Starting phenix.real_space_refine on Thu Mar 21 07:04:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g31_29687/03_2024/8g31_29687.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g31_29687/03_2024/8g31_29687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g31_29687/03_2024/8g31_29687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g31_29687/03_2024/8g31_29687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g31_29687/03_2024/8g31_29687.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g31_29687/03_2024/8g31_29687.pdb" } resolution = 3.2 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= 0.006 sd= 0.054 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 146 5.16 5 C 72704 2.51 5 N 26896 2.21 5 O 39956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 243": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "F TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "K ASP 55": "OD1" <-> "OD2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 70": "OD1" <-> "OD2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 178": "OE1" <-> "OE2" Residue "e TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 122": "OE1" <-> "OE2" Residue "i PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 10": "OD1" <-> "OD2" Residue "m GLU 86": "OE1" <-> "OE2" Residue "n ASP 48": "OD1" <-> "OD2" Residue "q TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ASP 81": "OD1" <-> "OD2" Residue "w GLU 174": "OE1" <-> "OE2" Residue "w PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 180": "OD1" <-> "OD2" 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: 144258 Number of models: 1 Model: "" Number of chains: 52 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: "6" Number of atoms: 3403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3403 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 409} 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': 5, 'rna2p_pyr': 4, 'rna3p_pur': 58, 'rna3p_pyr': 50} Link IDs: {'rna2p': 9, 'rna3p': 107} 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': 265, 'rna2p_pyr': 156, 'rna3p_pur': 1409, 'rna3p_pyr': 1073} Link IDs: {'rna2p': 421, 'rna3p': 2481} 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: "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': 125, 'rna2p_pyr': 100, 'rna3p_pur': 749, 'rna3p_pyr': 565} Link IDs: {'rna2p': 224, 'rna3p': 1314} Chain: "w" 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: "x" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1625 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 198} Time building chain proxies: 54.18, per 1000 atoms: 0.38 Number of scatterers: 144258 At special positions: 0 Unit cell: (247.2, 258.53, 272.95, 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 146 16.00 P 4556 15.00 O 39956 8.00 N 26896 7.00 C 72704 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: 56.03 Conformation dependent library (CDL) restraints added in 6.6 seconds 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10882 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 69 sheets defined 34.4% alpha, 15.1% beta 1451 base pairs and 2417 stacking pairs defined. Time for finding SS restraints: 47.99 Creating SS restraints... Processing helix chain '0' and resid 8 through 16 removed outlier: 3.644A pdb=" N ARG 0 16 " --> pdb=" O ARG 0 12 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 22 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: 3.877A pdb=" N LYS 4 34 " --> pdb=" O PRO 4 31 " (cutoff:3.500A) Processing helix chain '6' and resid 27 through 38 Processing helix chain '6' and resid 59 through 71 removed outlier: 4.729A pdb=" N GLU 6 68 " --> pdb=" O VAL 6 64 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ALA 6 69 " --> pdb=" O GLU 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 95 Processing helix chain '6' and resid 103 through 114 removed outlier: 4.868A pdb=" N ILE 6 110 " --> pdb=" O LEU 6 106 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE 6 111 " --> pdb=" O ILE 6 107 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 137 removed outlier: 3.827A pdb=" N ARG 6 135 " --> pdb=" O HIS 6 131 " (cutoff:3.500A) Processing helix chain '6' and resid 140 through 148 removed outlier: 3.599A pdb=" N GLY 6 148 " --> pdb=" O GLU 6 144 " (cutoff:3.500A) Processing helix chain '6' and resid 160 through 193 Processing helix chain '6' and resid 209 through 218 Processing helix chain '6' and resid 261 through 267 Processing helix chain '6' and resid 268 through 270 No H-bonds generated for 'chain '6' and resid 268 through 270' Processing helix chain '6' and resid 271 through 276 removed outlier: 3.869A pdb=" N ARG 6 275 " --> pdb=" O LEU 6 271 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN 6 276 " --> pdb=" O GLN 6 272 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 271 through 276' Processing helix chain '6' and resid 291 through 306 Processing helix chain '6' and resid 350 through 361 removed outlier: 3.942A pdb=" N LEU 6 361 " --> pdb=" O LEU 6 357 " (cutoff:3.500A) Processing helix chain '6' and resid 381 through 386 Processing helix chain '6' and resid 407 through 418 removed outlier: 4.355A pdb=" N CYS 6 415 " --> pdb=" O TRP 6 411 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS 6 416 " --> pdb=" O ARG 6 412 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU 6 418 " --> pdb=" O LEU 6 414 " (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 196 through 200 removed outlier: 3.589A pdb=" N HIS C 199 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 196 through 200' Processing helix chain 'C' and resid 206 through 214 removed outlier: 3.906A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.810A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.768A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'F' and resid 2 through 9 removed outlier: 3.650A pdb=" N ASP F 9 " --> pdb=" O ASP F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 15 removed outlier: 3.520A pdb=" N LEU F 15 " --> pdb=" O VAL F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 57 removed outlier: 4.340A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 107 Processing helix chain 'F' and resid 162 through 167 Processing helix chain 'G' and resid 59 through 80 Processing helix chain 'G' and resid 136 through 151 removed outlier: 4.379A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.658A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) 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 122 removed outlier: 3.782A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.534A pdb=" N GLN J 136 " --> pdb=" O ALA J 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 110 No H-bonds generated for 'chain 'K' and resid 108 through 110' Processing helix chain 'K' and resid 111 through 118 Processing helix chain 'L' and resid 82 through 86 removed outlier: 3.862A pdb=" N VAL L 85 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU L 86 " --> pdb=" O ALA L 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 82 through 86' Processing helix chain 'L' and resid 92 through 98 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 43 through 58 Processing helix chain 'M' and resid 109 through 124 Processing helix chain 'N' and resid 13 through 32 Processing helix chain 'N' and resid 38 through 55 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 'N' and resid 84 through 88 removed outlier: 3.606A pdb=" N ALA N 88 " --> pdb=" O PRO N 85 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 21 removed outlier: 4.950A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.238A 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 113 Processing helix chain 'Q' and resid 5 through 20 Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 30 through 72 removed outlier: 3.684A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 95 through 101 Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.567A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.086A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 4.110A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 60 Processing helix chain 'S' and resid 65 through 69 removed outlier: 3.531A pdb=" N LEU S 69 " --> pdb=" O ILE S 66 " (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 4 through 8 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 removed outlier: 3.864A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 57 removed outlier: 4.043A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 54 through 57' Processing helix chain 'X' and resid 52 through 62 Processing helix chain 'X' and resid 62 through 73 removed outlier: 3.541A pdb=" N VAL X 66 " --> pdb=" O GLY X 62 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 22 Processing helix chain 'Y' and resid 23 through 35 Processing helix chain 'Y' and resid 38 through 60 removed outlier: 4.764A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS Y 60 " --> pdb=" O LEU Y 56 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'Z' and resid 52 through 54 No H-bonds generated for 'chain 'Z' and resid 52 through 54' Processing helix chain 'c' and resid 6 through 15 removed outlier: 4.220A pdb=" N LEU c 10 " --> pdb=" O PRO c 6 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER c 11 " --> pdb=" O LYS c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 42 removed outlier: 4.449A pdb=" N ALA c 42 " --> pdb=" O GLN c 39 " (cutoff:3.500A) 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 164 Processing helix chain 'c' and resid 186 through 191 Processing helix chain 'c' and resid 195 through 204 removed outlier: 4.018A pdb=" N ILE c 199 " --> pdb=" O ASN c 195 " (cutoff:3.500A) 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 12 through 16 removed outlier: 4.655A pdb=" N GLU e 16 " --> pdb=" O ASP e 13 " (cutoff:3.500A) Processing helix chain 'e' and resid 17 through 32 Processing helix chain 'e' and resid 67 through 81 removed outlier: 3.560A pdb=" N ILE e 71 " --> pdb=" O PRO e 67 " (cutoff:3.500A) 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 Processing helix chain 'f' and resid 131 through 147 Processing helix chain 'g' and resid 4 through 20 Processing helix chain 'g' and resid 29 through 43 Processing helix chain 'g' and resid 93 through 98 removed outlier: 4.108A 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 43 through 53 Proline residue: h 50 - end of helix Processing helix chain 'h' and resid 70 through 90 Processing helix chain 'h' and resid 93 through 101 Processing helix chain 'i' and resid 14 through 33 Processing helix chain 'i' and resid 80 through 87 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: 3.791A pdb=" N ALA j 62 " --> pdb=" O THR j 58 " (cutoff:3.500A) Processing helix chain 'j' and resid 91 through 103 Processing helix chain 'k' and resid 2 through 9 Processing helix chain 'l' and resid 13 through 21 removed outlier: 4.230A pdb=" N ALA l 17 " --> pdb=" O HIS l 13 " (cutoff:3.500A) Processing helix chain 'l' and resid 26 through 37 Processing helix chain 'l' and resid 48 through 62 Processing helix chain 'l' and resid 66 through 83 removed outlier: 3.608A pdb=" N ARG l 70 " --> pdb=" O GLY l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 84 through 93 removed outlier: 4.020A pdb=" N LEU l 88 " --> pdb=" O CYS l 84 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY l 93 " --> pdb=" O ARG l 89 " (cutoff:3.500A) Processing helix chain 'l' and resid 105 through 110 Processing helix chain 'm' and resid 2 through 18 Processing helix chain 'm' and resid 22 through 32 Processing helix chain 'm' and resid 42 through 51 Processing helix chain 'm' and resid 52 through 56 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 44 removed outlier: 3.909A pdb=" N GLY n 40 " --> pdb=" O ASN n 36 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU n 44 " --> pdb=" O GLY n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 73 removed outlier: 4.034A 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 64 Processing helix chain 'o' and resid 68 through 78 Processing helix chain 'q' and resid 24 through 29 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 'r' and resid 40 through 44 removed outlier: 3.584A pdb=" N ILE r 44 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 's' and resid 4 through 41 removed outlier: 3.643A pdb=" N LYS s 8 " --> pdb=" O LYS s 4 " (cutoff:3.500A) Processing helix chain 's' and resid 42 through 64 removed outlier: 3.674A pdb=" N ALA s 46 " --> pdb=" O ASP s 42 " (cutoff:3.500A) Proline residue: s 55 - end of helix Processing helix chain 's' and resid 68 through 86 removed outlier: 4.029A pdb=" N ALA s 86 " --> pdb=" O ILE s 82 " (cutoff:3.500A) Processing helix chain 't' and resid 23 through 33 removed outlier: 4.281A pdb=" N ARG t 33 " --> pdb=" O ALA t 29 " (cutoff:3.500A) Processing helix chain 't' and resid 38 through 52 removed outlier: 4.444A pdb=" N THR t 42 " --> pdb=" O GLU t 38 " (cutoff:3.500A) Processing helix chain 'w' and resid 23 through 30 Proline residue: w 28 - end of helix Processing helix chain 'w' and resid 32 through 37 removed outlier: 3.963A pdb=" N LYS w 36 " --> pdb=" O GLY w 32 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 59 Proline residue: w 47 - end of helix Processing helix chain 'w' and resid 75 through 80 Processing helix chain 'w' and resid 102 through 118 removed outlier: 3.714A pdb=" N GLN w 108 " --> pdb=" O LYS w 104 " (cutoff:3.500A) Processing helix chain 'w' and resid 132 through 148 Processing helix chain 'w' and resid 149 through 154 Processing helix chain 'w' and resid 168 through 179 Processing helix chain 'w' and resid 205 through 218 Processing helix chain 'x' and resid 5 through 10 Processing helix chain 'x' and resid 27 through 46 Processing helix chain 'x' and resid 47 through 49 No H-bonds generated for 'chain 'x' and resid 47 through 49' Processing helix chain 'x' and resid 71 through 77 removed outlier: 3.916A pdb=" N VAL x 75 " --> pdb=" O ARG x 71 " (cutoff:3.500A) Processing helix chain 'x' and resid 80 through 95 Processing helix chain 'x' and resid 107 through 110 Processing helix chain 'x' and resid 111 through 125 Processing helix chain 'x' and resid 128 through 144 Processing helix chain 'x' and resid 155 through 159 removed outlier: 3.596A pdb=" N GLY x 158 " --> pdb=" O ARG x 155 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA x 159 " --> pdb=" O LEU x 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'x' and resid 155 through 159' Processing sheet with id=AA1, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain '1' and resid 8 through 11 removed outlier: 4.482A pdb=" N ILE 1 8 " --> pdb=" O THR 1 22 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N THR 1 22 " --> pdb=" O ILE 1 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 35 through 39 removed outlier: 3.834A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (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 '6' and resid 76 through 78 removed outlier: 5.564A pdb=" N SER 6 76 " --> pdb=" O ILE 6 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain '6' and resid 237 through 238 Processing sheet with id=AA8, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA9, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB1, first strand: chain 'C' and resid 75 through 81 removed outlier: 5.364A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 128 through 130 removed outlier: 3.677A pdb=" N VAL C 164 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ARG C 166 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR C 170 " --> pdb=" O ARG C 166 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 49 through 50 removed outlier: 3.557A pdb=" N VAL D 50 " --> pdb=" O TRP D 80 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TRP D 80 " --> pdb=" O VAL D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.553A pdb=" N GLY D 163 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 121 Processing sheet with id=AB6, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.641A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR F 34 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE F 153 " --> pdb=" O MET F 129 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 8 through 9 removed outlier: 3.636A pdb=" N VAL G 8 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU G 49 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY G 52 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU G 41 " --> pdb=" O GLY G 52 " (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 86 through 87 Processing sheet with id=AC1, first strand: chain 'G' and resid 93 through 98 removed outlier: 3.891A pdb=" N ALA G 96 " --> pdb=" O ASN G 103 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN G 103 " --> pdb=" O ALA G 96 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL G 112 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 123 through 124 removed outlier: 6.227A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'K' and resid 6 through 9 removed outlier: 6.797A pdb=" N LYS K 39 " --> pdb=" O ILE K 21 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL K 23 " --> pdb=" O ILE K 37 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE K 37 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA K 82 " --> pdb=" O VAL K 62 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N CYS K 83 " --> pdb=" O MET K 6 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ASN K 8 " --> pdb=" O CYS K 83 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU K 85 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 68 through 69 removed outlier: 3.552A pdb=" N VAL K 75 " --> pdb=" O VAL P 72 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 74 through 77 Processing sheet with id=AC7, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AC8, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.333A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.980A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE M 73 " --> pdb=" O TYR M 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 33 through 37 Processing sheet with id=AD2, first strand: chain 'O' and resid 47 through 52 removed outlier: 7.103A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER O 52 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE O 35 " --> pdb=" O SER O 52 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N LEU O 26 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'P' and resid 37 through 42 removed outlier: 4.244A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 89 through 90 removed outlier: 4.264A 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 15 removed outlier: 3.656A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 19 through 23 removed outlier: 7.403A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 72 through 78 removed outlier: 3.599A pdb=" N ARG R 78 " --> pdb=" O TYR R 83 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 7 through 10 removed outlier: 4.674A pdb=" N ARG S 8 " --> pdb=" O ILE S 103 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE S 103 " --> pdb=" O ARG S 8 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR S 104 " --> pdb=" O PHE S 75 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS S 73 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (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: 3.707A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.828A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (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 4 through 8 removed outlier: 7.566A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 32 through 34 Processing sheet with id=AE7, first strand: chain 'W' and resid 43 through 45 removed outlier: 6.431A pdb=" N PHE W 44 " --> pdb=" O ILE W 79 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE W 81 " --> pdb=" O PHE W 44 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG W 76 " --> pdb=" O LYS W 71 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'X' and resid 12 through 17 removed outlier: 3.619A pdb=" N ARG X 26 " --> pdb=" O GLY X 14 " (cutoff:3.500A) 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 3 through 7 removed outlier: 3.514A pdb=" N ILE Z 6 " --> pdb=" O VAL Z 35 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'c' and resid 127 through 128 removed outlier: 3.573A pdb=" N ASP c 140 " --> pdb=" O PHE c 181 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 11 through 21 removed outlier: 5.320A pdb=" N GLU d 12 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLY d 39 " --> pdb=" O GLU d 12 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU d 14 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL d 37 " --> pdb=" O LEU d 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA d 16 " --> pdb=" O LEU d 35 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'd' and resid 84 through 87 removed outlier: 6.616A pdb=" N ILE d 105 " --> pdb=" O ALA d 124 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ALA d 126 " --> pdb=" O ILE d 105 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'e' and resid 2 through 3 Processing sheet with id=AF6, first strand: chain 'e' and resid 40 through 51 removed outlier: 5.170A pdb=" N ASP e 41 " --> pdb=" O LEU e 61 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU e 61 " --> pdb=" O ASP e 41 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N HIS e 55 " --> pdb=" O LEU e 47 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG e 86 " --> pdb=" O MET e 9 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'f' and resid 72 through 76 Processing sheet with id=AF8, first strand: chain 'g' and resid 23 through 27 removed outlier: 3.960A pdb=" N ASP g 47 " --> pdb=" O THR g 61 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'g' and resid 73 through 76 Processing sheet with id=AG1, first strand: chain 'g' and resid 73 through 76 removed outlier: 6.162A pdb=" N ILE g 124 " --> pdb=" O SER g 104 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N SER g 104 " --> pdb=" O ILE g 124 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS g 126 " --> pdb=" O VAL g 102 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'h' and resid 10 through 11 removed outlier: 3.688A pdb=" N ARG h 11 " --> pdb=" O SER h 14 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'h' and resid 21 through 22 Processing sheet with id=AG4, first strand: chain 'i' and resid 40 through 51 removed outlier: 6.692A pdb=" N LEU i 73 " --> pdb=" O PRO i 41 " (cutoff:3.500A) removed outlier: 5.369A 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 51 removed outlier: 6.692A pdb=" N LEU i 73 " --> pdb=" O PRO i 41 " (cutoff:3.500A) removed outlier: 5.369A 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: 3.621A pdb=" N GLY j 18 " --> pdb=" O ASN j 80 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU j 81 " --> pdb=" O ASN j 108 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR j 110 " --> pdb=" O LEU j 81 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL j 83 " --> pdb=" O THR j 110 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 38 through 39 Processing sheet with id=AG8, first strand: chain 'k' and resid 38 through 39 removed outlier: 4.868A pdb=" N LYS k 50 " --> pdb=" O ILE k 66 " (cutoff:3.500A) removed outlier: 10.288A pdb=" N TYR k 94 " --> pdb=" O GLU k 61 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR k 63 " --> pdb=" O TYR k 94 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR k 96 " --> pdb=" O THR k 63 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N TYR k 65 " --> pdb=" O THR k 96 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'o' and resid 50 through 51 removed outlier: 3.640A pdb=" N GLU o 34 " --> pdb=" O VAL o 21 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL o 19 " --> pdb=" O VAL o 36 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N PHE o 38 " --> pdb=" O TYR o 17 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N TYR o 17 " --> pdb=" O PHE o 38 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL o 2 " --> pdb=" O THR o 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'p' and resid 6 through 13 removed outlier: 16.617A pdb=" N THR p 6 " --> pdb=" O PHE p 27 " (cutoff:3.500A) removed outlier: 12.867A pdb=" N PHE p 27 " --> pdb=" O THR p 6 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLN p 8 " --> pdb=" O GLU p 25 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N GLU p 25 " --> pdb=" O GLN p 8 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG p 10 " --> pdb=" O ALA p 23 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL p 21 " --> pdb=" O VAL p 12 " (cutoff:3.500A) removed outlier: 9.057A pdb=" N LYS p 70 " --> pdb=" O LYS p 42 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N HIS p 44 " --> pdb=" O LYS p 70 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP p 72 " --> pdb=" O HIS p 44 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER p 71 " --> pdb=" O CYS p 63 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'r' and resid 30 through 31 removed outlier: 6.538A pdb=" N LEU r 30 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N HIS r 51 " --> pdb=" O LEU r 30 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL r 57 " --> pdb=" O VAL r 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'u' and resid 158 through 164 removed outlier: 3.791A pdb=" N VAL u 160 " --> pdb=" O VAL u 171 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'w' and resid 183 through 186 removed outlier: 3.630A pdb=" N ALA w 184 " --> pdb=" O PHE w 197 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE w 199 " --> pdb=" O ALA w 184 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'x' and resid 19 through 21 removed outlier: 6.338A pdb=" N VAL x 65 " --> pdb=" O ASN x 101 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA x 103 " --> pdb=" O VAL x 65 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ILE x 67 " --> pdb=" O ALA x 103 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'x' and resid 164 through 170 removed outlier: 7.083A pdb=" N ASP x 180 " --> pdb=" O LYS x 203 " (cutoff:3.500A) 1763 hydrogen bonds defined for protein. 5052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3673 hydrogen bonds 5820 hydrogen bond angles 0 basepair planarities 1451 basepair parallelities 2417 stacking parallelities Total time for adding SS restraints: 241.38 Time building geometry restraints manager: 60.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 11980 1.29 - 1.43: 70292 1.43 - 1.56: 64970 1.56 - 1.69: 9135 1.69 - 1.83: 262 Bond restraints: 156639 Sorted by residual: bond pdb=" CG PRO E 76 " pdb=" CD PRO E 76 " ideal model delta sigma weight residual 1.503 1.210 0.293 3.40e-02 8.65e+02 7.42e+01 bond pdb=" CA VAL d 55 " pdb=" CB VAL d 55 " ideal model delta sigma weight residual 1.534 1.476 0.058 6.80e-03 2.16e+04 7.34e+01 bond pdb=" C LYS D 114 " pdb=" N GLY D 115 " ideal model delta sigma weight residual 1.331 1.260 0.071 1.46e-02 4.69e+03 2.36e+01 bond pdb=" CA VAL d 55 " pdb=" C VAL d 55 " ideal model delta sigma weight residual 1.520 1.562 -0.042 8.80e-03 1.29e+04 2.29e+01 bond pdb=" CD GLU f 122 " pdb=" OE1 GLU f 122 " ideal model delta sigma weight residual 1.249 1.161 0.088 1.90e-02 2.77e+03 2.16e+01 ... (remaining 156634 not shown) Histogram of bond angle deviations from ideal: 85.17 - 95.58: 6 95.58 - 106.00: 25841 106.00 - 116.42: 112433 116.42 - 126.83: 83062 126.83 - 137.25: 12756 Bond angle restraints: 234098 Sorted by residual: angle pdb=" N PRO E 76 " pdb=" CD PRO E 76 " pdb=" CG PRO E 76 " ideal model delta sigma weight residual 103.20 85.17 18.03 1.50e+00 4.44e-01 1.45e+02 angle pdb=" N VAL h 57 " pdb=" CA VAL h 57 " pdb=" C VAL h 57 " ideal model delta sigma weight residual 113.47 103.94 9.53 1.01e+00 9.80e-01 8.90e+01 angle pdb=" CA PRO 3 45 " pdb=" N PRO 3 45 " pdb=" CD PRO 3 45 " ideal model delta sigma weight residual 112.00 99.52 12.48 1.40e+00 5.10e-01 7.95e+01 angle pdb=" C3' C B1914 " pdb=" O3' C B1914 " pdb=" P U B1915 " ideal model delta sigma weight residual 120.20 108.68 11.52 1.50e+00 4.44e-01 5.89e+01 angle pdb=" CA PRO E 76 " pdb=" N PRO E 76 " pdb=" CD PRO E 76 " ideal model delta sigma weight residual 112.00 101.28 10.72 1.40e+00 5.10e-01 5.86e+01 ... (remaining 234093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 87281 35.91 - 71.82: 11717 71.82 - 107.73: 1248 107.73 - 143.64: 14 143.64 - 179.55: 44 Dihedral angle restraints: 100304 sinusoidal: 83441 harmonic: 16863 Sorted by residual: dihedral pdb=" O4' U B 652 " pdb=" C1' U B 652 " pdb=" N1 U B 652 " pdb=" C2 U B 652 " ideal model delta sinusoidal sigma weight residual 200.00 23.51 176.49 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U B1915 " pdb=" C1' U B1915 " pdb=" N1 U B1915 " pdb=" C2 U B1915 " ideal model delta sinusoidal sigma weight residual -160.00 13.49 -173.49 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U B 202 " pdb=" C1' U B 202 " pdb=" N1 U B 202 " pdb=" C2 U B 202 " ideal model delta sinusoidal sigma weight residual -160.00 0.58 -160.58 1 1.50e+01 4.44e-03 8.29e+01 ... (remaining 100301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 28528 0.108 - 0.215: 1233 0.215 - 0.323: 69 0.323 - 0.431: 30 0.431 - 0.539: 4 Chirality restraints: 29864 Sorted by residual: chirality pdb=" CB VAL h 46 " pdb=" CA VAL h 46 " pdb=" CG1 VAL h 46 " pdb=" CG2 VAL h 46 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.25e+00 chirality pdb=" P U B1911 " pdb=" OP1 U B1911 " pdb=" OP2 U B1911 " pdb=" O5' U B1911 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.43e+00 chirality pdb=" CB THR d 23 " pdb=" CA THR d 23 " pdb=" OG1 THR d 23 " pdb=" CG2 THR d 23 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 6.00e+00 ... (remaining 29861 not shown) Planarity restraints: 12746 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 6 259 " 0.154 5.00e-02 4.00e+02 2.25e-01 8.07e+01 pdb=" N PRO 6 260 " -0.387 5.00e-02 4.00e+02 pdb=" CA PRO 6 260 " 0.140 5.00e-02 4.00e+02 pdb=" CD PRO 6 260 " 0.092 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 6 " 0.104 5.00e-02 4.00e+02 1.52e-01 3.70e+01 pdb=" N PRO G 7 " -0.263 5.00e-02 4.00e+02 pdb=" CA PRO G 7 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO G 7 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE U 72 " -0.028 2.00e-02 2.50e+03 3.30e-02 1.91e+01 pdb=" CG PHE U 72 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE U 72 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE U 72 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE U 72 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE U 72 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE U 72 " -0.001 2.00e-02 2.50e+03 ... (remaining 12743 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 18970 2.74 - 3.28: 119114 3.28 - 3.82: 304592 3.82 - 4.36: 365079 4.36 - 4.90: 495928 Nonbonded interactions: 1303683 Sorted by model distance: nonbonded pdb=" NH1 ARG c 187 " pdb=" OE1 GLU c 196 " model vdw 2.203 2.520 nonbonded pdb=" O2' A B 526 " pdb=" O2 C B2043 " model vdw 2.212 2.440 nonbonded pdb=" O2' G v1316 " pdb=" OP2 A v1318 " model vdw 2.214 2.440 nonbonded pdb=" O2' C B 239 " pdb=" O2' G B 622 " model vdw 2.217 2.440 nonbonded pdb=" O2' C B2258 " pdb=" OP2 C B2427 " model vdw 2.221 2.440 ... (remaining 1303678 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: 1.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 13.320 Check model and map are aligned: 1.530 Set scattering table: 0.960 Process input model: 496.490 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 520.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3701 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.293 156639 Z= 0.395 Angle : 0.953 26.972 234098 Z= 0.471 Chirality : 0.051 0.539 29864 Planarity : 0.009 0.225 12746 Dihedral : 24.185 179.548 89422 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.16 % Favored : 93.79 % Rotamer: Outliers : 0.76 % Allowed : 31.53 % Favored : 67.71 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.51 % 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: -2.51 (0.09), residues: 5816 helix: -1.51 (0.10), residues: 1898 sheet: -0.34 (0.18), residues: 777 loop : -2.16 (0.09), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP w 22 HIS 0.020 0.003 HIS X 33 PHE 0.076 0.004 PHE U 72 TYR 0.062 0.003 TYR Q 31 ARG 0.031 0.001 ARG N 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 488 time to evaluate : 5.664 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: O 76 LYS cc_start: 0.6622 (ptmm) cc_final: 0.6378 (ptmm) REVERT: Y 1 MET cc_start: 0.0937 (mmt) cc_final: 0.0562 (mmt) REVERT: r 65 MET cc_start: 0.1432 (mtt) cc_final: -0.0147 (ptp) REVERT: x 68 HIS cc_start: 0.5949 (m-70) cc_final: 0.5407 (m90) REVERT: x 146 LYS cc_start: 0.7485 (mmtp) cc_final: 0.7174 (mmtp) outliers start: 37 outliers final: 12 residues processed: 518 average time/residue: 1.3523 time to fit residues: 1204.6281 Evaluate side-chains 432 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 420 time to evaluate : 5.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain Q residue 91 ARG Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain d residue 88 HIS Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain g residue 100 ILE Chi-restraints excluded: chain r residue 73 PHE Chi-restraints excluded: chain w residue 14 HIS Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain x residue 7 ASN Chi-restraints excluded: chain x residue 26 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 863 optimal weight: 6.9990 chunk 775 optimal weight: 5.9990 chunk 430 optimal weight: 1.9990 chunk 264 optimal weight: 9.9990 chunk 523 optimal weight: 0.0670 chunk 414 optimal weight: 10.0000 chunk 801 optimal weight: 0.9990 chunk 310 optimal weight: 6.9990 chunk 487 optimal weight: 0.2980 chunk 596 optimal weight: 5.9990 chunk 928 optimal weight: 9.9990 overall best weight: 1.8724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 16 HIS 3 23 HIS 3 42 HIS 6 173 GLN C 36 ASN C 43 ASN C 85 ASN C 89 ASN C 152 GLN C 196 ASN C 225 ASN F 36 ASN F 62 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN M 45 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS Q 71 ASN ** R 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS V 88 HIS ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 41 HIS c 119 HIS c 130 ASN ** d 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN e 3 HIS e 11 HIS ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN f 121 ASN ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 125 GLN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN l 99 GLN m 60 GLN ** q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 ASN w 119 GLN ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 122 GLN x 175 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5728 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.355 156639 Z= 0.314 Angle : 0.870 14.811 234098 Z= 0.430 Chirality : 0.046 0.532 29864 Planarity : 0.008 0.127 12746 Dihedral : 24.137 179.949 77750 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 6.46 % Allowed : 28.61 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.92 (0.10), residues: 5816 helix: -0.39 (0.11), residues: 1885 sheet: -0.78 (0.17), residues: 794 loop : -2.02 (0.10), residues: 3137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP F 96 HIS 0.017 0.003 HIS P 76 PHE 0.040 0.003 PHE M 130 TYR 0.041 0.003 TYR Q 46 ARG 0.039 0.001 ARG k 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 805 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 491 time to evaluate : 5.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 1 MET cc_start: 0.0859 (mtm) cc_final: 0.0049 (ttm) REVERT: 6 92 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5679 (mp) REVERT: 6 261 HIS cc_start: 0.1489 (OUTLIER) cc_final: 0.0017 (p-80) REVERT: C 264 LYS cc_start: 0.4262 (OUTLIER) cc_final: 0.3701 (pttt) REVERT: D 13 ARG cc_start: 0.4650 (tpt170) cc_final: 0.2572 (tpt170) REVERT: E 62 GLN cc_start: 0.3560 (OUTLIER) cc_final: 0.2971 (tt0) REVERT: G 74 MET cc_start: 0.6386 (ptp) cc_final: 0.6112 (ptp) REVERT: K 31 TYR cc_start: 0.4973 (t80) cc_final: 0.3761 (t80) REVERT: M 91 TYR cc_start: 0.5642 (p90) cc_final: 0.5403 (p90) REVERT: M 136 MET cc_start: -0.2287 (OUTLIER) cc_final: -0.3016 (ptt) REVERT: N 8 ARG cc_start: 0.5704 (OUTLIER) cc_final: 0.5386 (mtt180) REVERT: N 10 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.6042 (mt) REVERT: S 7 HIS cc_start: 0.6290 (OUTLIER) cc_final: 0.5615 (t-90) REVERT: T 1 MET cc_start: 0.3551 (tpp) cc_final: 0.3067 (tpp) REVERT: U 65 GLN cc_start: 0.6334 (tp40) cc_final: 0.6074 (mm-40) REVERT: U 67 SER cc_start: 0.5506 (OUTLIER) cc_final: 0.5272 (p) REVERT: Y 1 MET cc_start: 0.0919 (mmt) cc_final: 0.0573 (mmt) REVERT: Y 27 ASN cc_start: 0.5929 (OUTLIER) cc_final: 0.5584 (p0) REVERT: Z 50 VAL cc_start: 0.5700 (t) cc_final: 0.5356 (t) REVERT: Z 53 MET cc_start: 0.4597 (mtt) cc_final: 0.3479 (ttp) REVERT: c 13 ARG cc_start: 0.7417 (tpp-160) cc_final: 0.7089 (tpp-160) REVERT: d 67 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6686 (mtt90) REVERT: e 60 VAL cc_start: 0.6372 (OUTLIER) cc_final: 0.6131 (t) REVERT: e 77 THR cc_start: 0.7171 (m) cc_final: 0.6909 (t) REVERT: f 48 THR cc_start: 0.0282 (OUTLIER) cc_final: -0.0063 (m) REVERT: g 78 SER cc_start: 0.7804 (t) cc_final: 0.7520 (p) REVERT: h 38 PHE cc_start: 0.0747 (OUTLIER) cc_final: -0.1225 (p90) REVERT: k 110 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.7035 (mmtp) REVERT: m 43 ASN cc_start: 0.2128 (OUTLIER) cc_final: 0.1748 (p0) REVERT: m 65 ARG cc_start: 0.7493 (tpp80) cc_final: 0.7216 (ttm170) REVERT: p 16 MET cc_start: 0.3528 (mmt) cc_final: 0.2825 (mmt) REVERT: r 65 MET cc_start: 0.1680 (mtt) cc_final: 0.0932 (mtt) REVERT: x 19 SER cc_start: 0.7323 (m) cc_final: 0.6979 (p) REVERT: x 65 VAL cc_start: 0.7737 (OUTLIER) cc_final: 0.7494 (t) REVERT: x 184 ASN cc_start: 0.7790 (t0) cc_final: 0.7542 (t0) REVERT: x 187 GLU cc_start: 0.6160 (OUTLIER) cc_final: 0.5946 (tp30) outliers start: 314 outliers final: 88 residues processed: 742 average time/residue: 1.3219 time to fit residues: 1701.9782 Evaluate side-chains 557 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 451 time to evaluate : 5.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 92 LEU Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain 6 residue 180 ARG Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 221 ARG Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 139 VAL Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain Q residue 71 ASN Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 67 SER Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain W residue 50 VAL Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain c residue 123 MET Chi-restraints excluded: chain c residue 131 ILE Chi-restraints excluded: chain c residue 177 MET Chi-restraints excluded: chain c residue 203 TYR Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 136 VAL Chi-restraints excluded: chain d residue 151 MET Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 63 ASN Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 80 PHE Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 71 VAL Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 71 ILE Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain k residue 110 LYS Chi-restraints excluded: chain k residue 118 VAL Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 51 GLN Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain n residue 5 GLU Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 50 VAL Chi-restraints excluded: chain r residue 73 PHE Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain w residue 31 PHE Chi-restraints excluded: chain w residue 119 GLN Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 188 THR Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 187 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 516 optimal weight: 0.9990 chunk 288 optimal weight: 110.0000 chunk 773 optimal weight: 1.9990 chunk 632 optimal weight: 4.9990 chunk 256 optimal weight: 5.9990 chunk 930 optimal weight: 9.9990 chunk 1005 optimal weight: 4.9990 chunk 828 optimal weight: 30.0000 chunk 922 optimal weight: 6.9990 chunk 317 optimal weight: 8.9990 chunk 746 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 5 ASN 0 37 HIS 1 45 HIS 3 42 HIS 6 118 HIS ** 6 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 ASN C 89 ASN C 142 ASN C 152 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN U 44 HIS W 75 ASN c 73 ASN c 135 GLN ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 21 HIS j 37 GLN ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 26 ASN q 51 GLN r 51 HIS ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 35 ASN ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.9484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.170 156639 Z= 0.406 Angle : 0.875 15.594 234098 Z= 0.431 Chirality : 0.048 0.378 29864 Planarity : 0.007 0.139 12746 Dihedral : 24.084 179.668 77732 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.53 % Favored : 93.40 % Rotamer: Outliers : 5.97 % Allowed : 29.18 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.10), residues: 5816 helix: -0.36 (0.11), residues: 1893 sheet: -0.65 (0.18), residues: 801 loop : -2.09 (0.10), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP r 33 HIS 0.012 0.002 HIS V 88 PHE 0.027 0.003 PHE d 47 TYR 0.039 0.003 TYR e 59 ARG 0.016 0.001 ARG Q 57 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 484 time to evaluate : 5.804 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: 0 36 LYS cc_start: 0.7393 (OUTLIER) cc_final: 0.7088 (mttm) REVERT: 6 1 MET cc_start: 0.0875 (mtm) cc_final: 0.0121 (ttm) REVERT: 6 222 VAL cc_start: 0.4648 (t) cc_final: 0.3676 (m) REVERT: 6 235 THR cc_start: 0.6836 (OUTLIER) cc_final: 0.6605 (p) REVERT: 6 261 HIS cc_start: 0.1654 (OUTLIER) cc_final: -0.0126 (p-80) REVERT: C 33 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (mp) REVERT: C 102 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7349 (m-80) REVERT: C 224 MET cc_start: 0.8240 (tpp) cc_final: 0.7974 (mmt) REVERT: D 13 ARG cc_start: 0.3959 (tpt170) cc_final: 0.1939 (tpt90) REVERT: D 121 THR cc_start: 0.7766 (OUTLIER) cc_final: 0.7313 (p) REVERT: J 23 LYS cc_start: 0.6786 (ptmt) cc_final: 0.6582 (ptpt) REVERT: J 39 LYS cc_start: 0.7839 (mtpp) cc_final: 0.7634 (mmmm) REVERT: J 73 VAL cc_start: 0.8097 (p) cc_final: 0.7765 (t) REVERT: J 81 ILE cc_start: 0.6767 (OUTLIER) cc_final: 0.6556 (pt) REVERT: J 86 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7660 (pt0) REVERT: K 12 ASN cc_start: 0.5442 (OUTLIER) cc_final: 0.5230 (p0) REVERT: L 39 LYS cc_start: 0.7896 (ttmm) cc_final: 0.7680 (ttmt) REVERT: M 34 LYS cc_start: 0.6993 (OUTLIER) cc_final: 0.4923 (tttp) REVERT: M 53 MET cc_start: 0.7069 (mmm) cc_final: 0.6515 (mtt) REVERT: M 80 VAL cc_start: 0.7396 (p) cc_final: 0.7084 (t) REVERT: M 136 MET cc_start: -0.2375 (OUTLIER) cc_final: -0.2870 (ptt) REVERT: O 16 ARG cc_start: 0.5550 (mtm110) cc_final: 0.4270 (mtm180) REVERT: O 45 SER cc_start: 0.6503 (OUTLIER) cc_final: 0.6295 (t) REVERT: O 100 HIS cc_start: 0.4770 (t-90) cc_final: 0.4323 (t-90) REVERT: Q 4 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7588 (mtpt) REVERT: R 10 LYS cc_start: 0.8421 (ptpp) cc_final: 0.8191 (ptpp) REVERT: S 7 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7364 (t70) REVERT: S 85 ILE cc_start: 0.7682 (OUTLIER) cc_final: 0.7363 (tp) REVERT: V 48 MET cc_start: 0.6716 (mmm) cc_final: 0.6161 (mmm) REVERT: W 23 LYS cc_start: 0.3162 (OUTLIER) cc_final: 0.2462 (ptpp) REVERT: X 42 GLU cc_start: 0.6690 (mm-30) cc_final: 0.6307 (mm-30) REVERT: X 55 MET cc_start: 0.7347 (mtm) cc_final: 0.7113 (mtm) REVERT: Y 1 MET cc_start: 0.1021 (mmt) cc_final: 0.0765 (mmt) REVERT: c 115 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: c 120 LYS cc_start: 0.7366 (OUTLIER) cc_final: 0.7103 (mtmm) REVERT: c 136 VAL cc_start: 0.8120 (m) cc_final: 0.7739 (t) REVERT: c 146 GLU cc_start: 0.6015 (OUTLIER) cc_final: 0.5767 (tm-30) REVERT: c 201 GLU cc_start: 0.6279 (mt-10) cc_final: 0.6029 (mt-10) REVERT: d 9 GLU cc_start: 0.3121 (OUTLIER) cc_final: 0.2737 (pp20) REVERT: d 67 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6287 (mpt-90) REVERT: g 26 MET cc_start: 0.8112 (ptm) cc_final: 0.7806 (ptp) REVERT: h 38 PHE cc_start: 0.1837 (OUTLIER) cc_final: -0.0108 (p90) REVERT: h 45 MET cc_start: 0.3052 (tpt) cc_final: 0.2817 (tpt) REVERT: k 8 ARG cc_start: 0.6373 (OUTLIER) cc_final: 0.5840 (mpp80) REVERT: k 65 TYR cc_start: 0.8040 (t80) cc_final: 0.7828 (t80) REVERT: l 18 LEU cc_start: 0.5167 (OUTLIER) cc_final: 0.4856 (mt) REVERT: l 94 LEU cc_start: -0.0099 (OUTLIER) cc_final: -0.0533 (mt) REVERT: m 65 ARG cc_start: 0.7698 (tpp80) cc_final: 0.7326 (ttm170) REVERT: n 39 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7146 (mm110) REVERT: n 68 TYR cc_start: 0.7875 (t80) cc_final: 0.7213 (t80) REVERT: q 64 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7972 (mp) REVERT: r 65 MET cc_start: 0.1178 (mtt) cc_final: 0.0775 (mtt) REVERT: w 35 ASN cc_start: 0.5279 (OUTLIER) cc_final: 0.5017 (p0) REVERT: x 19 SER cc_start: 0.7566 (m) cc_final: 0.7323 (p) REVERT: x 143 LEU cc_start: 0.7157 (mt) cc_final: 0.6827 (mt) REVERT: x 174 LEU cc_start: 0.8058 (mt) cc_final: 0.7841 (mt) outliers start: 290 outliers final: 109 residues processed: 725 average time/residue: 1.3621 time to fit residues: 1685.8804 Evaluate side-chains 591 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 454 time to evaluate : 5.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 24 MET Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 180 ARG Chi-restraints excluded: chain 6 residue 221 ARG Chi-restraints excluded: chain 6 residue 235 THR Chi-restraints excluded: chain 6 residue 238 ARG Chi-restraints excluded: chain 6 residue 247 THR Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain 6 residue 264 VAL Chi-restraints excluded: chain 6 residue 370 LEU Chi-restraints excluded: chain 6 residue 379 LEU Chi-restraints excluded: chain 6 residue 386 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 161 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain K residue 12 ASN Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 34 LYS Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain O residue 8 ILE Chi-restraints excluded: chain O residue 45 SER Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain c residue 115 GLN Chi-restraints excluded: chain c residue 120 LYS Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 135 GLN Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain c residue 177 MET Chi-restraints excluded: chain d residue 9 GLU Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 121 ASN Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 62 MET Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain f residue 114 SER Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 59 LYS Chi-restraints excluded: chain h residue 71 ILE Chi-restraints excluded: chain h residue 92 SER Chi-restraints excluded: chain h residue 108 ARG Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 18 ILE Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain k residue 8 ARG Chi-restraints excluded: chain l residue 18 LEU Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 74 MET Chi-restraints excluded: chain l residue 80 MET Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain n residue 12 SER Chi-restraints excluded: chain n residue 39 GLN Chi-restraints excluded: chain n residue 46 LYS Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain q residue 64 LEU Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain w residue 35 ASN Chi-restraints excluded: chain w residue 101 THR Chi-restraints excluded: chain w residue 119 GLN Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 173 LYS Chi-restraints excluded: chain w residue 188 THR Chi-restraints excluded: chain x residue 42 LEU Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 168 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 919 optimal weight: 5.9990 chunk 699 optimal weight: 0.9980 chunk 483 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 444 optimal weight: 50.0000 chunk 624 optimal weight: 0.9980 chunk 934 optimal weight: 5.9990 chunk 988 optimal weight: 7.9990 chunk 487 optimal weight: 1.9990 chunk 885 optimal weight: 4.9990 chunk 266 optimal weight: 10.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN 6 118 HIS C 44 ASN C 225 ASN C 250 GLN D 67 HIS D 148 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS M 22 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 36 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 58 GLN c 73 ASN c 130 ASN ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 GLN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 3 GLN ** n 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 ASN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 176 ASN ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 1.0433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 156639 Z= 0.270 Angle : 0.631 11.331 234098 Z= 0.321 Chirality : 0.039 0.351 29864 Planarity : 0.005 0.091 12746 Dihedral : 23.766 179.985 77728 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.98 % Rotamer: Outliers : 5.47 % Allowed : 29.68 % Favored : 64.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.51 (0.10), residues: 5816 helix: 0.28 (0.12), residues: 1891 sheet: -0.44 (0.19), residues: 738 loop : -2.02 (0.10), residues: 3187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP r 33 HIS 0.010 0.001 HIS S 102 PHE 0.028 0.002 PHE 6 214 TYR 0.023 0.002 TYR e 59 ARG 0.013 0.001 ARG Y 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 488 time to evaluate : 5.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 10 SER cc_start: 0.7945 (t) cc_final: 0.7636 (p) REVERT: 0 36 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.7095 (mttm) REVERT: 0 38 LEU cc_start: 0.8215 (mt) cc_final: 0.7969 (mt) REVERT: 3 43 LEU cc_start: 0.8415 (mt) cc_final: 0.8186 (mt) REVERT: 6 1 MET cc_start: 0.0936 (mtm) cc_final: 0.0184 (ttm) REVERT: 6 175 GLN cc_start: 0.4432 (OUTLIER) cc_final: 0.3897 (pp30) REVERT: 6 222 VAL cc_start: 0.4687 (t) cc_final: 0.3963 (m) REVERT: 6 235 THR cc_start: 0.6849 (m) cc_final: 0.6648 (p) REVERT: 6 261 HIS cc_start: 0.1259 (OUTLIER) cc_final: -0.0370 (p-80) REVERT: C 33 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8043 (mp) REVERT: C 102 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7521 (m-80) REVERT: C 252 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7770 (mmtp) REVERT: D 13 ARG cc_start: 0.3570 (tpt170) cc_final: 0.1424 (tpt90) REVERT: D 104 VAL cc_start: -0.2131 (OUTLIER) cc_final: -0.2408 (m) REVERT: D 148 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.7118 (mt0) REVERT: D 208 LYS cc_start: 0.3655 (OUTLIER) cc_final: 0.3400 (tppt) REVERT: J 34 ARG cc_start: 0.8077 (ttp80) cc_final: 0.7591 (ttp-170) REVERT: M 20 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6781 (mt) REVERT: M 136 MET cc_start: -0.2496 (OUTLIER) cc_final: -0.2714 (ptt) REVERT: N 24 MET cc_start: 0.6986 (ttm) cc_final: 0.6783 (ttm) REVERT: N 32 GLU cc_start: 0.6117 (mm-30) cc_final: 0.5882 (mt-10) REVERT: O 16 ARG cc_start: 0.6143 (mtm110) cc_final: 0.5758 (mtp180) REVERT: P 74 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7579 (mm-40) REVERT: Q 5 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7259 (ptt180) REVERT: Q 108 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7214 (mt) REVERT: S 7 HIS cc_start: 0.8171 (OUTLIER) cc_final: 0.7938 (t-170) REVERT: S 85 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7234 (tp) REVERT: T 91 GLN cc_start: 0.1073 (OUTLIER) cc_final: 0.0166 (pt0) REVERT: U 53 GLN cc_start: -0.0247 (OUTLIER) cc_final: -0.2204 (tt0) REVERT: W 23 LYS cc_start: 0.3333 (OUTLIER) cc_final: 0.3011 (ptpp) REVERT: X 55 MET cc_start: 0.7465 (OUTLIER) cc_final: 0.7161 (mtm) REVERT: X 60 LYS cc_start: 0.7992 (tttp) cc_final: 0.7714 (tttt) REVERT: Y 1 MET cc_start: 0.0991 (mmt) cc_final: 0.0728 (mmt) REVERT: Y 27 ASN cc_start: 0.5991 (OUTLIER) cc_final: 0.5734 (p0) REVERT: c 77 GLU cc_start: 0.6006 (tp30) cc_final: 0.5789 (tp30) REVERT: c 136 VAL cc_start: 0.8003 (m) cc_final: 0.7586 (t) REVERT: c 201 GLU cc_start: 0.6291 (mt-10) cc_final: 0.6005 (mt-10) REVERT: d 67 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6735 (mpt-90) REVERT: f 48 THR cc_start: 0.1080 (OUTLIER) cc_final: 0.0826 (m) REVERT: g 26 MET cc_start: 0.8155 (ptm) cc_final: 0.7888 (ptp) REVERT: h 38 PHE cc_start: 0.1984 (OUTLIER) cc_final: -0.0009 (p90) REVERT: h 56 MET cc_start: -0.1036 (tpt) cc_final: -0.2315 (tpt) REVERT: h 121 ARG cc_start: 0.7090 (mmt90) cc_final: 0.6829 (mtt90) REVERT: i 47 GLU cc_start: 0.5549 (OUTLIER) cc_final: 0.5257 (mt-10) REVERT: i 88 MET cc_start: 0.3751 (OUTLIER) cc_final: 0.3491 (mpt) REVERT: j 112 VAL cc_start: 0.7542 (p) cc_final: 0.7215 (t) REVERT: k 8 ARG cc_start: 0.6346 (OUTLIER) cc_final: 0.5820 (mpp80) REVERT: k 28 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6520 (mp10) REVERT: k 54 VAL cc_start: 0.7042 (p) cc_final: 0.6700 (t) REVERT: k 80 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7225 (mp) REVERT: l 94 LEU cc_start: 0.0073 (OUTLIER) cc_final: -0.0440 (mt) REVERT: m 65 ARG cc_start: 0.7672 (tpp80) cc_final: 0.7323 (ttm170) REVERT: o 9 HIS cc_start: 0.7119 (OUTLIER) cc_final: 0.6187 (m170) REVERT: r 65 MET cc_start: 0.1023 (mtt) cc_final: 0.0815 (mtt) REVERT: w 20 ARG cc_start: 0.3621 (OUTLIER) cc_final: 0.2521 (mmp-170) REVERT: x 143 LEU cc_start: 0.7158 (mt) cc_final: 0.6792 (mt) REVERT: x 187 GLU cc_start: 0.6249 (OUTLIER) cc_final: 0.5919 (tp30) outliers start: 266 outliers final: 124 residues processed: 701 average time/residue: 1.3165 time to fit residues: 1570.5616 Evaluate side-chains 618 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 463 time to evaluate : 5.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 22 MET Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 33 LEU Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain 6 residue 175 GLN Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain 6 residue 394 MET Chi-restraints excluded: chain 6 residue 411 TRP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 45 ASN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 148 GLN Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 22 GLN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 18 GLN Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 91 GLN Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 121 ASN Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 51 ILE Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 48 THR Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain f residue 114 SER Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain h residue 4 GLN Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain i residue 88 MET Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain k residue 8 ARG Chi-restraints excluded: chain k residue 28 GLN Chi-restraints excluded: chain k residue 80 LEU Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain l residue 51 GLN Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain o residue 9 HIS Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 61 VAL Chi-restraints excluded: chain p residue 20 ILE Chi-restraints excluded: chain p residue 61 ARG Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain w residue 20 ARG Chi-restraints excluded: chain w residue 31 PHE Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 160 LEU Chi-restraints excluded: chain w residue 162 VAL Chi-restraints excluded: chain w residue 173 LYS Chi-restraints excluded: chain w residue 188 THR Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain x residue 187 GLU Chi-restraints excluded: chain x residue 201 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 823 optimal weight: 4.9990 chunk 561 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 736 optimal weight: 0.7980 chunk 407 optimal weight: 5.9990 chunk 843 optimal weight: 7.9990 chunk 683 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 504 optimal weight: 3.9990 chunk 887 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN 4 35 GLN 4 37 GLN ** 6 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 113 GLN 6 387 GLN C 44 ASN D 126 ASN D 134 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS Q 19 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS T 92 ASN ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN Y 27 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN ** g 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 125 GLN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 74 HIS ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 1.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 156639 Z= 0.264 Angle : 0.626 9.980 234098 Z= 0.319 Chirality : 0.038 0.323 29864 Planarity : 0.005 0.066 12746 Dihedral : 23.725 179.903 77728 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.96 % Favored : 92.98 % Rotamer: Outliers : 5.54 % Allowed : 29.64 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.10), residues: 5816 helix: 0.39 (0.12), residues: 1882 sheet: -0.47 (0.19), residues: 751 loop : -1.95 (0.10), residues: 3183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP T 80 HIS 0.008 0.001 HIS O 29 PHE 0.019 0.002 PHE e 8 TYR 0.019 0.002 TYR e 59 ARG 0.010 0.001 ARG c 110 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 456 time to evaluate : 5.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 10 SER cc_start: 0.7928 (t) cc_final: 0.7614 (p) REVERT: 0 36 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7142 (mttm) REVERT: 0 38 LEU cc_start: 0.8192 (mt) cc_final: 0.7953 (mt) REVERT: 4 35 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: 6 1 MET cc_start: 0.1200 (mtm) cc_final: 0.0494 (ttm) REVERT: 6 175 GLN cc_start: 0.4502 (OUTLIER) cc_final: 0.3957 (pp30) REVERT: 6 222 VAL cc_start: 0.5090 (t) cc_final: 0.4337 (m) REVERT: 6 261 HIS cc_start: 0.1042 (OUTLIER) cc_final: -0.0516 (p-80) REVERT: C 33 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8034 (mp) REVERT: C 102 TYR cc_start: 0.7698 (OUTLIER) cc_final: 0.7476 (m-80) REVERT: C 145 MET cc_start: 0.5895 (mpp) cc_final: 0.5573 (mtt) REVERT: C 203 VAL cc_start: 0.7383 (OUTLIER) cc_final: 0.7089 (t) REVERT: C 252 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7710 (mptt) REVERT: D 15 PHE cc_start: 0.2126 (OUTLIER) cc_final: 0.1533 (t80) REVERT: D 104 VAL cc_start: -0.2135 (OUTLIER) cc_final: -0.2402 (m) REVERT: D 175 LEU cc_start: 0.2296 (OUTLIER) cc_final: 0.2033 (pp) REVERT: E 62 GLN cc_start: 0.3661 (OUTLIER) cc_final: 0.3457 (tt0) REVERT: E 112 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7824 (mp) REVERT: E 141 MET cc_start: 0.6535 (mpp) cc_final: 0.5742 (mpp) REVERT: F 37 MET cc_start: 0.0211 (mtm) cc_final: -0.0016 (mtm) REVERT: J 81 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6584 (pt) REVERT: K 6 MET cc_start: 0.7331 (mmm) cc_final: 0.7101 (mmm) REVERT: K 70 ARG cc_start: 0.7433 (mmt-90) cc_final: 0.7047 (mmt-90) REVERT: M 118 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6779 (mmmm) REVERT: N 8 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6981 (ptt180) REVERT: N 24 MET cc_start: 0.6999 (ttm) cc_final: 0.6768 (ttm) REVERT: N 30 ARG cc_start: 0.7477 (ttm170) cc_final: 0.7273 (ttm170) REVERT: O 47 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7538 (p) REVERT: P 74 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7679 (mm-40) REVERT: Q 5 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7154 (ptt180) REVERT: S 85 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7350 (tp) REVERT: W 23 LYS cc_start: 0.4482 (OUTLIER) cc_final: 0.4233 (ptpp) REVERT: X 55 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7273 (mtm) REVERT: Y 1 MET cc_start: 0.0905 (mmt) cc_final: 0.0676 (mmt) REVERT: Y 56 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.8030 (mt) REVERT: c 77 GLU cc_start: 0.5956 (tp30) cc_final: 0.5733 (tp30) REVERT: c 171 GLU cc_start: 0.5891 (mp0) cc_final: 0.5326 (mp0) REVERT: c 201 GLU cc_start: 0.6234 (mt-10) cc_final: 0.5989 (mt-10) REVERT: d 67 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6719 (mpt-90) REVERT: f 143 MET cc_start: 0.3292 (mmt) cc_final: 0.2680 (mmm) REVERT: g 26 MET cc_start: 0.8222 (ptm) cc_final: 0.8000 (ptp) REVERT: g 37 ASN cc_start: 0.7889 (t0) cc_final: 0.7597 (t0) REVERT: h 38 PHE cc_start: 0.2206 (OUTLIER) cc_final: 0.0129 (p90) REVERT: h 45 MET cc_start: 0.3275 (tpt) cc_final: 0.3067 (tpt) REVERT: h 56 MET cc_start: -0.0888 (tpt) cc_final: -0.2283 (tpt) REVERT: i 47 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5257 (mt-10) REVERT: i 88 MET cc_start: 0.4055 (mpt) cc_final: 0.3232 (mpt) REVERT: k 8 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.5754 (mpp80) REVERT: k 54 VAL cc_start: 0.7138 (OUTLIER) cc_final: 0.6854 (t) REVERT: k 80 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7322 (mp) REVERT: l 94 LEU cc_start: 0.0066 (OUTLIER) cc_final: -0.0506 (mt) REVERT: m 65 ARG cc_start: 0.7652 (tpp80) cc_final: 0.7304 (ttm170) REVERT: n 9 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7568 (ttpp) REVERT: p 61 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6932 (ptt-90) REVERT: t 53 LYS cc_start: -0.0695 (OUTLIER) cc_final: -0.1726 (mmtm) REVERT: w 178 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7140 (mp) REVERT: w 199 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7235 (tt) REVERT: x 35 ASP cc_start: 0.6823 (m-30) cc_final: 0.6438 (m-30) REVERT: x 143 LEU cc_start: 0.7186 (mt) cc_final: 0.6838 (mt) REVERT: x 174 LEU cc_start: 0.8130 (mt) cc_final: 0.7930 (mt) REVERT: x 187 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.6019 (tp30) outliers start: 269 outliers final: 140 residues processed: 661 average time/residue: 1.3591 time to fit residues: 1523.3667 Evaluate side-chains 617 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 443 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 2 residue 1 MET Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 60 CYS Chi-restraints excluded: chain 4 residue 35 GLN Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 6 residue 45 ILE Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain 6 residue 175 GLN Chi-restraints excluded: chain 6 residue 238 ARG Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain 6 residue 264 VAL Chi-restraints excluded: chain 6 residue 379 LEU Chi-restraints excluded: chain 6 residue 394 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 118 LYS Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 133 SER Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 MET Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 121 ASN Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 62 MET Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 57 GLU Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 8 THR Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 80 HIS Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain j residue 14 GLN Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain j residue 124 LYS Chi-restraints excluded: chain k residue 8 ARG Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 80 LEU Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain l residue 13 HIS Chi-restraints excluded: chain l residue 51 GLN Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 74 MET Chi-restraints excluded: chain l residue 94 LEU Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain n residue 7 THR Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 61 ARG Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain t residue 53 LYS Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 160 LEU Chi-restraints excluded: chain w residue 162 VAL Chi-restraints excluded: chain w residue 173 LYS Chi-restraints excluded: chain w residue 178 LEU Chi-restraints excluded: chain w residue 188 THR Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 105 VAL Chi-restraints excluded: chain x residue 187 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 332 optimal weight: 7.9990 chunk 890 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 580 optimal weight: 0.9990 chunk 244 optimal weight: 8.9990 chunk 989 optimal weight: 9.9990 chunk 821 optimal weight: 0.3980 chunk 458 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 519 optimal weight: 0.6980 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN ** 6 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 113 GLN ** 6 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS C 199 HIS J 58 ASN K 4 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 45 GLN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS P 76 HIS ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS U 68 ASN ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 36 GLN c 73 ASN ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN h 3 ASN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 34 GLN q 51 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 1.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 156639 Z= 0.301 Angle : 0.659 10.893 234098 Z= 0.334 Chirality : 0.040 0.365 29864 Planarity : 0.005 0.067 12746 Dihedral : 23.724 179.634 77727 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.07 % Favored : 92.86 % Rotamer: Outliers : 5.25 % Allowed : 30.17 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.10), residues: 5816 helix: 0.32 (0.12), residues: 1893 sheet: -0.42 (0.19), residues: 733 loop : -2.01 (0.10), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP r 33 HIS 0.009 0.002 HIS S 102 PHE 0.025 0.002 PHE j 26 TYR 0.022 0.002 TYR Q 31 ARG 0.014 0.001 ARG 4 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 474 time to evaluate : 8.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 10 SER cc_start: 0.7956 (t) cc_final: 0.7601 (p) REVERT: 0 36 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7240 (mttm) REVERT: 6 1 MET cc_start: 0.1208 (mtm) cc_final: 0.0512 (ttm) REVERT: 6 175 GLN cc_start: 0.4535 (OUTLIER) cc_final: 0.4007 (pp30) REVERT: 6 261 HIS cc_start: 0.0831 (OUTLIER) cc_final: -0.0753 (p-80) REVERT: C 102 TYR cc_start: 0.7655 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: C 145 MET cc_start: 0.6056 (mpp) cc_final: 0.5766 (mtt) REVERT: C 261 ARG cc_start: 0.7926 (ttp80) cc_final: 0.7724 (ttp80) REVERT: D 104 VAL cc_start: -0.2228 (OUTLIER) cc_final: -0.2505 (m) REVERT: E 102 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7730 (mtt180) REVERT: E 117 ARG cc_start: 0.7627 (mtp180) cc_final: 0.7402 (mtp180) REVERT: E 141 MET cc_start: 0.6459 (mpp) cc_final: 0.5615 (mpp) REVERT: E 196 VAL cc_start: 0.7923 (p) cc_final: 0.7656 (t) REVERT: G 43 LYS cc_start: 0.5400 (OUTLIER) cc_final: 0.4970 (pttm) REVERT: J 81 ILE cc_start: 0.7131 (OUTLIER) cc_final: 0.6770 (pt) REVERT: J 102 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6864 (mt-10) REVERT: M 34 LYS cc_start: 0.6196 (OUTLIER) cc_final: 0.3771 (tttp) REVERT: O 17 LYS cc_start: 0.7757 (tppt) cc_final: 0.7465 (tptt) REVERT: O 47 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7565 (p) REVERT: Q 5 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7142 (ptt180) REVERT: S 25 ARG cc_start: 0.7759 (ttm110) cc_final: 0.7488 (ttm110) REVERT: S 85 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7407 (tp) REVERT: U 53 GLN cc_start: -0.0643 (OUTLIER) cc_final: -0.2657 (tt0) REVERT: X 25 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7727 (mttm) REVERT: X 55 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7330 (mtp) REVERT: Y 56 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7955 (mt) REVERT: Z 10 ARG cc_start: 0.7524 (mmm-85) cc_final: 0.6623 (mtm-85) REVERT: c 77 GLU cc_start: 0.5981 (tp30) cc_final: 0.5754 (tp30) REVERT: c 128 VAL cc_start: 0.7601 (OUTLIER) cc_final: 0.7389 (p) REVERT: d 9 GLU cc_start: 0.3426 (OUTLIER) cc_final: 0.2828 (pp20) REVERT: d 31 SER cc_start: 0.7805 (OUTLIER) cc_final: 0.7449 (m) REVERT: d 67 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6717 (mpt-90) REVERT: d 110 MET cc_start: 0.7572 (mtp) cc_final: 0.7117 (mtp) REVERT: e 1 MET cc_start: 0.4527 (tpp) cc_final: 0.4231 (tpp) REVERT: e 33 GLU cc_start: 0.4176 (OUTLIER) cc_final: 0.3691 (pp20) REVERT: f 14 ASP cc_start: 0.0686 (OUTLIER) cc_final: 0.0276 (p0) REVERT: g 37 ASN cc_start: 0.7901 (t0) cc_final: 0.7643 (t0) REVERT: h 38 PHE cc_start: 0.2640 (OUTLIER) cc_final: 0.0542 (p90) REVERT: h 45 MET cc_start: 0.3527 (tpt) cc_final: 0.3258 (tpt) REVERT: h 56 MET cc_start: -0.0506 (tpt) cc_final: -0.2075 (tpt) REVERT: h 121 ARG cc_start: 0.7849 (mmt90) cc_final: 0.7521 (mtt90) REVERT: i 47 GLU cc_start: 0.5422 (OUTLIER) cc_final: 0.5214 (mt-10) REVERT: i 88 MET cc_start: 0.4075 (mpt) cc_final: 0.3460 (mpt) REVERT: k 8 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5692 (mpp80) REVERT: m 65 ARG cc_start: 0.7705 (tpp80) cc_final: 0.7355 (ttm170) REVERT: n 9 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7632 (ttpp) REVERT: o 9 HIS cc_start: 0.7155 (OUTLIER) cc_final: 0.6930 (m-70) REVERT: r 65 MET cc_start: -0.0010 (mtt) cc_final: -0.0844 (tpt) REVERT: t 53 LYS cc_start: -0.0166 (OUTLIER) cc_final: -0.1447 (mmtm) REVERT: w 20 ARG cc_start: 0.3580 (OUTLIER) cc_final: 0.3029 (mmp-170) REVERT: w 199 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7194 (tt) REVERT: x 35 ASP cc_start: 0.6831 (m-30) cc_final: 0.6430 (m-30) REVERT: x 143 LEU cc_start: 0.7229 (mt) cc_final: 0.6905 (mt) outliers start: 255 outliers final: 143 residues processed: 673 average time/residue: 1.3595 time to fit residues: 1546.6082 Evaluate side-chains 646 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 474 time to evaluate : 5.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 33 LEU Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain 6 residue 175 GLN Chi-restraints excluded: chain 6 residue 238 ARG Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain 6 residue 264 VAL Chi-restraints excluded: chain 6 residue 370 LEU Chi-restraints excluded: chain 6 residue 411 TRP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 34 LYS Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 53 GLN Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain Y residue 27 ASN Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain c residue 117 VAL Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 177 MET Chi-restraints excluded: chain d residue 9 GLU Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 121 ASN Chi-restraints excluded: chain e residue 33 GLU Chi-restraints excluded: chain e residue 46 GLN Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 57 GLU Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 3 ASN Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 86 LEU Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain j residue 118 ASN Chi-restraints excluded: chain k residue 8 ARG Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain l residue 13 HIS Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain m residue 32 ASP Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain m residue 53 ARG Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain o residue 9 HIS Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain t residue 53 LYS Chi-restraints excluded: chain w residue 20 ARG Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 160 LEU Chi-restraints excluded: chain w residue 162 VAL Chi-restraints excluded: chain w residue 173 LYS Chi-restraints excluded: chain w residue 188 THR Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 83 VAL Chi-restraints excluded: chain x residue 105 VAL Chi-restraints excluded: chain x residue 142 ARG Chi-restraints excluded: chain x residue 163 ARG Chi-restraints excluded: chain x residue 194 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 954 optimal weight: 6.9990 chunk 111 optimal weight: 20.0000 chunk 563 optimal weight: 3.9990 chunk 722 optimal weight: 1.9990 chunk 560 optimal weight: 2.9990 chunk 833 optimal weight: 5.9990 chunk 552 optimal weight: 5.9990 chunk 986 optimal weight: 2.9990 chunk 617 optimal weight: 3.9990 chunk 601 optimal weight: 7.9990 chunk 455 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN ** 6 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 128 GLN C 44 ASN M 45 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS ** Y 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN e 94 HIS ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 64 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 19 HIS ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 1.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 156639 Z= 0.253 Angle : 0.606 13.627 234098 Z= 0.309 Chirality : 0.037 0.325 29864 Planarity : 0.005 0.061 12746 Dihedral : 23.655 179.455 77725 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.15 % Favored : 92.78 % Rotamer: Outliers : 4.55 % Allowed : 31.26 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.10), residues: 5816 helix: 0.46 (0.12), residues: 1890 sheet: -0.42 (0.18), residues: 757 loop : -1.93 (0.10), residues: 3169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP T 80 HIS 0.008 0.001 HIS i 56 PHE 0.020 0.002 PHE e 8 TYR 0.022 0.002 TYR h 5 ARG 0.006 0.001 ARG c 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 473 time to evaluate : 5.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 10 SER cc_start: 0.7976 (t) cc_final: 0.7618 (p) REVERT: 0 36 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7227 (mttm) REVERT: 3 46 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7619 (mttm) REVERT: 6 1 MET cc_start: 0.1382 (mtm) cc_final: 0.0720 (ttm) REVERT: 6 175 GLN cc_start: 0.4536 (OUTLIER) cc_final: 0.4029 (pp30) REVERT: 6 214 PHE cc_start: 0.4684 (t80) cc_final: 0.3909 (t80) REVERT: 6 261 HIS cc_start: 0.0913 (OUTLIER) cc_final: -0.0581 (p-80) REVERT: C 102 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: C 145 MET cc_start: 0.5971 (mpp) cc_final: 0.5751 (mtt) REVERT: C 202 ARG cc_start: 0.6429 (tmm-80) cc_final: 0.6206 (tmm-80) REVERT: C 203 VAL cc_start: 0.7492 (OUTLIER) cc_final: 0.7199 (t) REVERT: C 261 ARG cc_start: 0.7911 (ttp80) cc_final: 0.7701 (ttp80) REVERT: D 104 VAL cc_start: -0.1865 (OUTLIER) cc_final: -0.2083 (m) REVERT: D 155 VAL cc_start: 0.8215 (m) cc_final: 0.8013 (m) REVERT: E 141 MET cc_start: 0.6331 (mpp) cc_final: 0.5567 (mpp) REVERT: F 25 MET cc_start: 0.2981 (pmm) cc_final: 0.2144 (pmm) REVERT: J 81 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6784 (pt) REVERT: M 34 LYS cc_start: 0.6151 (OUTLIER) cc_final: 0.3810 (tttp) REVERT: M 40 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7564 (mtt90) REVERT: N 8 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.6890 (ptt180) REVERT: O 13 ARG cc_start: 0.6930 (mmt90) cc_final: 0.6638 (mmt90) REVERT: O 17 LYS cc_start: 0.7759 (tppt) cc_final: 0.7497 (tptt) REVERT: O 47 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7571 (p) REVERT: O 102 ARG cc_start: 0.7456 (ttp-110) cc_final: 0.7167 (ttm-80) REVERT: Q 5 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7095 (ptt180) REVERT: Q 27 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7407 (mtp85) REVERT: R 23 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: S 85 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7473 (tp) REVERT: X 25 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7629 (mttm) REVERT: X 55 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.7377 (mtp) REVERT: Y 56 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8179 (mt) REVERT: c 77 GLU cc_start: 0.5951 (tp30) cc_final: 0.5723 (tp30) REVERT: c 171 GLU cc_start: 0.5677 (mp0) cc_final: 0.5470 (mp0) REVERT: d 67 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6750 (mpt-90) REVERT: d 110 MET cc_start: 0.7577 (mtp) cc_final: 0.7094 (mtp) REVERT: f 14 ASP cc_start: 0.0668 (OUTLIER) cc_final: 0.0237 (p0) REVERT: f 143 MET cc_start: 0.3424 (mmt) cc_final: 0.3171 (tpp) REVERT: g 37 ASN cc_start: 0.7907 (t0) cc_final: 0.7631 (t0) REVERT: h 38 PHE cc_start: 0.2766 (OUTLIER) cc_final: 0.0614 (p90) REVERT: h 45 MET cc_start: 0.3653 (tpt) cc_final: 0.3388 (tpt) REVERT: h 56 MET cc_start: -0.0735 (tpt) cc_final: -0.2414 (tpt) REVERT: h 121 ARG cc_start: 0.7944 (mmt90) cc_final: 0.7677 (mtt90) REVERT: i 47 GLU cc_start: 0.5428 (OUTLIER) cc_final: 0.5223 (mt-10) REVERT: i 88 MET cc_start: 0.4059 (mpt) cc_final: 0.3545 (mpt) REVERT: k 8 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.5671 (mpp80) REVERT: k 54 VAL cc_start: 0.7167 (OUTLIER) cc_final: 0.6912 (t) REVERT: l 74 MET cc_start: 0.2809 (mpp) cc_final: 0.2450 (mpp) REVERT: m 65 ARG cc_start: 0.7587 (tpp80) cc_final: 0.7243 (ttm170) REVERT: n 9 LYS cc_start: 0.7853 (OUTLIER) cc_final: 0.7533 (ttpp) REVERT: r 65 MET cc_start: -0.0074 (mtt) cc_final: -0.0887 (tpt) REVERT: r 80 ARG cc_start: 0.2082 (OUTLIER) cc_final: 0.1701 (ptp-170) REVERT: w 178 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7507 (mt) REVERT: w 199 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7185 (tt) REVERT: x 35 ASP cc_start: 0.6797 (m-30) cc_final: 0.6396 (m-30) REVERT: x 143 LEU cc_start: 0.7150 (mt) cc_final: 0.6836 (mt) outliers start: 221 outliers final: 130 residues processed: 639 average time/residue: 1.3964 time to fit residues: 1495.6849 Evaluate side-chains 625 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 467 time to evaluate : 5.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 46 LYS Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain 6 residue 175 GLN Chi-restraints excluded: chain 6 residue 197 VAL Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain 6 residue 264 VAL Chi-restraints excluded: chain 6 residue 314 LEU Chi-restraints excluded: chain 6 residue 370 LEU Chi-restraints excluded: chain 6 residue 411 TRP Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 34 LYS Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 177 MET Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 121 ASN Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 62 MET Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 57 GLU Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 80 HIS Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain j residue 14 GLN Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain j residue 124 LYS Chi-restraints excluded: chain k residue 8 ARG Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain l residue 13 HIS Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain t residue 53 LYS Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 160 LEU Chi-restraints excluded: chain w residue 162 VAL Chi-restraints excluded: chain w residue 173 LYS Chi-restraints excluded: chain w residue 178 LEU Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 63 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 610 optimal weight: 3.9990 chunk 393 optimal weight: 20.0000 chunk 588 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 193 optimal weight: 40.0000 chunk 191 optimal weight: 7.9990 chunk 626 optimal weight: 0.5980 chunk 671 optimal weight: 0.7980 chunk 487 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 775 optimal weight: 7.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN ** 6 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 92 HIS ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 31 GLN Y 39 GLN c 73 ASN ** e 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 1.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 156639 Z= 0.374 Angle : 0.720 15.254 234098 Z= 0.363 Chirality : 0.043 0.377 29864 Planarity : 0.006 0.062 12746 Dihedral : 23.754 179.843 77725 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.08 % Favored : 91.85 % Rotamer: Outliers : 5.08 % Allowed : 30.66 % Favored : 64.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.10), residues: 5816 helix: 0.10 (0.12), residues: 1905 sheet: -0.55 (0.18), residues: 763 loop : -2.04 (0.10), residues: 3148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 60 HIS 0.011 0.002 HIS i 56 PHE 0.044 0.002 PHE w 31 TYR 0.027 0.002 TYR Q 31 ARG 0.028 0.001 ARG 6 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 482 time to evaluate : 5.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 36 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7247 (mttm) REVERT: 6 1 MET cc_start: 0.1404 (mtm) cc_final: 0.0731 (ttm) REVERT: 6 175 GLN cc_start: 0.4363 (OUTLIER) cc_final: 0.3853 (pp30) REVERT: 6 261 HIS cc_start: 0.0740 (OUTLIER) cc_final: -0.0785 (p-80) REVERT: C 102 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: C 202 ARG cc_start: 0.6385 (tmm-80) cc_final: 0.6135 (tmm-80) REVERT: C 261 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7590 (ttp80) REVERT: D 13 ARG cc_start: 0.3363 (tpt170) cc_final: 0.1026 (tpt90) REVERT: D 104 VAL cc_start: -0.1973 (OUTLIER) cc_final: -0.2243 (m) REVERT: E 1 MET cc_start: 0.0776 (ttp) cc_final: 0.0126 (ttp) REVERT: E 141 MET cc_start: 0.6413 (mpp) cc_final: 0.5622 (mpp) REVERT: G 43 LYS cc_start: 0.5621 (OUTLIER) cc_final: 0.5235 (pttm) REVERT: G 140 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7417 (tt) REVERT: K 6 MET cc_start: 0.7238 (mmm) cc_final: 0.7009 (mmm) REVERT: L 21 ARG cc_start: 0.7825 (tpp80) cc_final: 0.7275 (mmt-90) REVERT: L 132 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7296 (ptm160) REVERT: M 34 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.3818 (tttp) REVERT: N 8 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.6985 (ptt180) REVERT: N 24 MET cc_start: 0.6954 (ttm) cc_final: 0.6691 (ttm) REVERT: Q 5 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7239 (ptt180) REVERT: Q 27 ARG cc_start: 0.7648 (OUTLIER) cc_final: 0.7435 (mtp85) REVERT: R 23 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: S 25 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7509 (ttm110) REVERT: S 85 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7590 (tp) REVERT: U 86 PHE cc_start: 0.8063 (m-10) cc_final: 0.7631 (m-80) REVERT: X 25 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7953 (mttm) REVERT: X 55 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7339 (mtp) REVERT: Y 20 ASN cc_start: 0.7367 (OUTLIER) cc_final: 0.7146 (m-40) REVERT: Y 56 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8042 (mt) REVERT: c 59 LYS cc_start: 0.8274 (ttpp) cc_final: 0.7935 (ttpp) REVERT: c 77 GLU cc_start: 0.5954 (tp30) cc_final: 0.5712 (tp30) REVERT: c 128 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7431 (p) REVERT: c 171 GLU cc_start: 0.5805 (mp0) cc_final: 0.5538 (mp0) REVERT: d 31 SER cc_start: 0.7807 (OUTLIER) cc_final: 0.7433 (m) REVERT: d 67 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6439 (mpt-90) REVERT: d 110 MET cc_start: 0.7584 (mtp) cc_final: 0.7091 (mtp) REVERT: e 1 MET cc_start: 0.4644 (tpp) cc_final: 0.4372 (tpp) REVERT: e 33 GLU cc_start: 0.4361 (OUTLIER) cc_final: 0.3902 (pp20) REVERT: f 14 ASP cc_start: 0.0827 (OUTLIER) cc_final: 0.0438 (p0) REVERT: f 117 LEU cc_start: 0.3864 (OUTLIER) cc_final: 0.3215 (tt) REVERT: g 37 ASN cc_start: 0.7976 (t0) cc_final: 0.7717 (t0) REVERT: h 38 PHE cc_start: 0.2936 (OUTLIER) cc_final: 0.0868 (p90) REVERT: h 56 MET cc_start: -0.0352 (tpt) cc_final: -0.1966 (tpt) REVERT: h 121 ARG cc_start: 0.8056 (mmt90) cc_final: 0.7763 (mtt90) REVERT: i 47 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.5190 (mt-10) REVERT: i 88 MET cc_start: 0.4129 (mpt) cc_final: 0.3702 (mpt) REVERT: k 8 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5686 (mpp80) REVERT: k 54 VAL cc_start: 0.7159 (OUTLIER) cc_final: 0.6936 (t) REVERT: m 65 ARG cc_start: 0.7628 (tpp80) cc_final: 0.7243 (ttm170) REVERT: n 9 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7628 (ttpp) REVERT: n 39 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: r 65 MET cc_start: 0.0272 (mtt) cc_final: -0.0833 (tpt) REVERT: r 80 ARG cc_start: 0.2259 (OUTLIER) cc_final: 0.1929 (ptp-170) REVERT: w 199 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.7164 (tt) REVERT: x 20 THR cc_start: 0.7700 (OUTLIER) cc_final: 0.7417 (p) REVERT: x 35 ASP cc_start: 0.6889 (m-30) cc_final: 0.6467 (m-30) REVERT: x 143 LEU cc_start: 0.7246 (mt) cc_final: 0.6933 (mt) outliers start: 247 outliers final: 166 residues processed: 672 average time/residue: 1.3592 time to fit residues: 1532.1946 Evaluate side-chains 681 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 482 time to evaluate : 5.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 6 residue 22 LYS Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 33 LEU Chi-restraints excluded: chain 6 residue 34 VAL Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain 6 residue 175 GLN Chi-restraints excluded: chain 6 residue 197 VAL Chi-restraints excluded: chain 6 residue 202 LEU Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain 6 residue 264 VAL Chi-restraints excluded: chain 6 residue 314 LEU Chi-restraints excluded: chain 6 residue 370 LEU Chi-restraints excluded: chain 6 residue 399 SER Chi-restraints excluded: chain 6 residue 411 TRP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain J residue 9 GLU Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 25 ASP Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 34 LYS Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 45 GLN Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 110 MET Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 70 LYS Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 11 GLU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 MET Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 121 ASN Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 33 GLU Chi-restraints excluded: chain e residue 46 GLN Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 57 GLU Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 80 HIS Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 47 GLU Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 14 GLN Chi-restraints excluded: chain j residue 113 THR Chi-restraints excluded: chain j residue 124 LYS Chi-restraints excluded: chain k residue 8 ARG Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain l residue 13 HIS Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 39 GLN Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain r residue 3 SER Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 53 LYS Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 160 LEU Chi-restraints excluded: chain w residue 162 VAL Chi-restraints excluded: chain w residue 173 LYS Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 163 ARG Chi-restraints excluded: chain x residue 190 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 896 optimal weight: 5.9990 chunk 944 optimal weight: 8.9990 chunk 861 optimal weight: 4.9990 chunk 918 optimal weight: 5.9990 chunk 553 optimal weight: 0.1980 chunk 400 optimal weight: 6.9990 chunk 721 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 830 optimal weight: 4.9990 chunk 869 optimal weight: 7.9990 chunk 915 optimal weight: 4.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN 6 113 GLN ** 6 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** U 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN f 121 ASN h 3 ASN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 42 ASN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 HIS ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 1.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 156639 Z= 0.398 Angle : 0.727 14.659 234098 Z= 0.365 Chirality : 0.044 0.366 29864 Planarity : 0.006 0.068 12746 Dihedral : 23.762 179.807 77725 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.98 % Favored : 91.94 % Rotamer: Outliers : 4.84 % Allowed : 30.77 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.10), residues: 5816 helix: -0.04 (0.12), residues: 1898 sheet: -0.58 (0.18), residues: 773 loop : -2.12 (0.10), residues: 3145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP f 102 HIS 0.016 0.002 HIS i 56 PHE 0.038 0.002 PHE 6 214 TYR 0.025 0.002 TYR Q 31 ARG 0.018 0.001 ARG 6 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 499 time to evaluate : 5.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 36 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7154 (ptpp) REVERT: 6 1 MET cc_start: 0.1470 (mtm) cc_final: 0.0792 (ttm) REVERT: 6 175 GLN cc_start: 0.4377 (OUTLIER) cc_final: 0.3877 (pp30) REVERT: 6 261 HIS cc_start: -0.0087 (OUTLIER) cc_final: -0.1796 (p-80) REVERT: C 102 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: D 104 VAL cc_start: -0.1861 (OUTLIER) cc_final: -0.2118 (m) REVERT: E 1 MET cc_start: 0.1104 (ttp) cc_final: 0.0376 (ttp) REVERT: E 141 MET cc_start: 0.6399 (mpp) cc_final: 0.5735 (mpp) REVERT: G 43 LYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5267 (pttm) REVERT: G 140 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7505 (tt) REVERT: J 108 MET cc_start: 0.7430 (mtp) cc_final: 0.7216 (mtt) REVERT: K 94 ILE cc_start: 0.7598 (mm) cc_final: 0.7136 (mm) REVERT: L 21 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7298 (mmt-90) REVERT: L 132 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7217 (ptm160) REVERT: M 34 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.3730 (tttp) REVERT: N 8 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6938 (ptt180) REVERT: N 24 MET cc_start: 0.6848 (ttm) cc_final: 0.6585 (ttm) REVERT: Q 5 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7209 (ptt180) REVERT: Q 27 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.7419 (mtp85) REVERT: R 23 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: S 85 ILE cc_start: 0.7803 (OUTLIER) cc_final: 0.7595 (tp) REVERT: S 90 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7931 (mttt) REVERT: U 3 LYS cc_start: 0.6288 (ttmt) cc_final: 0.6011 (ttmt) REVERT: U 86 PHE cc_start: 0.7778 (m-10) cc_final: 0.7517 (m-80) REVERT: X 25 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7927 (mttm) REVERT: X 55 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7348 (mtp) REVERT: Y 56 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8047 (mt) REVERT: c 128 VAL cc_start: 0.7587 (OUTLIER) cc_final: 0.7370 (p) REVERT: c 171 GLU cc_start: 0.5851 (mp0) cc_final: 0.5546 (mp0) REVERT: d 31 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7387 (m) REVERT: d 67 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6737 (mpt-90) REVERT: d 110 MET cc_start: 0.7589 (mtp) cc_final: 0.7085 (mtp) REVERT: e 1 MET cc_start: 0.4644 (tpp) cc_final: 0.4422 (tpp) REVERT: e 33 GLU cc_start: 0.4163 (OUTLIER) cc_final: 0.3734 (pp20) REVERT: f 14 ASP cc_start: 0.1009 (OUTLIER) cc_final: 0.0574 (p0) REVERT: g 37 ASN cc_start: 0.7970 (t0) cc_final: 0.7711 (t0) REVERT: h 38 PHE cc_start: 0.3133 (OUTLIER) cc_final: 0.1014 (p90) REVERT: h 56 MET cc_start: -0.0296 (tpt) cc_final: -0.1967 (tpt) REVERT: h 87 MET cc_start: 0.1375 (mmt) cc_final: 0.1094 (mmt) REVERT: h 121 ARG cc_start: 0.8015 (mmt90) cc_final: 0.7793 (mtt180) REVERT: j 97 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6708 (mtp85) REVERT: k 8 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.5672 (mpp80) REVERT: k 54 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6923 (t) REVERT: m 65 ARG cc_start: 0.7623 (tpp80) cc_final: 0.6990 (mtt-85) REVERT: n 9 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7614 (ttpp) REVERT: r 65 MET cc_start: 0.0339 (mtt) cc_final: -0.0868 (tpt) REVERT: r 80 ARG cc_start: 0.2477 (OUTLIER) cc_final: 0.2204 (ptp-170) REVERT: w 147 LEU cc_start: 0.5306 (OUTLIER) cc_final: 0.5061 (mt) REVERT: w 199 ILE cc_start: 0.7544 (OUTLIER) cc_final: 0.7196 (tt) REVERT: x 20 THR cc_start: 0.7616 (OUTLIER) cc_final: 0.7326 (p) REVERT: x 35 ASP cc_start: 0.6863 (m-30) cc_final: 0.6430 (m-30) REVERT: x 41 TYR cc_start: 0.7036 (t80) cc_final: 0.6776 (t80) REVERT: x 143 LEU cc_start: 0.7236 (mt) cc_final: 0.6931 (mt) REVERT: x 169 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6447 (tm-30) outliers start: 235 outliers final: 164 residues processed: 675 average time/residue: 1.3635 time to fit residues: 1548.4269 Evaluate side-chains 690 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 494 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 33 LEU Chi-restraints excluded: chain 6 residue 81 ASP Chi-restraints excluded: chain 6 residue 124 VAL Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain 6 residue 175 GLN Chi-restraints excluded: chain 6 residue 197 VAL Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain 6 residue 264 VAL Chi-restraints excluded: chain 6 residue 314 LEU Chi-restraints excluded: chain 6 residue 370 LEU Chi-restraints excluded: chain 6 residue 379 LEU Chi-restraints excluded: chain 6 residue 394 MET Chi-restraints excluded: chain 6 residue 399 SER Chi-restraints excluded: chain 6 residue 411 TRP Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain K residue 89 ASN Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 132 ARG Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 34 LYS Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 96 ILE Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain Y residue 28 LEU Chi-restraints excluded: chain Y residue 30 MET Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 146 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 177 MET Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 121 ASN Chi-restraints excluded: chain e residue 18 VAL Chi-restraints excluded: chain e residue 33 GLU Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 62 MET Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 57 GLU Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 20 ILE Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 80 HIS Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 14 GLN Chi-restraints excluded: chain j residue 97 ARG Chi-restraints excluded: chain j residue 124 LYS Chi-restraints excluded: chain k residue 8 ARG Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain l residue 13 HIS Chi-restraints excluded: chain m residue 5 MET Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 64 LEU Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 53 LYS Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 160 LEU Chi-restraints excluded: chain w residue 162 VAL Chi-restraints excluded: chain w residue 173 LYS Chi-restraints excluded: chain w residue 180 ILE Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 163 ARG Chi-restraints excluded: chain x residue 169 GLU Chi-restraints excluded: chain x residue 190 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 603 optimal weight: 4.9990 chunk 971 optimal weight: 10.0000 chunk 593 optimal weight: 7.9990 chunk 460 optimal weight: 3.9990 chunk 675 optimal weight: 0.7980 chunk 1019 optimal weight: 4.9990 chunk 938 optimal weight: 4.9990 chunk 811 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 626 optimal weight: 0.9980 chunk 497 optimal weight: 8.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN 4 37 GLN ** 6 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 113 GLN ** 6 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN K 92 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 70 HIS V 51 GLN c 73 ASN ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 63 ASN f 121 ASN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 99 GLN ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 1.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 156639 Z= 0.310 Angle : 0.657 14.662 234098 Z= 0.334 Chirality : 0.040 0.337 29864 Planarity : 0.005 0.074 12746 Dihedral : 23.694 179.979 77725 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.87 % Favored : 92.04 % Rotamer: Outliers : 4.22 % Allowed : 31.14 % Favored : 64.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.10), residues: 5816 helix: 0.15 (0.12), residues: 1902 sheet: -0.58 (0.18), residues: 783 loop : -2.07 (0.10), residues: 3131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 92 HIS 0.015 0.002 HIS S 7 PHE 0.033 0.002 PHE U 72 TYR 0.021 0.002 TYR Q 31 ARG 0.008 0.001 ARG K 70 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11632 Ramachandran restraints generated. 5816 Oldfield, 0 Emsley, 5816 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 476 time to evaluate : 5.881 Fit side-chains revert: symmetry clash REVERT: 0 36 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7110 (ptpp) REVERT: 6 1 MET cc_start: 0.1472 (mtm) cc_final: 0.0774 (ttm) REVERT: 6 77 VAL cc_start: 0.7225 (t) cc_final: 0.7010 (m) REVERT: 6 175 GLN cc_start: 0.4141 (OUTLIER) cc_final: 0.3635 (pp30) REVERT: 6 261 HIS cc_start: -0.0196 (OUTLIER) cc_final: -0.1785 (p-80) REVERT: C 102 TYR cc_start: 0.7694 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: C 173 LEU cc_start: 0.7265 (mt) cc_final: 0.7055 (mp) REVERT: C 261 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7629 (ttp80) REVERT: D 13 ARG cc_start: 0.4765 (tpt90) cc_final: 0.2486 (tpt170) REVERT: D 104 VAL cc_start: -0.1835 (OUTLIER) cc_final: -0.2160 (m) REVERT: E 1 MET cc_start: 0.1047 (ttp) cc_final: 0.0428 (ttp) REVERT: E 141 MET cc_start: 0.6448 (mpp) cc_final: 0.5773 (mpp) REVERT: G 43 LYS cc_start: 0.5569 (OUTLIER) cc_final: 0.5251 (pttm) REVERT: J 108 MET cc_start: 0.7355 (mtp) cc_final: 0.7136 (mtt) REVERT: K 94 ILE cc_start: 0.7717 (mm) cc_final: 0.7284 (mm) REVERT: L 21 ARG cc_start: 0.7778 (tpp80) cc_final: 0.7212 (mmt-90) REVERT: M 34 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.3810 (tttp) REVERT: N 8 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6919 (ptt180) REVERT: N 24 MET cc_start: 0.6847 (ttm) cc_final: 0.6584 (ttm) REVERT: Q 5 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7085 (ptt180) REVERT: Q 27 ARG cc_start: 0.7619 (OUTLIER) cc_final: 0.7392 (mtp85) REVERT: R 23 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6290 (mp0) REVERT: S 25 ARG cc_start: 0.7740 (ttm110) cc_final: 0.7418 (ttm110) REVERT: T 1 MET cc_start: 0.4130 (mmp) cc_final: 0.3315 (mmp) REVERT: U 3 LYS cc_start: 0.6322 (ttmt) cc_final: 0.5999 (ttmt) REVERT: U 86 PHE cc_start: 0.7576 (m-10) cc_final: 0.7286 (m-80) REVERT: X 25 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7726 (mttm) REVERT: X 55 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7336 (mtp) REVERT: Y 56 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8024 (mt) REVERT: c 21 LYS cc_start: 0.5943 (ttmt) cc_final: 0.5387 (tttm) REVERT: c 128 VAL cc_start: 0.7595 (OUTLIER) cc_final: 0.7376 (p) REVERT: c 171 GLU cc_start: 0.5857 (mp0) cc_final: 0.5543 (mp0) REVERT: d 31 SER cc_start: 0.7760 (OUTLIER) cc_final: 0.7394 (m) REVERT: d 67 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.6692 (mpt-90) REVERT: d 110 MET cc_start: 0.7600 (mtp) cc_final: 0.7075 (mtp) REVERT: e 33 GLU cc_start: 0.4156 (OUTLIER) cc_final: 0.3753 (pp20) REVERT: f 14 ASP cc_start: 0.0913 (OUTLIER) cc_final: 0.0533 (p0) REVERT: f 117 LEU cc_start: 0.3601 (OUTLIER) cc_final: 0.3092 (tt) REVERT: g 37 ASN cc_start: 0.7945 (t0) cc_final: 0.7690 (t0) REVERT: h 38 PHE cc_start: 0.3106 (OUTLIER) cc_final: 0.0936 (p90) REVERT: h 56 MET cc_start: -0.0487 (tpt) cc_final: -0.2102 (tpt) REVERT: h 87 MET cc_start: 0.1196 (mmt) cc_final: 0.0764 (mmt) REVERT: h 121 ARG cc_start: 0.8036 (mmt90) cc_final: 0.7816 (mtt180) REVERT: j 97 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6672 (mtp85) REVERT: k 8 ARG cc_start: 0.6362 (OUTLIER) cc_final: 0.5687 (mpp80) REVERT: k 54 VAL cc_start: 0.7176 (OUTLIER) cc_final: 0.6938 (t) REVERT: m 65 ARG cc_start: 0.7619 (tpp80) cc_final: 0.6960 (mtt-85) REVERT: n 9 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7610 (ttpp) REVERT: r 39 ILE cc_start: -0.1026 (OUTLIER) cc_final: -0.1391 (mp) REVERT: r 65 MET cc_start: 0.0204 (mtt) cc_final: -0.0947 (tpt) REVERT: r 80 ARG cc_start: 0.2450 (OUTLIER) cc_final: 0.2165 (ptp-170) REVERT: w 199 ILE cc_start: 0.7532 (OUTLIER) cc_final: 0.7175 (tt) REVERT: x 20 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.7315 (p) REVERT: x 35 ASP cc_start: 0.6830 (m-30) cc_final: 0.6397 (m-30) REVERT: x 41 TYR cc_start: 0.7000 (t80) cc_final: 0.6681 (t80) REVERT: x 143 LEU cc_start: 0.7213 (mt) cc_final: 0.6927 (mt) REVERT: x 187 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5878 (tp30) outliers start: 205 outliers final: 156 residues processed: 629 average time/residue: 1.3881 time to fit residues: 1465.4575 Evaluate side-chains 660 residues out of total 4865 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 474 time to evaluate : 5.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 LYS Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 46 LYS Chi-restraints excluded: chain 6 residue 27 LEU Chi-restraints excluded: chain 6 residue 126 LEU Chi-restraints excluded: chain 6 residue 131 HIS Chi-restraints excluded: chain 6 residue 175 GLN Chi-restraints excluded: chain 6 residue 197 VAL Chi-restraints excluded: chain 6 residue 236 LEU Chi-restraints excluded: chain 6 residue 238 ARG Chi-restraints excluded: chain 6 residue 261 HIS Chi-restraints excluded: chain 6 residue 264 VAL Chi-restraints excluded: chain 6 residue 314 LEU Chi-restraints excluded: chain 6 residue 370 LEU Chi-restraints excluded: chain 6 residue 379 LEU Chi-restraints excluded: chain 6 residue 394 MET Chi-restraints excluded: chain 6 residue 399 SER Chi-restraints excluded: chain 6 residue 411 TRP Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 161 MET Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 120 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 55 MET Chi-restraints excluded: chain L residue 84 LYS Chi-restraints excluded: chain L residue 103 ILE Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 106 GLU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 34 LYS Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 136 MET Chi-restraints excluded: chain N residue 8 ARG Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 69 ASP Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 109 ILE Chi-restraints excluded: chain Q residue 5 ARG Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 27 ARG Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 23 GLU Chi-restraints excluded: chain R residue 82 HIS Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 59 GLU Chi-restraints excluded: chain S residue 86 MET Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 54 GLU Chi-restraints excluded: chain T residue 55 VAL Chi-restraints excluded: chain U residue 6 ARG Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 36 GLU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 102 ILE Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 18 SER Chi-restraints excluded: chain X residue 25 LYS Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 55 MET Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 36 GLU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain c residue 128 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 173 ASP Chi-restraints excluded: chain c residue 177 MET Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 25 LYS Chi-restraints excluded: chain d residue 31 SER Chi-restraints excluded: chain d residue 67 ARG Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 113 VAL Chi-restraints excluded: chain d residue 121 ASN Chi-restraints excluded: chain e residue 33 GLU Chi-restraints excluded: chain e residue 46 GLN Chi-restraints excluded: chain e residue 56 LYS Chi-restraints excluded: chain e residue 60 VAL Chi-restraints excluded: chain e residue 62 MET Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 37 THR Chi-restraints excluded: chain f residue 41 ILE Chi-restraints excluded: chain f residue 117 LEU Chi-restraints excluded: chain g residue 54 THR Chi-restraints excluded: chain g residue 57 GLU Chi-restraints excluded: chain g residue 89 ASP Chi-restraints excluded: chain g residue 109 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain h residue 38 PHE Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain i residue 10 LEU Chi-restraints excluded: chain i residue 44 THR Chi-restraints excluded: chain i residue 57 VAL Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 96 VAL Chi-restraints excluded: chain i residue 102 LEU Chi-restraints excluded: chain j residue 14 GLN Chi-restraints excluded: chain j residue 97 ARG Chi-restraints excluded: chain j residue 124 LYS Chi-restraints excluded: chain k residue 8 ARG Chi-restraints excluded: chain k residue 36 VAL Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain l residue 13 HIS Chi-restraints excluded: chain m residue 43 ASN Chi-restraints excluded: chain n residue 9 LYS Chi-restraints excluded: chain n residue 44 GLU Chi-restraints excluded: chain o residue 20 VAL Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 64 LEU Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 47 THR Chi-restraints excluded: chain r residue 80 ARG Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 53 LYS Chi-restraints excluded: chain w residue 147 LEU Chi-restraints excluded: chain w residue 160 LEU Chi-restraints excluded: chain w residue 162 VAL Chi-restraints excluded: chain w residue 173 LYS Chi-restraints excluded: chain w residue 199 ILE Chi-restraints excluded: chain x residue 20 THR Chi-restraints excluded: chain x residue 55 VAL Chi-restraints excluded: chain x residue 63 ILE Chi-restraints excluded: chain x residue 163 ARG Chi-restraints excluded: chain x residue 187 GLU Chi-restraints excluded: chain x residue 190 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1023 random chunks: chunk 644 optimal weight: 1.9990 chunk 864 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 748 optimal weight: 0.0770 chunk 119 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 812 optimal weight: 2.9990 chunk 340 optimal weight: 6.9990 chunk 834 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 13 ASN ** 6 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 ASN J 128 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS c 73 ASN ** e 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 121 ASN f 129 ASN ** i 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.165111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.131121 restraints weight = 199622.605| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.12 r_work: 0.3355 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 1.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 156639 Z= 0.335 Angle : 0.684 16.570 234098 Z= 0.347 Chirality : 0.041 0.344 29864 Planarity : 0.005 0.106 12746 Dihedral : 23.698 179.593 77725 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.24 % Favored : 91.68 % Rotamer: Outliers : 4.12 % Allowed : 31.45 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.10), residues: 5816 helix: 0.06 (0.12), residues: 1907 sheet: -0.56 (0.18), residues: 801 loop : -2.09 (0.10), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP M 92 HIS 0.017 0.002 HIS 6 82 PHE 0.032 0.002 PHE U 72 TYR 0.022 0.002 TYR Q 31 ARG 0.014 0.001 ARG 6 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27572.97 seconds wall clock time: 487 minutes 48.19 seconds (29268.19 seconds total)