 ASP Chi-restraints excluded: chain o residue 78 VAL Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 67 LEU Chi-restraints excluded: chain q residue 70 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 495 optimal weight: 5.9990 chunk 276 optimal weight: 7.9990 chunk 741 optimal weight: 20.0000 chunk 606 optimal weight: 20.0000 chunk 245 optimal weight: 50.0000 chunk 892 optimal weight: 10.0000 chunk 964 optimal weight: 20.0000 chunk 794 optimal weight: 10.0000 chunk 885 optimal weight: 10.0000 chunk 304 optimal weight: 7.9990 chunk 715 optimal weight: 10.0000 overall best weight: 8.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN 2 29 GLN 4 35 GLN C 20 ASN C 69 ASN D 49 GLN D 58 ASN D 67 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS K 92 GLN L 54 GLN ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 23 ASN O 29 HIS ** O 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN P 76 HIS Q 51 GLN U 39 ASN b 24 ASN ** c 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 197 HIS d 81 GLN d 131 ASN e 52 ASN f 67 ASN f 121 ASN f 129 ASN g 3 GLN ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 ASN p 46 HIS q 30 ASN r 68 HIS u 177 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 1.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.127 153183 Z= 0.563 Angle : 0.894 16.516 229421 Z= 0.449 Chirality : 0.052 0.631 29329 Planarity : 0.008 0.123 12128 Dihedral : 23.954 179.638 77250 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.70 % Favored : 93.25 % Rotamer: Outliers : 6.41 % Allowed : 21.20 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.10), residues: 5392 helix: -0.26 (0.12), residues: 1752 sheet: -0.73 (0.16), residues: 932 loop : -1.85 (0.10), residues: 2708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP M 64 HIS 0.022 0.003 HIS K 28 PHE 0.045 0.003 PHE Q 56 TYR 0.031 0.003 TYR T 84 ARG 0.022 0.001 ARG S 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 724 time to evaluate : 5.657 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: 0 21 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7839 (mp) REVERT: 3 5 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8617 (p) REVERT: 3 48 MET cc_start: 0.8332 (mmm) cc_final: 0.7986 (mmm) REVERT: C 23 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 27 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8191 (mptt) REVERT: E 139 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7329 (tttp) REVERT: E 164 LEU cc_start: 0.8456 (mt) cc_final: 0.8090 (mt) REVERT: F 25 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7169 (mmp) REVERT: G 44 HIS cc_start: 0.5589 (OUTLIER) cc_final: 0.5030 (p90) REVERT: J 136 GLN cc_start: 0.8323 (mt0) cc_final: 0.8116 (mt0) REVERT: K 31 TYR cc_start: 0.4495 (t80) cc_final: 0.3757 (t80) REVERT: N 32 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: O 81 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7198 (mpp80) REVERT: O 111 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6693 (mpp80) REVERT: P 28 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8246 (mmtp) REVERT: S 22 ASP cc_start: 0.7639 (m-30) cc_final: 0.7340 (m-30) REVERT: W 70 VAL cc_start: 0.8646 (OUTLIER) cc_final: 0.8351 (t) REVERT: Y 7 ARG cc_start: 0.5171 (OUTLIER) cc_final: 0.4080 (mpp80) REVERT: d 53 ARG cc_start: 0.7129 (mmm-85) cc_final: 0.6884 (mmm-85) REVERT: d 67 ARG cc_start: 0.7847 (mpt-90) cc_final: 0.7540 (mpt-90) REVERT: e 9 MET cc_start: 0.7243 (OUTLIER) cc_final: 0.6872 (ptp) REVERT: h 56 MET cc_start: 0.4541 (OUTLIER) cc_final: 0.4185 (ptp) REVERT: k 113 ARG cc_start: 0.6775 (OUTLIER) cc_final: 0.5403 (tmm-80) REVERT: o 25 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7003 (mpt-90) outliers start: 288 outliers final: 104 residues processed: 916 average time/residue: 2.1061 time to fit residues: 2763.0144 Evaluate side-chains 737 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 616 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 21 LEU Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 16 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 139 LYS Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain O residue 111 ARG Chi-restraints excluded: chain P residue 28 LYS Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 70 VAL Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Y residue 7 ARG Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 178 LEU Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 150 VAL Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 140 VAL Chi-restraints excluded: chain g residue 77 VAL Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 102 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain h residue 109 GLN Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain l residue 2 ARG Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain l residue 76 ILE Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain m residue 56 SER Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain o residue 25 ARG Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 28 VAL Chi-restraints excluded: chain p residue 57 VAL Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain s residue 23 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 881 optimal weight: 30.0000 chunk 670 optimal weight: 3.9990 chunk 463 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 425 optimal weight: 0.2980 chunk 599 optimal weight: 0.2980 chunk 895 optimal weight: 10.0000 chunk 948 optimal weight: 30.0000 chunk 467 optimal weight: 1.9990 chunk 848 optimal weight: 40.0000 chunk 255 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN 3 30 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN K 28 HIS ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 18 GLN ** O 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN P 2 ASN P 51 ASN Q 70 GLN R 86 GLN S 7 HIS T 48 GLN V 12 GLN V 24 ASN ** c 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 70 GLN c 84 ASN d 96 GLN d 131 ASN h 31 GLN ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 ASN q 53 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 1.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 153183 Z= 0.176 Angle : 0.558 12.265 229421 Z= 0.290 Chirality : 0.035 0.334 29329 Planarity : 0.005 0.064 12128 Dihedral : 23.693 179.986 77250 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.93 % Favored : 95.01 % Rotamer: Outliers : 3.96 % Allowed : 25.03 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.11), residues: 5392 helix: 0.60 (0.12), residues: 1759 sheet: -0.32 (0.17), residues: 934 loop : -1.63 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 60 HIS 0.032 0.001 HIS G 44 PHE 0.027 0.001 PHE J 4 TYR 0.021 0.001 TYR c 50 ARG 0.012 0.001 ARG P 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 703 time to evaluate : 5.684 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: 3 51 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7943 (tptp) REVERT: C 186 ASP cc_start: 0.7448 (m-30) cc_final: 0.7154 (m-30) REVERT: C 228 ASP cc_start: 0.8159 (m-30) cc_final: 0.7928 (m-30) REVERT: D 203 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8420 (t) REVERT: E 1 MET cc_start: 0.5838 (mtp) cc_final: 0.5581 (mtt) REVERT: J 17 VAL cc_start: 0.8522 (OUTLIER) cc_final: 0.8179 (t) REVERT: N 27 SER cc_start: 0.8695 (t) cc_final: 0.8470 (m) REVERT: N 32 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: R 73 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6833 (mmpt) REVERT: d 11 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6629 (pt0) REVERT: d 53 ARG cc_start: 0.7053 (mmm-85) cc_final: 0.6832 (mmm-85) REVERT: e 9 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6899 (ptp) REVERT: g 91 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7539 (pp) REVERT: h 56 MET cc_start: 0.4405 (OUTLIER) cc_final: 0.3937 (ptt) REVERT: n 39 GLN cc_start: 0.6086 (tm-30) cc_final: 0.5849 (tm-30) REVERT: p 59 GLU cc_start: 0.6365 (pt0) cc_final: 0.6161 (pt0) REVERT: s 12 GLN cc_start: 0.6954 (mt0) cc_final: 0.6736 (tt0) outliers start: 178 outliers final: 59 residues processed: 805 average time/residue: 2.0729 time to fit residues: 2394.5613 Evaluate side-chains 701 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 633 time to evaluate : 5.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 46 LYS Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain b residue 68 HIS Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 12 GLU Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain j residue 118 ASN Chi-restraints excluded: chain l residue 2 ARG Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain m residue 66 GLN Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain o residue 53 ASP Chi-restraints excluded: chain s residue 25 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 789 optimal weight: 10.0000 chunk 538 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 706 optimal weight: 5.9990 chunk 391 optimal weight: 1.9990 chunk 809 optimal weight: 20.0000 chunk 655 optimal weight: 0.0020 chunk 1 optimal weight: 9.9990 chunk 484 optimal weight: 2.9990 chunk 851 optimal weight: 20.0000 chunk 239 optimal weight: 7.9990 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 29 GLN C 116 GLN C 225 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS J 128 ASN K 28 HIS K 87 ASN K 92 GLN O 29 HIS Q 70 GLN S 7 HIS S 15 GLN V 24 ASN ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 ASN c 88 ASN d 96 GLN d 120 HIS e 52 ASN f 129 ASN ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 64 GLN k 45 ASN ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 111 GLN q 53 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 1.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 153183 Z= 0.197 Angle : 0.552 12.561 229421 Z= 0.286 Chirality : 0.034 0.325 29329 Planarity : 0.005 0.063 12128 Dihedral : 23.598 179.352 77250 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.84 % Favored : 94.10 % Rotamer: Outliers : 4.54 % Allowed : 24.78 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 5392 helix: 0.93 (0.12), residues: 1767 sheet: -0.25 (0.17), residues: 937 loop : -1.55 (0.11), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP p 72 HIS 0.008 0.001 HIS G 44 PHE 0.020 0.001 PHE h 38 TYR 0.016 0.001 TYR Q 31 ARG 0.013 0.001 ARG S 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 671 time to evaluate : 5.769 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: 3 51 LYS cc_start: 0.8246 (tptm) cc_final: 0.7977 (tptp) REVERT: C 186 ASP cc_start: 0.7501 (m-30) cc_final: 0.7210 (m-30) REVERT: C 228 ASP cc_start: 0.8188 (m-30) cc_final: 0.7975 (m-30) REVERT: D 203 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8400 (t) REVERT: E 1 MET cc_start: 0.5746 (mtp) cc_final: 0.5511 (mtt) REVERT: E 88 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.7454 (mmp80) REVERT: E 199 MET cc_start: 0.7656 (ptm) cc_final: 0.7393 (ptm) REVERT: F 37 MET cc_start: 0.7896 (mtp) cc_final: 0.7489 (ttm) REVERT: J 16 TYR cc_start: 0.8592 (m-80) cc_final: 0.8351 (m-80) REVERT: K 31 TYR cc_start: 0.3262 (t80) cc_final: 0.2880 (t80) REVERT: N 32 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: O 104 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: R 73 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.6904 (mmpt) REVERT: Y 55 THR cc_start: 0.7858 (t) cc_final: 0.7599 (t) REVERT: d 11 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6538 (pt0) REVERT: d 53 ARG cc_start: 0.7080 (mmm-85) cc_final: 0.6858 (mmm-85) REVERT: d 67 ARG cc_start: 0.7735 (mpt-90) cc_final: 0.7524 (mpt-90) REVERT: e 9 MET cc_start: 0.7126 (OUTLIER) cc_final: 0.6741 (ptp) REVERT: g 91 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7546 (pp) REVERT: h 56 MET cc_start: 0.4507 (OUTLIER) cc_final: 0.4164 (ptp) REVERT: h 87 MET cc_start: 0.5419 (mmp) cc_final: 0.5170 (mmp) REVERT: i 40 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6748 (pp) REVERT: k 113 ARG cc_start: 0.6217 (OUTLIER) cc_final: 0.5189 (tmm-80) REVERT: q 24 ASP cc_start: 0.7296 (p0) cc_final: 0.7025 (p0) outliers start: 204 outliers final: 95 residues processed: 802 average time/residue: 2.1077 time to fit residues: 2423.9850 Evaluate side-chains 757 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 651 time to evaluate : 5.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 28 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain F residue 59 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 93 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain b residue 105 VAL Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 195 ASN Chi-restraints excluded: chain d residue 11 GLN Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain e residue 9 MET Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain k residue 45 ASN Chi-restraints excluded: chain k residue 55 ARG Chi-restraints excluded: chain k residue 102 ASP Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain l residue 2 ARG Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain m residue 66 GLN Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain o residue 42 ILE Chi-restraints excluded: chain o residue 53 ASP Chi-restraints excluded: chain o residue 66 THR Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 319 optimal weight: 10.0000 chunk 853 optimal weight: 20.0000 chunk 187 optimal weight: 40.0000 chunk 556 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 949 optimal weight: 30.0000 chunk 787 optimal weight: 20.0000 chunk 439 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 313 optimal weight: 30.0000 chunk 498 optimal weight: 20.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 29 GLN C 24 HIS C 162 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** G 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN G 44 HIS J 67 ASN K 28 HIS N 18 GLN O 34 HIS Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS V 78 GLN a 23 ASN ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 ASN c 88 ASN d 96 GLN d 120 HIS ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 13 HIS n 49 HIS o 18 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 1.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 153183 Z= 0.515 Angle : 0.781 11.769 229421 Z= 0.395 Chirality : 0.048 0.694 29329 Planarity : 0.007 0.087 12128 Dihedral : 23.748 179.969 77250 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.95 % Favored : 92.97 % Rotamer: Outliers : 5.65 % Allowed : 24.63 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.11), residues: 5392 helix: 0.60 (0.12), residues: 1762 sheet: -0.42 (0.17), residues: 933 loop : -1.67 (0.11), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 125 HIS 0.011 0.002 HIS P 76 PHE 0.028 0.003 PHE Q 56 TYR 0.029 0.003 TYR 0 48 ARG 0.013 0.001 ARG 0 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 661 time to evaluate : 5.822 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: 3 51 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7881 (tptm) REVERT: 4 4 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7531 (ptp-170) REVERT: C 186 ASP cc_start: 0.7378 (m-30) cc_final: 0.7154 (m-30) REVERT: D 1 MET cc_start: 0.5521 (OUTLIER) cc_final: 0.4975 (mmm) REVERT: E 1 MET cc_start: 0.5645 (mtp) cc_final: 0.5432 (mtt) REVERT: E 21 ARG cc_start: 0.7484 (ttt-90) cc_final: 0.7206 (ttt-90) REVERT: E 199 MET cc_start: 0.7675 (ptm) cc_final: 0.7472 (ptm) REVERT: F 21 TYR cc_start: 0.0085 (OUTLIER) cc_final: -0.1954 (t80) REVERT: J 16 TYR cc_start: 0.8678 (m-80) cc_final: 0.8433 (m-80) REVERT: J 85 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8370 (ptpp) REVERT: K 31 TYR cc_start: 0.4207 (t80) cc_final: 0.3898 (t80) REVERT: L 144 GLU cc_start: 0.7199 (pm20) cc_final: 0.6569 (mt-10) REVERT: M 6 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6681 (ptm-80) REVERT: N 32 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7978 (mt-10) REVERT: O 34 HIS cc_start: 0.8491 (m90) cc_final: 0.8125 (m-70) REVERT: O 102 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.6551 (ttp80) REVERT: O 104 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: P 12 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.7829 (mtm) REVERT: P 73 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.6935 (p90) REVERT: Q 14 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8367 (ttpt) REVERT: R 70 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: R 73 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6906 (mmpt) REVERT: S 22 ASP cc_start: 0.7782 (m-30) cc_final: 0.7382 (m-30) REVERT: T 66 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8026 (mtpt) REVERT: U 21 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7780 (ptm160) REVERT: U 93 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7868 (ptt180) REVERT: c 98 ASP cc_start: 0.6162 (p0) cc_final: 0.5937 (p0) REVERT: g 91 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7741 (pp) REVERT: h 56 MET cc_start: 0.4691 (OUTLIER) cc_final: 0.4344 (ptp) REVERT: i 7 ARG cc_start: 0.5361 (ptp-170) cc_final: 0.5152 (ptm160) REVERT: i 40 ILE cc_start: 0.7096 (OUTLIER) cc_final: 0.6800 (pp) REVERT: k 113 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.5996 (tmm-80) REVERT: m 11 LYS cc_start: 0.6710 (OUTLIER) cc_final: 0.6451 (ptmm) REVERT: r 11 ASP cc_start: 0.6052 (OUTLIER) cc_final: 0.5669 (p0) outliers start: 254 outliers final: 135 residues processed: 834 average time/residue: 2.0658 time to fit residues: 2473.2394 Evaluate side-chains 794 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 636 time to evaluate : 5.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain 4 residue 4 ARG Chi-restraints excluded: chain 4 residue 6 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 102 ARG Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Z residue 34 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 133 SER Chi-restraints excluded: chain c residue 137 SER Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 63 ASN Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain i residue 71 LEU Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain m residue 66 GLN Chi-restraints excluded: chain n residue 17 ASP Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain o residue 42 ILE Chi-restraints excluded: chain o residue 66 THR Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 78 VAL Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 11 ASP Chi-restraints excluded: chain t residue 31 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 915 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 540 optimal weight: 0.9980 chunk 693 optimal weight: 10.0000 chunk 537 optimal weight: 0.9990 chunk 798 optimal weight: 3.9990 chunk 530 optimal weight: 0.9990 chunk 945 optimal weight: 30.0000 chunk 591 optimal weight: 0.8980 chunk 576 optimal weight: 3.9990 chunk 436 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 GLN C 116 GLN C 162 GLN G 29 ASN G 44 HIS G 115 GLN J 130 HIS K 87 ASN N 18 GLN P 9 GLN Q 70 GLN S 7 HIS U 45 GLN V 24 ASN Y 45 GLN ** c 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 ASN c 197 HIS d 96 GLN d 120 HIS e 11 HIS ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 109 GLN k 45 ASN ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 1.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 153183 Z= 0.134 Angle : 0.539 12.412 229421 Z= 0.280 Chirality : 0.033 0.360 29329 Planarity : 0.004 0.057 12128 Dihedral : 23.648 179.704 77250 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.21 % Favored : 94.75 % Rotamer: Outliers : 3.45 % Allowed : 27.43 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.11), residues: 5392 helix: 1.02 (0.12), residues: 1774 sheet: -0.21 (0.17), residues: 926 loop : -1.53 (0.11), residues: 2692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP p 72 HIS 0.008 0.001 HIS s 19 PHE 0.040 0.001 PHE J 4 TYR 0.029 0.001 TYR q 22 ARG 0.011 0.001 ARG p 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 669 time to evaluate : 5.765 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: 3 51 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8061 (tptp) REVERT: C 186 ASP cc_start: 0.7391 (m-30) cc_final: 0.7191 (m-30) REVERT: C 228 ASP cc_start: 0.8190 (m-30) cc_final: 0.7963 (m-30) REVERT: D 203 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8457 (t) REVERT: E 1 MET cc_start: 0.5515 (mtp) cc_final: 0.5248 (mtt) REVERT: E 199 MET cc_start: 0.7674 (ptm) cc_final: 0.7407 (ptm) REVERT: F 21 TYR cc_start: -0.0042 (OUTLIER) cc_final: -0.1939 (t80) REVERT: F 37 MET cc_start: 0.8086 (mtp) cc_final: 0.7766 (ttm) REVERT: J 16 TYR cc_start: 0.8559 (m-80) cc_final: 0.8327 (m-80) REVERT: J 85 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8292 (ptpp) REVERT: L 143 GLU cc_start: 0.6733 (mp0) cc_final: 0.6423 (mp0) REVERT: L 144 GLU cc_start: 0.7096 (pm20) cc_final: 0.6670 (mt-10) REVERT: N 27 SER cc_start: 0.8674 (t) cc_final: 0.8432 (m) REVERT: N 32 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: O 33 ARG cc_start: 0.5203 (OUTLIER) cc_final: 0.4132 (tpt170) REVERT: O 102 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.6777 (ttp80) REVERT: O 104 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8274 (tt0) REVERT: P 62 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7988 (tttt) REVERT: P 73 PHE cc_start: 0.7024 (OUTLIER) cc_final: 0.6569 (p90) REVERT: R 70 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7280 (tt0) REVERT: Z 10 ARG cc_start: 0.7903 (mtt-85) cc_final: 0.7634 (mtt-85) REVERT: a 26 MET cc_start: 0.4361 (ppp) cc_final: 0.3959 (ppp) REVERT: c 98 ASP cc_start: 0.6006 (p0) cc_final: 0.5792 (p0) REVERT: h 56 MET cc_start: 0.4420 (OUTLIER) cc_final: 0.4203 (ptp) REVERT: i 40 ILE cc_start: 0.6982 (OUTLIER) cc_final: 0.6728 (pp) REVERT: k 45 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6910 (p0) REVERT: k 113 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.5586 (tmm-80) REVERT: m 11 LYS cc_start: 0.6584 (OUTLIER) cc_final: 0.6303 (ptmm) REVERT: p 20 ILE cc_start: 0.6469 (pt) cc_final: 0.6246 (pt) REVERT: q 62 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6680 (mtp180) REVERT: r 11 ASP cc_start: 0.5734 (OUTLIER) cc_final: 0.5517 (p0) outliers start: 155 outliers final: 75 residues processed: 773 average time/residue: 2.1154 time to fit residues: 2335.8202 Evaluate side-chains 720 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 627 time to evaluate : 5.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain O residue 33 ARG Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 102 ARG Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 105 VAL Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 137 SER Chi-restraints excluded: chain c residue 195 ASN Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain f residue 74 VAL Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 45 ASN Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain m residue 66 GLN Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain p residue 36 PHE Chi-restraints excluded: chain q residue 62 ARG Chi-restraints excluded: chain r residue 11 ASP Chi-restraints excluded: chain t residue 31 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 584 optimal weight: 1.9990 chunk 377 optimal weight: 7.9990 chunk 564 optimal weight: 0.5980 chunk 284 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 601 optimal weight: 8.9990 chunk 644 optimal weight: 10.0000 chunk 467 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 743 optimal weight: 0.5980 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 GLN C 162 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN G 44 HIS N 18 GLN O 34 HIS Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS U 45 GLN ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN c 84 ASN d 96 GLN d 120 HIS e 52 ASN e 63 ASN ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 GLN s 19 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 1.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 153183 Z= 0.282 Angle : 0.597 14.777 229421 Z= 0.307 Chirality : 0.037 0.404 29329 Planarity : 0.005 0.059 12128 Dihedral : 23.589 179.780 77250 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 3.83 % Allowed : 27.61 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.65 (0.11), residues: 5392 helix: 1.01 (0.12), residues: 1768 sheet: -0.24 (0.17), residues: 938 loop : -1.52 (0.11), residues: 2686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP p 72 HIS 0.008 0.001 HIS S 7 PHE 0.026 0.002 PHE J 4 TYR 0.024 0.002 TYR q 22 ARG 0.012 0.001 ARG k 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 623 time to evaluate : 5.697 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: 3 51 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.8002 (tptp) REVERT: D 1 MET cc_start: 0.5336 (OUTLIER) cc_final: 0.4903 (mmm) REVERT: D 203 VAL cc_start: 0.8693 (OUTLIER) cc_final: 0.8319 (t) REVERT: E 199 MET cc_start: 0.7761 (ptm) cc_final: 0.7549 (ptm) REVERT: F 21 TYR cc_start: 0.0285 (OUTLIER) cc_final: -0.1841 (t80) REVERT: J 16 TYR cc_start: 0.8642 (m-80) cc_final: 0.8394 (m-80) REVERT: J 85 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8432 (ptpp) REVERT: L 144 GLU cc_start: 0.7171 (pm20) cc_final: 0.6775 (mt-10) REVERT: N 32 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7807 (mt-10) REVERT: O 102 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.6794 (ttp80) REVERT: O 104 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: P 73 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.6931 (p90) REVERT: R 70 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: S 22 ASP cc_start: 0.7713 (m-30) cc_final: 0.7355 (m-30) REVERT: T 66 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7722 (mtpt) REVERT: U 93 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7631 (ptt180) REVERT: a 22 TRP cc_start: 0.5344 (OUTLIER) cc_final: 0.5013 (p90) REVERT: g 91 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7469 (pp) REVERT: h 56 MET cc_start: 0.4482 (OUTLIER) cc_final: 0.4204 (ptp) REVERT: i 7 ARG cc_start: 0.5352 (ptp-170) cc_final: 0.5054 (ptm160) REVERT: i 40 ILE cc_start: 0.7088 (OUTLIER) cc_final: 0.6795 (pp) REVERT: k 113 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.5853 (tmm-80) REVERT: m 11 LYS cc_start: 0.6651 (OUTLIER) cc_final: 0.6344 (ptmm) REVERT: p 20 ILE cc_start: 0.6644 (pt) cc_final: 0.6416 (pt) REVERT: q 62 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6684 (mtp180) REVERT: r 11 ASP cc_start: 0.5992 (OUTLIER) cc_final: 0.5707 (p0) REVERT: s 78 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6970 (mp) outliers start: 172 outliers final: 101 residues processed: 736 average time/residue: 2.0517 time to fit residues: 2164.2510 Evaluate side-chains 722 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 600 time to evaluate : 5.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 3 residue 53 ASP Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain J residue 2 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain K residue 16 ARG Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 102 ARG Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 22 TRP Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 105 VAL Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 137 SER Chi-restraints excluded: chain c residue 195 ASN Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 55 HIS Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 54 VAL Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain p residue 36 PHE Chi-restraints excluded: chain q residue 62 ARG Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 11 ASP Chi-restraints excluded: chain s residue 78 LEU Chi-restraints excluded: chain t residue 31 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 860 optimal weight: 10.0000 chunk 905 optimal weight: 10.0000 chunk 826 optimal weight: 40.0000 chunk 881 optimal weight: 30.0000 chunk 530 optimal weight: 4.9990 chunk 383 optimal weight: 4.9990 chunk 691 optimal weight: 30.0000 chunk 270 optimal weight: 8.9990 chunk 796 optimal weight: 8.9990 chunk 833 optimal weight: 20.0000 chunk 878 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN G 29 ASN G 44 HIS J 130 HIS N 18 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS T 59 ASN ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN c 84 ASN d 96 GLN d 120 HIS g 3 GLN ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 13 HIS n 39 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 1.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.081 153183 Z= 0.497 Angle : 0.764 19.795 229421 Z= 0.387 Chirality : 0.048 0.684 29329 Planarity : 0.006 0.089 12128 Dihedral : 23.742 179.928 77250 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.27 % Favored : 92.64 % Rotamer: Outliers : 4.34 % Allowed : 27.59 % Favored : 68.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.11), residues: 5392 helix: 0.70 (0.12), residues: 1758 sheet: -0.37 (0.17), residues: 928 loop : -1.67 (0.11), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 78 HIS 0.033 0.002 HIS G 44 PHE 0.030 0.003 PHE P 73 TYR 0.033 0.003 TYR K 31 ARG 0.010 0.001 ARG 0 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 636 time to evaluate : 5.776 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: 3 51 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7858 (tptm) REVERT: D 1 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.4803 (mmm) REVERT: F 21 TYR cc_start: 0.0817 (OUTLIER) cc_final: -0.1578 (t80) REVERT: J 16 TYR cc_start: 0.8658 (m-80) cc_final: 0.8421 (m-80) REVERT: J 85 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8479 (ptpp) REVERT: L 144 GLU cc_start: 0.7342 (pm20) cc_final: 0.6858 (mt-10) REVERT: M 6 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6676 (ptm-80) REVERT: N 32 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7973 (mt-10) REVERT: O 102 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.6429 (ttp80) REVERT: O 104 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: Q 14 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8377 (ttpt) REVERT: R 70 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: R 73 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.6941 (mmpt) REVERT: S 22 ASP cc_start: 0.7742 (m-30) cc_final: 0.7362 (m-30) REVERT: T 66 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7951 (mtpt) REVERT: U 93 ARG cc_start: 0.8462 (OUTLIER) cc_final: 0.7744 (ptt180) REVERT: V 12 GLN cc_start: 0.8127 (mp10) cc_final: 0.7860 (mt0) REVERT: Z 38 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7154 (pt0) REVERT: a 22 TRP cc_start: 0.5498 (OUTLIER) cc_final: 0.5225 (p90) REVERT: a 26 MET cc_start: 0.4986 (ppp) cc_final: 0.4574 (ppp) REVERT: a 153 MET cc_start: 0.5251 (tmm) cc_final: 0.4800 (ttt) REVERT: g 91 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7644 (pp) REVERT: h 56 MET cc_start: 0.4826 (OUTLIER) cc_final: 0.4439 (ptp) REVERT: i 40 ILE cc_start: 0.7132 (OUTLIER) cc_final: 0.6889 (pp) REVERT: i 91 ASP cc_start: -0.0248 (OUTLIER) cc_final: -0.1837 (p0) REVERT: k 45 ASN cc_start: 0.7203 (p0) cc_final: 0.6894 (p0) REVERT: k 113 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.6122 (tmm-80) REVERT: m 11 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6402 (ptmm) REVERT: q 56 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7518 (ttm110) REVERT: q 62 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.6872 (mtp180) REVERT: r 11 ASP cc_start: 0.6215 (OUTLIER) cc_final: 0.5957 (p0) outliers start: 195 outliers final: 116 residues processed: 764 average time/residue: 2.1097 time to fit residues: 2302.9449 Evaluate side-chains 751 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 612 time to evaluate : 5.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 97 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 6 ARG Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 102 ARG Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain U residue 93 ARG Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 78 GLN Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 22 TRP Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 137 SER Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 55 HIS Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain f residue 67 ASN Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain k residue 114 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain o residue 42 ILE Chi-restraints excluded: chain p residue 36 PHE Chi-restraints excluded: chain q residue 62 ARG Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 11 ASP Chi-restraints excluded: chain t residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 578 optimal weight: 3.9990 chunk 931 optimal weight: 50.0000 chunk 568 optimal weight: 8.9990 chunk 442 optimal weight: 0.9990 chunk 647 optimal weight: 5.9990 chunk 977 optimal weight: 10.0000 chunk 899 optimal weight: 10.0000 chunk 778 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 601 optimal weight: 7.9990 chunk 477 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 GLN C 116 GLN ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN G 44 HIS N 18 GLN P 9 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN Y 45 GLN ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN c 84 ASN d 120 HIS ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 13 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 1.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 153183 Z= 0.219 Angle : 0.594 17.443 229421 Z= 0.307 Chirality : 0.036 0.423 29329 Planarity : 0.005 0.072 12128 Dihedral : 23.677 179.986 77250 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.14 % Favored : 93.81 % Rotamer: Outliers : 3.47 % Allowed : 28.90 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.77 (0.11), residues: 5392 helix: 0.90 (0.12), residues: 1769 sheet: -0.32 (0.17), residues: 932 loop : -1.58 (0.11), residues: 2691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP a 103 HIS 0.010 0.001 HIS V 80 PHE 0.021 0.002 PHE P 73 TYR 0.023 0.002 TYR q 22 ARG 0.016 0.001 ARG a 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 617 time to evaluate : 5.976 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: 3 51 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7934 (tptp) REVERT: D 1 MET cc_start: 0.5294 (OUTLIER) cc_final: 0.4816 (mmm) REVERT: D 203 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8332 (t) REVERT: F 21 TYR cc_start: 0.0765 (OUTLIER) cc_final: -0.1586 (t80) REVERT: J 16 TYR cc_start: 0.8611 (m-80) cc_final: 0.8368 (m-80) REVERT: J 85 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8297 (ptpp) REVERT: K 90 SER cc_start: 0.8737 (p) cc_final: 0.8443 (p) REVERT: L 144 GLU cc_start: 0.7306 (pm20) cc_final: 0.6846 (mt-10) REVERT: N 32 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: O 102 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.6797 (ttp80) REVERT: O 104 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: P 73 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7044 (p90) REVERT: R 70 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: R 73 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.6940 (mmpt) REVERT: T 66 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.7777 (mtpt) REVERT: Z 38 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: a 26 MET cc_start: 0.4959 (ppp) cc_final: 0.4368 (ppp) REVERT: g 91 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7611 (pp) REVERT: g 106 SER cc_start: 0.7634 (t) cc_final: 0.7049 (m) REVERT: h 56 MET cc_start: 0.4614 (OUTLIER) cc_final: 0.4322 (ptp) REVERT: i 40 ILE cc_start: 0.7068 (OUTLIER) cc_final: 0.6810 (pp) REVERT: k 45 ASN cc_start: 0.7177 (p0) cc_final: 0.6930 (p0) REVERT: k 113 ARG cc_start: 0.7006 (OUTLIER) cc_final: 0.6025 (tmm-80) REVERT: m 11 LYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6429 (ptmm) REVERT: q 62 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6715 (mtp180) outliers start: 156 outliers final: 103 residues processed: 723 average time/residue: 2.1289 time to fit residues: 2198.9167 Evaluate side-chains 725 residues out of total 4501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 603 time to evaluate : 5.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 36 LYS Chi-restraints excluded: chain 2 residue 44 VAL Chi-restraints excluded: chain 3 residue 51 LYS Chi-restraints excluded: chain 4 residue 2 LYS Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 87 SER Chi-restraints excluded: chain C residue 193 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain F residue 21 TYR Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 57 TYR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 85 LYS Chi-restraints excluded: chain K residue 84 VAL Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 78 LEU Chi-restraints excluded: chain N residue 15 SER Chi-restraints excluded: chain N residue 32 GLU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 102 ARG Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 58 PHE Chi-restraints excluded: chain P residue 62 LYS Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 73 PHE Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 71 VAL Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 69 ARG Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain W residue 19 ARG Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 34 SER Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain X residue 47 THR Chi-restraints excluded: chain X residue 51 SER Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 69 VAL Chi-restraints excluded: chain a residue 147 LEU Chi-restraints excluded: chain a residue 185 ILE Chi-restraints excluded: chain a residue 188 THR Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 86 LEU Chi-restraints excluded: chain b residue 105 VAL Chi-restraints excluded: chain b residue 120 THR Chi-restraints excluded: chain b residue 190 THR Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 118 SER Chi-restraints excluded: chain c residue 137 SER Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 55 HIS Chi-restraints excluded: chain e residue 64 VAL Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain f residue 93 VAL Chi-restraints excluded: chain f residue 100 MET Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain g residue 79 ARG Chi-restraints excluded: chain g residue 91 LEU Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 29 ILE Chi-restraints excluded: chain h residue 48 ARG Chi-restraints excluded: chain h residue 56 MET Chi-restraints excluded: chain h residue 93 LEU Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain j residue 19 VAL Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 113 ARG Chi-restraints excluded: chain k residue 114 SER Chi-restraints excluded: chain l residue 15 VAL Chi-restraints excluded: chain l residue 65 GLU Chi-restraints excluded: chain m residue 11 LYS Chi-restraints excluded: chain m residue 66 GLN Chi-restraints excluded: chain n residue 32 THR Chi-restraints excluded: chain n residue 38 LEU Chi-restraints excluded: chain p residue 36 PHE Chi-restraints excluded: chain q residue 62 ARG Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain t residue 31 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 981 random chunks: chunk 618 optimal weight: 4.9990 chunk 829 optimal weight: 20.0000 chunk 238 optimal weight: 7.9990 chunk 717 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 chunk 216 optimal weight: 8.9990 chunk 779 optimal weight: 4.9990 chunk 326 optimal weight: 0.2980 chunk 800 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 143 optimal weight: 50.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 44 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN G 29 ASN G 44 HIS N 18 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS V 78 GLN ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 84 ASN d 96 GLN e 52 ASN e 63 ASN ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 13 HIS ** r 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.124616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100449 restraints weight = 210285.791| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.23 r_work: 0.2647 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 1.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 153183 Z= 0.348 Angle : 0.656 20.872 229421 Z= 0.336 Chirality : 0.041 0.506 29329 Planarity : 0.006 0.081 12128 Dihedral : 23.653 179.999 77250 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.05 % Favored : 92.88 % Rotamer: Outliers : 3.69 % Allowed : 28.79 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.81 (0.11), residues: 5392 helix: 0.85 (0.12), residues: 1766 sheet: -0.31 (0.17), residues: 917 loop : -1.59 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 103 HIS 0.029 0.002 HIS G 44 PHE 0.023 0.002 PHE P 73 TYR 0.030 0.002 TYR K 31 ARG 0.018 0.001 ARG a 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36100.20 seconds wall clock time: 631 minutes 34.76 seconds (37894.76 seconds total)