Starting phenix.real_space_refine on Sat Oct 12 13:02:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/10_2024/8jou_36462.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/10_2024/8jou_36462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/10_2024/8jou_36462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/10_2024/8jou_36462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/10_2024/8jou_36462.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jou_36462/10_2024/8jou_36462.cif" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.105 sd= 2.608 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 39340 2.51 5 N 10805 2.21 5 O 12250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 62425 Number of models: 1 Model: "" Number of chains: 70 Chain: "a" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "b" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "c" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "d" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "e" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "f" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "g" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "h" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "i" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "j" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "A" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "D" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "B" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "C" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "E" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "G" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "H" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "I" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "J" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "K" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "L" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "M" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "N" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "O" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "P" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "Q" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "R" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "S" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "T" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "U" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "V" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "W" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "X" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "Y" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "Z" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "0" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "1" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "2" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "3" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "4" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "5" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "6" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "7" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "8" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "9" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "k" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "l" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "m" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "n" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "o" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "p" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "q" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "r" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "s" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "t" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "u" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "v" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "w" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "x" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "y" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "z" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AA" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AB" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AC" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AD" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 990 Classifications: {'peptide': 136} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 126} Chain: "AE" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 590 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 118 Planarities with less than four sites: {'UNK:plan-1': 118} Unresolved non-hydrogen planarities: 118 Chain: "AF" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "AG" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Chain: "AH" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 665 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 3, 'TRANS': 85} Time building chain proxies: 27.13, per 1000 atoms: 0.43 Number of scatterers: 62425 At special positions: 0 Unit cell: (698.5, 670.56, 199.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 12250 8.00 N 10805 7.00 C 39340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.58 Conformation dependent library (CDL) restraints added in 6.0 seconds 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15680 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 160 sheets defined 8.5% alpha, 21.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.54 Creating SS restraints... Processing helix chain 'a' and resid 5 through 17 Processing helix chain 'b' and resid 5 through 17 Processing helix chain 'c' and resid 5 through 17 Processing helix chain 'd' and resid 5 through 17 Processing helix chain 'e' and resid 5 through 17 Processing helix chain 'f' and resid 5 through 17 Processing helix chain 'g' and resid 5 through 18 Processing helix chain 'h' and resid 5 through 17 Processing helix chain 'i' and resid 5 through 17 Processing helix chain 'j' and resid 5 through 17 Processing helix chain 'D' and resid 38 through 40 No H-bonds generated for 'chain 'D' and resid 38 through 40' Processing helix chain 'B' and resid 20 through 23 Processing helix chain 'E' and resid 5 through 17 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'G' and resid 5 through 17 Processing helix chain 'H' and resid 5 through 17 Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'J' and resid 5 through 17 Processing helix chain 'K' and resid 5 through 18 Processing helix chain 'L' and resid 5 through 17 Processing helix chain 'M' and resid 5 through 17 Processing helix chain 'N' and resid 5 through 17 Processing helix chain 'P' and resid 38 through 40 No H-bonds generated for 'chain 'P' and resid 38 through 40' Processing helix chain 'Q' and resid 20 through 23 Processing helix chain 'S' and resid 5 through 17 Processing helix chain 'T' and resid 5 through 17 Processing helix chain 'U' and resid 5 through 17 Processing helix chain 'V' and resid 5 through 17 Processing helix chain 'W' and resid 5 through 17 Processing helix chain 'X' and resid 5 through 17 Processing helix chain 'Y' and resid 5 through 18 Processing helix chain 'Z' and resid 5 through 17 Processing helix chain '0' and resid 5 through 17 Processing helix chain '1' and resid 5 through 17 Processing helix chain '3' and resid 38 through 40 No H-bonds generated for 'chain '3' and resid 38 through 40' Processing helix chain '4' and resid 20 through 23 Processing helix chain '6' and resid 5 through 17 Processing helix chain '7' and resid 5 through 17 Processing helix chain '8' and resid 5 through 17 Processing helix chain '9' and resid 5 through 17 Processing helix chain 'k' and resid 5 through 17 Processing helix chain 'l' and resid 5 through 17 Processing helix chain 'm' and resid 5 through 18 Processing helix chain 'n' and resid 5 through 17 Processing helix chain 'o' and resid 5 through 17 Processing helix chain 'p' and resid 5 through 17 Processing helix chain 'r' and resid 38 through 40 No H-bonds generated for 'chain 'r' and resid 38 through 40' Processing helix chain 's' and resid 20 through 23 Processing helix chain 'u' and resid 5 through 17 Processing helix chain 'v' and resid 5 through 17 Processing helix chain 'w' and resid 5 through 17 Processing helix chain 'x' and resid 5 through 17 Processing helix chain 'y' and resid 5 through 17 Processing helix chain 'z' and resid 5 through 17 Processing helix chain 'AA' and resid 5 through 18 Processing helix chain 'AB' and resid 5 through 17 Processing helix chain 'AC' and resid 5 through 17 Processing helix chain 'AD' and resid 5 through 17 Processing helix chain 'AF' and resid 38 through 40 No H-bonds generated for 'chain 'AF' and resid 38 through 40' Processing helix chain 'AG' and resid 20 through 23 Processing sheet with id=1, first strand: chain 'a' and resid 29 through 33 removed outlier: 3.552A pdb=" N TYR a 99 " --> pdb=" O ALA a 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE a 112 " --> pdb=" O VAL a 101 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'a' and resid 83 through 84 Processing sheet with id=3, first strand: chain 'a' and resid 94 through 95 Processing sheet with id=4, first strand: chain 'a' and resid 136 through 137 Processing sheet with id=5, first strand: chain 'b' and resid 29 through 33 removed outlier: 6.772A pdb=" N HIS b 98 " --> pdb=" O VAL b 118 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N VAL b 118 " --> pdb=" O HIS b 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA b 100 " --> pdb=" O LEU b 116 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N LEU b 116 " --> pdb=" O ALA b 100 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE b 102 " --> pdb=" O ALA b 114 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N ALA b 114 " --> pdb=" O PHE b 102 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'c' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS c 98 " --> pdb=" O VAL c 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL c 118 " --> pdb=" O HIS c 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA c 100 " --> pdb=" O LEU c 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU c 116 " --> pdb=" O ALA c 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE c 102 " --> pdb=" O ALA c 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA c 114 " --> pdb=" O PHE c 102 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'c' and resid 83 through 84 Processing sheet with id=8, first strand: chain 'c' and resid 136 through 137 Processing sheet with id=9, first strand: chain 'd' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG d 57 " --> pdb=" O VAL d 30 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N THR d 95 " --> pdb=" O VAL d 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL d 118 " --> pdb=" O THR d 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR d 97 " --> pdb=" O LEU d 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE d 112 " --> pdb=" O VAL d 101 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'd' and resid 83 through 84 Processing sheet with id=11, first strand: chain 'e' and resid 29 through 33 removed outlier: 3.640A pdb=" N HIS e 98 " --> pdb=" O HIS e 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG e 120 " --> pdb=" O VAL e 96 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N HIS e 98 " --> pdb=" O VAL e 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL e 118 " --> pdb=" O HIS e 98 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ALA e 100 " --> pdb=" O LEU e 116 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU e 116 " --> pdb=" O ALA e 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE e 102 " --> pdb=" O ALA e 114 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N ALA e 114 " --> pdb=" O PHE e 102 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'e' and resid 83 through 84 Processing sheet with id=13, first strand: chain 'e' and resid 136 through 137 Processing sheet with id=14, first strand: chain 'f' and resid 29 through 33 removed outlier: 7.215A pdb=" N TYR f 99 " --> pdb=" O LYS f 113 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS f 113 " --> pdb=" O TYR f 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL f 101 " --> pdb=" O LEU f 111 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'f' and resid 83 through 84 Processing sheet with id=16, first strand: chain 'f' and resid 94 through 95 Processing sheet with id=17, first strand: chain 'g' and resid 57 through 58 removed outlier: 3.904A pdb=" N ARG g 57 " --> pdb=" O VAL g 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL g 94 " --> pdb=" O LEU g 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS g 98 " --> pdb=" O VAL g 118 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N VAL g 118 " --> pdb=" O HIS g 98 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALA g 100 " --> pdb=" O LEU g 116 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N LEU g 116 " --> pdb=" O ALA g 100 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N PHE g 102 " --> pdb=" O ALA g 114 " (cutoff:3.500A) removed outlier: 13.048A pdb=" N ALA g 114 " --> pdb=" O PHE g 102 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'g' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEU g 83 " --> pdb=" O PHE g 130 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'h' and resid 29 through 33 removed outlier: 10.300A pdb=" N THR h 95 " --> pdb=" O VAL h 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL h 118 " --> pdb=" O THR h 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR h 97 " --> pdb=" O LEU h 116 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'h' and resid 83 through 84 removed outlier: 3.913A pdb=" N LEU h 83 " --> pdb=" O PHE h 130 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'i' and resid 29 through 33 removed outlier: 7.008A pdb=" N HIS i 98 " --> pdb=" O VAL i 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VAL i 118 " --> pdb=" O HIS i 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA i 100 " --> pdb=" O LEU i 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU i 116 " --> pdb=" O ALA i 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE i 102 " --> pdb=" O ALA i 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALA i 114 " --> pdb=" O PHE i 102 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'i' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEU i 83 " --> pdb=" O PHE i 130 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'i' and resid 136 through 137 Processing sheet with id=24, first strand: chain 'j' and resid 29 through 33 removed outlier: 3.657A pdb=" N HIS j 98 " --> pdb=" O HIS j 33 " (cutoff:3.500A) removed outlier: 15.203A pdb=" N THR j 95 " --> pdb=" O THR j 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR j 117 " --> pdb=" O THR j 95 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR j 97 " --> pdb=" O PRO j 115 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR j 99 " --> pdb=" O LYS j 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS j 113 " --> pdb=" O TYR j 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL j 101 " --> pdb=" O LEU j 111 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'j' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEU j 83 " --> pdb=" O PHE j 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL j 129 " --> pdb=" O UNK A 101 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'j' and resid 136 through 138 removed outlier: 5.770A pdb=" N THR j 136 " --> pdb=" O UNK A 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=26 Processing sheet with id=27, first strand: chain 'A' and resid 3 through 4 removed outlier: 3.537A pdb=" N ASP D 18 " --> pdb=" O UNK A 3 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 5 through 8 removed outlier: 5.796A pdb=" N GLN D 6 " --> pdb=" O ARG D 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA D 75 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER D 31 " --> pdb=" O ALA D 75 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'B' and resid 5 through 8 removed outlier: 5.781A pdb=" N GLN B 6 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA B 75 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER B 31 " --> pdb=" O ALA B 75 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASP B 51 " --> pdb=" O VAL B 54 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'C' and resid 5 through 8 removed outlier: 6.104A pdb=" N GLN C 6 " --> pdb=" O ARG C 89 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA C 75 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER C 31 " --> pdb=" O ALA C 75 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=33, first strand: chain 'E' and resid 29 through 33 removed outlier: 3.553A pdb=" N TYR E 99 " --> pdb=" O ALA E 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE E 112 " --> pdb=" O VAL E 101 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 83 through 84 Processing sheet with id=35, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=36, first strand: chain 'E' and resid 136 through 137 Processing sheet with id=37, first strand: chain 'F' and resid 29 through 33 removed outlier: 6.772A pdb=" N HIS F 98 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N VAL F 118 " --> pdb=" O HIS F 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA F 100 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N LEU F 116 " --> pdb=" O ALA F 100 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE F 102 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N ALA F 114 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'G' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS G 98 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL G 118 " --> pdb=" O HIS G 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA G 100 " --> pdb=" O LEU G 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU G 116 " --> pdb=" O ALA G 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE G 102 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA G 114 " --> pdb=" O PHE G 102 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'G' and resid 83 through 84 Processing sheet with id=40, first strand: chain 'G' and resid 136 through 137 Processing sheet with id=41, first strand: chain 'H' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG H 57 " --> pdb=" O VAL H 30 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N THR H 95 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL H 118 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR H 97 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE H 112 " --> pdb=" O VAL H 101 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'H' and resid 83 through 84 Processing sheet with id=43, first strand: chain 'I' and resid 29 through 33 removed outlier: 3.640A pdb=" N HIS I 98 " --> pdb=" O HIS I 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG I 120 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N HIS I 98 " --> pdb=" O VAL I 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL I 118 " --> pdb=" O HIS I 98 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N ALA I 100 " --> pdb=" O LEU I 116 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N LEU I 116 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE I 102 " --> pdb=" O ALA I 114 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N ALA I 114 " --> pdb=" O PHE I 102 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'I' and resid 83 through 84 Processing sheet with id=45, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=46, first strand: chain 'J' and resid 29 through 33 removed outlier: 7.214A pdb=" N TYR J 99 " --> pdb=" O LYS J 113 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS J 113 " --> pdb=" O TYR J 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL J 101 " --> pdb=" O LEU J 111 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'J' and resid 83 through 84 Processing sheet with id=48, first strand: chain 'J' and resid 94 through 95 Processing sheet with id=49, first strand: chain 'K' and resid 57 through 58 removed outlier: 3.903A pdb=" N ARG K 57 " --> pdb=" O VAL K 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL K 94 " --> pdb=" O LEU K 122 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N HIS K 98 " --> pdb=" O VAL K 118 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N VAL K 118 " --> pdb=" O HIS K 98 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALA K 100 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N LEU K 116 " --> pdb=" O ALA K 100 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N PHE K 102 " --> pdb=" O ALA K 114 " (cutoff:3.500A) removed outlier: 13.047A pdb=" N ALA K 114 " --> pdb=" O PHE K 102 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'K' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEU K 83 " --> pdb=" O PHE K 130 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'L' and resid 29 through 33 removed outlier: 10.300A pdb=" N THR L 95 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL L 118 " --> pdb=" O THR L 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR L 97 " --> pdb=" O LEU L 116 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'L' and resid 83 through 84 removed outlier: 3.913A pdb=" N LEU L 83 " --> pdb=" O PHE L 130 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'M' and resid 29 through 33 removed outlier: 7.008A pdb=" N HIS M 98 " --> pdb=" O VAL M 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VAL M 118 " --> pdb=" O HIS M 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA M 100 " --> pdb=" O LEU M 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU M 116 " --> pdb=" O ALA M 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE M 102 " --> pdb=" O ALA M 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALA M 114 " --> pdb=" O PHE M 102 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'M' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEU M 83 " --> pdb=" O PHE M 130 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'M' and resid 136 through 137 Processing sheet with id=56, first strand: chain 'N' and resid 29 through 33 removed outlier: 3.657A pdb=" N HIS N 98 " --> pdb=" O HIS N 33 " (cutoff:3.500A) removed outlier: 15.203A pdb=" N THR N 95 " --> pdb=" O THR N 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR N 117 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N THR N 97 " --> pdb=" O PRO N 115 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYR N 99 " --> pdb=" O LYS N 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS N 113 " --> pdb=" O TYR N 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL N 101 " --> pdb=" O LEU N 111 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'N' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEU N 83 " --> pdb=" O PHE N 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL N 129 " --> pdb=" O UNK O 101 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'N' and resid 136 through 138 removed outlier: 5.770A pdb=" N THR N 136 " --> pdb=" O UNK O 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=58 Processing sheet with id=59, first strand: chain 'O' and resid 3 through 4 removed outlier: 3.538A pdb=" N ASP P 18 " --> pdb=" O UNK O 3 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'P' and resid 5 through 8 removed outlier: 5.796A pdb=" N GLN P 6 " --> pdb=" O ARG P 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA P 75 " --> pdb=" O SER P 31 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER P 31 " --> pdb=" O ALA P 75 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'Q' and resid 5 through 8 removed outlier: 5.780A pdb=" N GLN Q 6 " --> pdb=" O ARG Q 89 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA Q 75 " --> pdb=" O SER Q 31 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER Q 31 " --> pdb=" O ALA Q 75 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'Q' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASP Q 51 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'R' and resid 5 through 8 removed outlier: 6.104A pdb=" N GLN R 6 " --> pdb=" O ARG R 89 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ALA R 75 " --> pdb=" O SER R 31 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER R 31 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'R' and resid 16 through 18 Processing sheet with id=65, first strand: chain 'S' and resid 29 through 33 removed outlier: 3.552A pdb=" N TYR S 99 " --> pdb=" O ALA S 114 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE S 112 " --> pdb=" O VAL S 101 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'S' and resid 83 through 84 Processing sheet with id=67, first strand: chain 'S' and resid 94 through 95 Processing sheet with id=68, first strand: chain 'S' and resid 136 through 137 Processing sheet with id=69, first strand: chain 'T' and resid 29 through 33 removed outlier: 6.772A pdb=" N HIS T 98 " --> pdb=" O VAL T 118 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N VAL T 118 " --> pdb=" O HIS T 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA T 100 " --> pdb=" O LEU T 116 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N LEU T 116 " --> pdb=" O ALA T 100 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE T 102 " --> pdb=" O ALA T 114 " (cutoff:3.500A) removed outlier: 12.569A pdb=" N ALA T 114 " --> pdb=" O PHE T 102 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'U' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS U 98 " --> pdb=" O VAL U 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL U 118 " --> pdb=" O HIS U 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA U 100 " --> pdb=" O LEU U 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU U 116 " --> pdb=" O ALA U 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE U 102 " --> pdb=" O ALA U 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA U 114 " --> pdb=" O PHE U 102 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'U' and resid 83 through 84 Processing sheet with id=72, first strand: chain 'U' and resid 136 through 137 Processing sheet with id=73, first strand: chain 'V' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG V 57 " --> pdb=" O VAL V 30 " (cutoff:3.500A) removed outlier: 10.114A pdb=" N THR V 95 " --> pdb=" O VAL V 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL V 118 " --> pdb=" O THR V 95 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR V 97 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE V 112 " --> pdb=" O VAL V 101 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'V' and resid 83 through 84 Processing sheet with id=75, first strand: chain 'W' and resid 29 through 33 removed outlier: 3.639A pdb=" N HIS W 98 " --> pdb=" O HIS W 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG W 120 " --> pdb=" O VAL W 96 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N HIS W 98 " --> pdb=" O VAL W 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL W 118 " --> pdb=" O HIS W 98 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ALA W 100 " --> pdb=" O LEU W 116 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU W 116 " --> pdb=" O ALA W 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE W 102 " --> pdb=" O ALA W 114 " (cutoff:3.500A) removed outlier: 12.477A pdb=" N ALA W 114 " --> pdb=" O PHE W 102 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'W' and resid 83 through 84 Processing sheet with id=77, first strand: chain 'W' and resid 136 through 137 Processing sheet with id=78, first strand: chain 'X' and resid 29 through 33 removed outlier: 7.215A pdb=" N TYR X 99 " --> pdb=" O LYS X 113 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS X 113 " --> pdb=" O TYR X 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL X 101 " --> pdb=" O LEU X 111 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'X' and resid 83 through 84 Processing sheet with id=80, first strand: chain 'X' and resid 94 through 95 Processing sheet with id=81, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.904A pdb=" N ARG Y 57 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL Y 94 " --> pdb=" O LEU Y 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS Y 98 " --> pdb=" O VAL Y 118 " (cutoff:3.500A) removed outlier: 10.966A pdb=" N VAL Y 118 " --> pdb=" O HIS Y 98 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N ALA Y 100 " --> pdb=" O LEU Y 116 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N LEU Y 116 " --> pdb=" O ALA Y 100 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N PHE Y 102 " --> pdb=" O ALA Y 114 " (cutoff:3.500A) removed outlier: 13.047A pdb=" N ALA Y 114 " --> pdb=" O PHE Y 102 " (cutoff:3.500A) Processing sheet with id=82, first strand: chain 'Y' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEU Y 83 " --> pdb=" O PHE Y 130 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'Z' and resid 29 through 33 removed outlier: 10.300A pdb=" N THR Z 95 " --> pdb=" O VAL Z 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL Z 118 " --> pdb=" O THR Z 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR Z 97 " --> pdb=" O LEU Z 116 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'Z' and resid 83 through 84 removed outlier: 3.912A pdb=" N LEU Z 83 " --> pdb=" O PHE Z 130 " (cutoff:3.500A) Processing sheet with id=85, first strand: chain '0' and resid 29 through 33 removed outlier: 7.007A pdb=" N HIS 0 98 " --> pdb=" O VAL 0 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VAL 0 118 " --> pdb=" O HIS 0 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA 0 100 " --> pdb=" O LEU 0 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU 0 116 " --> pdb=" O ALA 0 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE 0 102 " --> pdb=" O ALA 0 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALA 0 114 " --> pdb=" O PHE 0 102 " (cutoff:3.500A) Processing sheet with id=86, first strand: chain '0' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEU 0 83 " --> pdb=" O PHE 0 130 " (cutoff:3.500A) Processing sheet with id=87, first strand: chain '0' and resid 136 through 137 Processing sheet with id=88, first strand: chain '1' and resid 29 through 33 removed outlier: 3.657A pdb=" N HIS 1 98 " --> pdb=" O HIS 1 33 " (cutoff:3.500A) removed outlier: 15.204A pdb=" N THR 1 95 " --> pdb=" O THR 1 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR 1 117 " --> pdb=" O THR 1 95 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR 1 97 " --> pdb=" O PRO 1 115 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR 1 99 " --> pdb=" O LYS 1 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS 1 113 " --> pdb=" O TYR 1 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL 1 101 " --> pdb=" O LEU 1 111 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain '1' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEU 1 83 " --> pdb=" O PHE 1 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL 1 129 " --> pdb=" O UNK 2 101 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain '1' and resid 136 through 138 removed outlier: 5.770A pdb=" N THR 1 136 " --> pdb=" O UNK 2 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=90 Processing sheet with id=91, first strand: chain '2' and resid 3 through 4 removed outlier: 3.537A pdb=" N ASP 3 18 " --> pdb=" O UNK 2 3 " (cutoff:3.500A) Processing sheet with id=92, first strand: chain '3' and resid 5 through 8 removed outlier: 5.797A pdb=" N GLN 3 6 " --> pdb=" O ARG 3 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA 3 75 " --> pdb=" O SER 3 31 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER 3 31 " --> pdb=" O ALA 3 75 " (cutoff:3.500A) Processing sheet with id=93, first strand: chain '4' and resid 5 through 8 removed outlier: 5.781A pdb=" N GLN 4 6 " --> pdb=" O ARG 4 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA 4 75 " --> pdb=" O SER 4 31 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SER 4 31 " --> pdb=" O ALA 4 75 " (cutoff:3.500A) Processing sheet with id=94, first strand: chain '4' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASP 4 51 " --> pdb=" O VAL 4 54 " (cutoff:3.500A) Processing sheet with id=95, first strand: chain '5' and resid 5 through 8 removed outlier: 6.104A pdb=" N GLN 5 6 " --> pdb=" O ARG 5 89 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA 5 75 " --> pdb=" O SER 5 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SER 5 31 " --> pdb=" O ALA 5 75 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain '5' and resid 16 through 18 Processing sheet with id=97, first strand: chain '6' and resid 29 through 33 removed outlier: 3.553A pdb=" N TYR 6 99 " --> pdb=" O ALA 6 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE 6 112 " --> pdb=" O VAL 6 101 " (cutoff:3.500A) Processing sheet with id=98, first strand: chain '6' and resid 83 through 84 Processing sheet with id=99, first strand: chain '6' and resid 94 through 95 Processing sheet with id=100, first strand: chain '6' and resid 136 through 137 Processing sheet with id=101, first strand: chain '7' and resid 29 through 33 removed outlier: 6.771A pdb=" N HIS 7 98 " --> pdb=" O VAL 7 118 " (cutoff:3.500A) removed outlier: 10.518A pdb=" N VAL 7 118 " --> pdb=" O HIS 7 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA 7 100 " --> pdb=" O LEU 7 116 " (cutoff:3.500A) removed outlier: 10.795A pdb=" N LEU 7 116 " --> pdb=" O ALA 7 100 " (cutoff:3.500A) removed outlier: 10.941A pdb=" N PHE 7 102 " --> pdb=" O ALA 7 114 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N ALA 7 114 " --> pdb=" O PHE 7 102 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '8' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS 8 98 " --> pdb=" O VAL 8 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL 8 118 " --> pdb=" O HIS 8 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA 8 100 " --> pdb=" O LEU 8 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU 8 116 " --> pdb=" O ALA 8 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE 8 102 " --> pdb=" O ALA 8 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA 8 114 " --> pdb=" O PHE 8 102 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain '8' and resid 83 through 84 Processing sheet with id=104, first strand: chain '8' and resid 136 through 137 Processing sheet with id=105, first strand: chain '9' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG 9 57 " --> pdb=" O VAL 9 30 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N THR 9 95 " --> pdb=" O VAL 9 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL 9 118 " --> pdb=" O THR 9 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR 9 97 " --> pdb=" O LEU 9 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE 9 112 " --> pdb=" O VAL 9 101 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain '9' and resid 83 through 84 Processing sheet with id=107, first strand: chain 'k' and resid 29 through 33 removed outlier: 3.639A pdb=" N HIS k 98 " --> pdb=" O HIS k 33 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG k 120 " --> pdb=" O VAL k 96 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N HIS k 98 " --> pdb=" O VAL k 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL k 118 " --> pdb=" O HIS k 98 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ALA k 100 " --> pdb=" O LEU k 116 " (cutoff:3.500A) removed outlier: 10.914A pdb=" N LEU k 116 " --> pdb=" O ALA k 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE k 102 " --> pdb=" O ALA k 114 " (cutoff:3.500A) removed outlier: 12.476A pdb=" N ALA k 114 " --> pdb=" O PHE k 102 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'k' and resid 83 through 84 Processing sheet with id=109, first strand: chain 'k' and resid 136 through 137 Processing sheet with id=110, first strand: chain 'l' and resid 29 through 33 removed outlier: 7.215A pdb=" N TYR l 99 " --> pdb=" O LYS l 113 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS l 113 " --> pdb=" O TYR l 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL l 101 " --> pdb=" O LEU l 111 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'l' and resid 83 through 84 Processing sheet with id=112, first strand: chain 'l' and resid 94 through 95 Processing sheet with id=113, first strand: chain 'm' and resid 57 through 58 removed outlier: 3.903A pdb=" N ARG m 57 " --> pdb=" O VAL m 30 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL m 94 " --> pdb=" O LEU m 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS m 98 " --> pdb=" O VAL m 118 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N VAL m 118 " --> pdb=" O HIS m 98 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALA m 100 " --> pdb=" O LEU m 116 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N LEU m 116 " --> pdb=" O ALA m 100 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N PHE m 102 " --> pdb=" O ALA m 114 " (cutoff:3.500A) removed outlier: 13.048A pdb=" N ALA m 114 " --> pdb=" O PHE m 102 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'm' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEU m 83 " --> pdb=" O PHE m 130 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'n' and resid 29 through 33 removed outlier: 10.300A pdb=" N THR n 95 " --> pdb=" O VAL n 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VAL n 118 " --> pdb=" O THR n 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR n 97 " --> pdb=" O LEU n 116 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'n' and resid 83 through 84 removed outlier: 3.913A pdb=" N LEU n 83 " --> pdb=" O PHE n 130 " (cutoff:3.500A) Processing sheet with id=117, first strand: chain 'o' and resid 29 through 33 removed outlier: 7.007A pdb=" N HIS o 98 " --> pdb=" O VAL o 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VAL o 118 " --> pdb=" O HIS o 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALA o 100 " --> pdb=" O LEU o 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEU o 116 " --> pdb=" O ALA o 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE o 102 " --> pdb=" O ALA o 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALA o 114 " --> pdb=" O PHE o 102 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'o' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEU o 83 " --> pdb=" O PHE o 130 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'o' and resid 136 through 137 Processing sheet with id=120, first strand: chain 'p' and resid 29 through 33 removed outlier: 3.656A pdb=" N HIS p 98 " --> pdb=" O HIS p 33 " (cutoff:3.500A) removed outlier: 15.203A pdb=" N THR p 95 " --> pdb=" O THR p 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THR p 117 " --> pdb=" O THR p 95 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THR p 97 " --> pdb=" O PRO p 115 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N TYR p 99 " --> pdb=" O LYS p 113 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS p 113 " --> pdb=" O TYR p 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL p 101 " --> pdb=" O LEU p 111 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain 'p' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEU p 83 " --> pdb=" O PHE p 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL p 129 " --> pdb=" O UNK q 101 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'p' and resid 136 through 138 removed outlier: 5.770A pdb=" N THR p 136 " --> pdb=" O UNK q 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=122 Processing sheet with id=123, first strand: chain 'q' and resid 3 through 4 removed outlier: 3.537A pdb=" N ASP r 18 " --> pdb=" O UNK q 3 " (cutoff:3.500A) Processing sheet with id=124, first strand: chain 'r' and resid 5 through 8 removed outlier: 5.796A pdb=" N GLN r 6 " --> pdb=" O ARG r 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALA r 75 " --> pdb=" O SER r 31 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER r 31 " --> pdb=" O ALA r 75 " (cutoff:3.500A) Processing sheet with id=125, first strand: chain 's' and resid 5 through 8 removed outlier: 5.781A pdb=" N GLN s 6 " --> pdb=" O ARG s 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALA s 75 " --> pdb=" O SER s 31 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N SER s 31 " --> pdb=" O ALA s 75 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 's' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASP s 51 " --> pdb=" O VAL s 54 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 't' and resid 5 through 8 removed outlier: 6.105A pdb=" N GLN t 6 " --> pdb=" O ARG t 89 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA t 75 " --> pdb=" O SER t 31 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER t 31 " --> pdb=" O ALA t 75 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 't' and resid 16 through 18 Processing sheet with id=129, first strand: chain 'u' and resid 29 through 33 removed outlier: 3.552A pdb=" N TYR u 99 " --> pdb=" O ALA u 114 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE u 112 " --> pdb=" O VAL u 101 " (cutoff:3.500A) Processing sheet with id=130, first strand: chain 'u' and resid 83 through 84 Processing sheet with id=131, first strand: chain 'u' and resid 94 through 95 Processing sheet with id=132, first strand: chain 'u' and resid 136 through 137 Processing sheet with id=133, first strand: chain 'v' and resid 29 through 33 removed outlier: 6.772A pdb=" N HIS v 98 " --> pdb=" O VAL v 118 " (cutoff:3.500A) removed outlier: 10.517A pdb=" N VAL v 118 " --> pdb=" O HIS v 98 " (cutoff:3.500A) removed outlier: 11.076A pdb=" N ALA v 100 " --> pdb=" O LEU v 116 " (cutoff:3.500A) removed outlier: 10.796A pdb=" N LEU v 116 " --> pdb=" O ALA v 100 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N PHE v 102 " --> pdb=" O ALA v 114 " (cutoff:3.500A) removed outlier: 12.570A pdb=" N ALA v 114 " --> pdb=" O PHE v 102 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'w' and resid 29 through 33 removed outlier: 7.143A pdb=" N HIS w 98 " --> pdb=" O VAL w 118 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N VAL w 118 " --> pdb=" O HIS w 98 " (cutoff:3.500A) removed outlier: 11.239A pdb=" N ALA w 100 " --> pdb=" O LEU w 116 " (cutoff:3.500A) removed outlier: 11.087A pdb=" N LEU w 116 " --> pdb=" O ALA w 100 " (cutoff:3.500A) removed outlier: 11.482A pdb=" N PHE w 102 " --> pdb=" O ALA w 114 " (cutoff:3.500A) removed outlier: 12.883A pdb=" N ALA w 114 " --> pdb=" O PHE w 102 " (cutoff:3.500A) Processing sheet with id=135, first strand: chain 'w' and resid 83 through 84 Processing sheet with id=136, first strand: chain 'w' and resid 136 through 137 Processing sheet with id=137, first strand: chain 'x' and resid 57 through 58 removed outlier: 3.931A pdb=" N ARG x 57 " --> pdb=" O VAL x 30 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N THR x 95 " --> pdb=" O VAL x 118 " (cutoff:3.500A) removed outlier: 11.357A pdb=" N VAL x 118 " --> pdb=" O THR x 95 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR x 97 " --> pdb=" O LEU x 116 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE x 112 " --> pdb=" O VAL x 101 " (cutoff:3.500A) Processing sheet with id=138, first strand: chain 'x' and resid 83 through 84 Processing sheet with id=139, first strand: chain 'y' and resid 29 through 33 removed outlier: 3.640A pdb=" N HIS y 98 " --> pdb=" O HIS y 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG y 120 " --> pdb=" O VAL y 96 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N HIS y 98 " --> pdb=" O VAL y 118 " (cutoff:3.500A) removed outlier: 10.847A pdb=" N VAL y 118 " --> pdb=" O HIS y 98 " (cutoff:3.500A) removed outlier: 11.118A pdb=" N ALA y 100 " --> pdb=" O LEU y 116 " (cutoff:3.500A) removed outlier: 10.915A pdb=" N LEU y 116 " --> pdb=" O ALA y 100 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N PHE y 102 " --> pdb=" O ALA y 114 " (cutoff:3.500A) removed outlier: 12.477A pdb=" N ALA y 114 " --> pdb=" O PHE y 102 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain 'y' and resid 83 through 84 Processing sheet with id=141, first strand: chain 'y' and resid 136 through 137 Processing sheet with id=142, first strand: chain 'z' and resid 29 through 33 removed outlier: 7.215A pdb=" N TYR z 99 " --> pdb=" O LYS z 113 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LYS z 113 " --> pdb=" O TYR z 99 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL z 101 " --> pdb=" O LEU z 111 " (cutoff:3.500A) Processing sheet with id=143, first strand: chain 'z' and resid 83 through 84 Processing sheet with id=144, first strand: chain 'z' and resid 94 through 95 Processing sheet with id=145, first strand: chain 'AA' and resid 57 through 58 removed outlier: 3.904A pdb=" N ARGAA 57 " --> pdb=" O VALAA 30 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VALAA 94 " --> pdb=" O LEUAA 122 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HISAA 98 " --> pdb=" O VALAA 118 " (cutoff:3.500A) removed outlier: 10.965A pdb=" N VALAA 118 " --> pdb=" O HISAA 98 " (cutoff:3.500A) removed outlier: 11.564A pdb=" N ALAAA 100 " --> pdb=" O LEUAA 116 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N LEUAA 116 " --> pdb=" O ALAAA 100 " (cutoff:3.500A) removed outlier: 11.752A pdb=" N PHEAA 102 " --> pdb=" O ALAAA 114 " (cutoff:3.500A) removed outlier: 13.048A pdb=" N ALAAA 114 " --> pdb=" O PHEAA 102 " (cutoff:3.500A) Processing sheet with id=146, first strand: chain 'AA' and resid 83 through 84 removed outlier: 3.810A pdb=" N LEUAA 83 " --> pdb=" O PHEAA 130 " (cutoff:3.500A) Processing sheet with id=147, first strand: chain 'AB' and resid 29 through 33 removed outlier: 10.300A pdb=" N THRAB 95 " --> pdb=" O VALAB 118 " (cutoff:3.500A) removed outlier: 11.495A pdb=" N VALAB 118 " --> pdb=" O THRAB 95 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THRAB 97 " --> pdb=" O LEUAB 116 " (cutoff:3.500A) Processing sheet with id=148, first strand: chain 'AB' and resid 83 through 84 removed outlier: 3.913A pdb=" N LEUAB 83 " --> pdb=" O PHEAB 130 " (cutoff:3.500A) Processing sheet with id=149, first strand: chain 'AC' and resid 29 through 33 removed outlier: 7.007A pdb=" N HISAC 98 " --> pdb=" O VALAC 118 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N VALAC 118 " --> pdb=" O HISAC 98 " (cutoff:3.500A) removed outlier: 10.560A pdb=" N ALAAC 100 " --> pdb=" O LEUAC 116 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N LEUAC 116 " --> pdb=" O ALAAC 100 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHEAC 102 " --> pdb=" O ALAAC 114 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N ALAAC 114 " --> pdb=" O PHEAC 102 " (cutoff:3.500A) Processing sheet with id=150, first strand: chain 'AC' and resid 83 through 84 removed outlier: 4.159A pdb=" N LEUAC 83 " --> pdb=" O PHEAC 130 " (cutoff:3.500A) Processing sheet with id=151, first strand: chain 'AC' and resid 136 through 137 Processing sheet with id=152, first strand: chain 'AD' and resid 29 through 33 removed outlier: 3.657A pdb=" N HISAD 98 " --> pdb=" O HISAD 33 " (cutoff:3.500A) removed outlier: 15.203A pdb=" N THRAD 95 " --> pdb=" O THRAD 117 " (cutoff:3.500A) removed outlier: 12.746A pdb=" N THRAD 117 " --> pdb=" O THRAD 95 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N THRAD 97 " --> pdb=" O PROAD 115 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N TYRAD 99 " --> pdb=" O LYSAD 113 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYSAD 113 " --> pdb=" O TYRAD 99 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VALAD 101 " --> pdb=" O LEUAD 111 " (cutoff:3.500A) Processing sheet with id=153, first strand: chain 'AD' and resid 83 through 84 removed outlier: 3.740A pdb=" N LEUAD 83 " --> pdb=" O PHEAD 130 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VALAD 129 " --> pdb=" O UNKAE 101 " (cutoff:3.500A) Processing sheet with id=154, first strand: chain 'AD' and resid 136 through 138 removed outlier: 5.770A pdb=" N THRAD 136 " --> pdb=" O UNKAE 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=154 Processing sheet with id=155, first strand: chain 'AE' and resid 3 through 4 removed outlier: 3.538A pdb=" N ASPAF 18 " --> pdb=" O UNKAE 3 " (cutoff:3.500A) Processing sheet with id=156, first strand: chain 'AF' and resid 5 through 8 removed outlier: 5.796A pdb=" N GLNAF 6 " --> pdb=" O ARGAF 89 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ALAAF 75 " --> pdb=" O SERAF 31 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SERAF 31 " --> pdb=" O ALAAF 75 " (cutoff:3.500A) Processing sheet with id=157, first strand: chain 'AG' and resid 5 through 8 removed outlier: 5.781A pdb=" N GLNAG 6 " --> pdb=" O ARGAG 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ALAAG 75 " --> pdb=" O SERAG 31 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N SERAG 31 " --> pdb=" O ALAAG 75 " (cutoff:3.500A) Processing sheet with id=158, first strand: chain 'AG' and resid 16 through 18 removed outlier: 3.563A pdb=" N ASPAG 51 " --> pdb=" O VALAG 54 " (cutoff:3.500A) Processing sheet with id=159, first strand: chain 'AH' and resid 5 through 8 removed outlier: 6.104A pdb=" N GLNAH 6 " --> pdb=" O ARGAH 89 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALAAH 75 " --> pdb=" O SERAH 31 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N SERAH 31 " --> pdb=" O ALAAH 75 " (cutoff:3.500A) Processing sheet with id=160, first strand: chain 'AH' and resid 16 through 18 1275 hydrogen bonds defined for protein. 3330 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 22.44 Time building geometry restraints manager: 13.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19052 1.33 - 1.45: 9918 1.45 - 1.57: 34715 1.57 - 1.69: 5 1.69 - 1.81: 45 Bond restraints: 63735 Sorted by residual: bond pdb=" CA UNK q 58 " pdb=" C UNK q 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 9.13e+00 bond pdb=" CA UNKAE 58 " pdb=" C UNKAE 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 9.13e+00 bond pdb=" CA UNK A 58 " pdb=" C UNK A 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 9.09e+00 bond pdb=" CA UNK O 58 " pdb=" C UNK O 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 9.06e+00 bond pdb=" CA UNK 2 58 " pdb=" C UNK 2 58 " ideal model delta sigma weight residual 1.525 1.462 0.063 2.10e-02 2.27e+03 8.98e+00 ... (remaining 63730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 86393 2.88 - 5.76: 1002 5.76 - 8.64: 105 8.64 - 11.53: 50 11.53 - 14.41: 10 Bond angle restraints: 87560 Sorted by residual: angle pdb=" N ASP s 39 " pdb=" CA ASP s 39 " pdb=" C ASP s 39 " ideal model delta sigma weight residual 111.02 125.43 -14.41 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N ASP Q 39 " pdb=" CA ASP Q 39 " pdb=" C ASP Q 39 " ideal model delta sigma weight residual 111.02 125.40 -14.38 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N ASP 4 39 " pdb=" CA ASP 4 39 " pdb=" C ASP 4 39 " ideal model delta sigma weight residual 111.02 125.39 -14.37 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N ASP B 39 " pdb=" CA ASP B 39 " pdb=" C ASP B 39 " ideal model delta sigma weight residual 111.02 125.38 -14.36 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N ASPAG 39 " pdb=" CA ASPAG 39 " pdb=" C ASPAG 39 " ideal model delta sigma weight residual 111.02 125.38 -14.36 1.22e+00 6.72e-01 1.39e+02 ... (remaining 87555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 34201 17.90 - 35.80: 2139 35.80 - 53.70: 335 53.70 - 71.60: 50 71.60 - 89.49: 15 Dihedral angle restraints: 36740 sinusoidal: 12110 harmonic: 24630 Sorted by residual: dihedral pdb=" CA THR t 63 " pdb=" C THR t 63 " pdb=" N ALA t 64 " pdb=" CA ALA t 64 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THRAH 63 " pdb=" C THRAH 63 " pdb=" N ALAAH 64 " pdb=" CA ALAAH 64 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA THR C 63 " pdb=" C THR C 63 " pdb=" N ALA C 64 " pdb=" CA ALA C 64 " ideal model delta harmonic sigma weight residual 180.00 159.96 20.04 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 36737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 9751 0.096 - 0.191: 605 0.191 - 0.287: 24 0.287 - 0.383: 10 0.383 - 0.478: 15 Chirality restraints: 10405 Sorted by residual: chirality pdb=" CA ASP Q 39 " pdb=" N ASP Q 39 " pdb=" C ASP Q 39 " pdb=" CB ASP Q 39 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CA ASP B 39 " pdb=" N ASP B 39 " pdb=" C ASP B 39 " pdb=" CB ASP B 39 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA ASPAG 39 " pdb=" N ASPAG 39 " pdb=" C ASPAG 39 " pdb=" CB ASPAG 39 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 10402 not shown) Planarity restraints: 11555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP I 51 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO I 52 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO I 52 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO I 52 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP W 51 " 0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO W 52 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO W 52 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO W 52 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP e 51 " -0.072 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO e 52 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO e 52 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO e 52 " -0.058 5.00e-02 4.00e+02 ... (remaining 11552 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.59: 20 1.59 - 2.42: 355 2.42 - 3.24: 66034 3.24 - 4.07: 150760 4.07 - 4.90: 264705 Warning: very small nonbonded interaction distances. Nonbonded interactions: 481874 Sorted by model distance: nonbonded pdb=" N LEU 5 13 " pdb=" NH1 ARG r 80 " model vdw 0.759 3.200 nonbonded pdb=" NH1 ARG D 80 " pdb=" N LEUAH 13 " model vdw 0.759 3.200 nonbonded pdb=" N LEU R 13 " pdb=" NH1 ARG 3 80 " model vdw 0.759 3.200 nonbonded pdb=" N LEU t 13 " pdb=" NH1 ARGAF 80 " model vdw 0.759 3.200 nonbonded pdb=" N LEU C 13 " pdb=" NH1 ARG P 80 " model vdw 0.759 3.200 ... (remaining 481869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'AA' selection = chain 'AB' selection = chain 'AC' selection = chain 'AD' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } ncs_group { reference = chain '2' selection = chain 'A' selection = chain 'AE' selection = chain 'O' selection = chain 'q' } ncs_group { reference = chain '3' selection = chain '4' selection = chain '5' selection = chain 'AF' selection = chain 'AG' selection = chain 'AH' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'r' selection = chain 's' selection = chain 't' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.310 Check model and map are aligned: 0.350 Set scattering table: 0.430 Process input model: 107.130 Find NCS groups from input model: 2.160 Set up NCS constraints: 1.030 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3779 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 63735 Z= 0.269 Angle : 0.832 14.407 87560 Z= 0.484 Chirality : 0.051 0.478 10405 Planarity : 0.007 0.108 11555 Dihedral : 12.095 89.494 21060 Min Nonbonded Distance : 0.759 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 1.87 % Allowed : 7.71 % Favored : 90.42 % Rotamer: Outliers : 0.49 % Allowed : 0.43 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.54 (0.09), residues: 8005 helix: 1.04 (0.17), residues: 650 sheet: 1.15 (0.14), residues: 1235 loop : -1.91 (0.07), residues: 6120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP o 69 HIS 0.015 0.002 HIS 9 98 PHE 0.042 0.002 PHE Y 128 TYR 0.035 0.002 TYRAG 15 ARG 0.004 0.001 ARG V 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1137 time to evaluate : 4.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 48 LEU cc_start: 0.6713 (tp) cc_final: 0.6346 (mt) REVERT: i 97 THR cc_start: 0.7045 (p) cc_final: 0.6677 (p) REVERT: N 65 ILE cc_start: 0.4451 (tp) cc_final: 0.4229 (tp) REVERT: Z 65 ILE cc_start: 0.5157 (tp) cc_final: 0.4876 (tp) REVERT: 8 105 PRO cc_start: 0.5133 (Cg_exo) cc_final: 0.4878 (Cg_endo) REVERT: o 7 TYR cc_start: 0.5417 (t80) cc_final: 0.5137 (t80) outliers start: 30 outliers final: 6 residues processed: 1165 average time/residue: 0.6098 time to fit residues: 1202.8311 Evaluate side-chains 552 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 546 time to evaluate : 4.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 696 optimal weight: 4.9990 chunk 625 optimal weight: 50.0000 chunk 346 optimal weight: 8.9990 chunk 213 optimal weight: 0.0670 chunk 421 optimal weight: 20.0000 chunk 334 optimal weight: 9.9990 chunk 646 optimal weight: 0.3980 chunk 250 optimal weight: 5.9990 chunk 393 optimal weight: 20.0000 chunk 481 optimal weight: 50.0000 chunk 749 optimal weight: 8.9990 overall best weight: 4.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 138 GLN ** b 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 89 ASN f 76 GLN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 GLN F 98 HIS G 89 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 98 HIS ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 ASN ** M 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 ASN S 81 ASN ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS T 109 ASN ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 81 ASN U 89 ASN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 109 ASN ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 6 GLN ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 69 ASN 6 82 GLN 7 109 ASN 8 81 ASN 8 89 ASN 8 138 GLN ** l 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 14 ASN ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 88 ASN r 6 GLN ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 12 GLN ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 76 GLN ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 109 ASN AD 14 ASN ** AD 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AH 12 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3973 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 63735 Z= 0.194 Angle : 0.667 9.609 87560 Z= 0.351 Chirality : 0.043 0.293 10405 Planarity : 0.006 0.080 11555 Dihedral : 4.574 23.742 9210 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 1.82 % Allowed : 6.68 % Favored : 91.49 % Rotamer: Outliers : 0.15 % Allowed : 3.92 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.29 (0.09), residues: 8005 helix: 1.57 (0.19), residues: 650 sheet: 1.47 (0.14), residues: 1175 loop : -1.77 (0.07), residues: 6180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP x 51 HIS 0.010 0.002 HIS L 98 PHE 0.024 0.001 PHE Z 112 TYR 0.025 0.002 TYRAA 85 ARG 0.009 0.001 ARG j 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 763 time to evaluate : 5.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 36 ASP cc_start: 0.6438 (t0) cc_final: 0.6231 (t0) REVERT: e 36 ASP cc_start: 0.6732 (t0) cc_final: 0.6433 (t70) REVERT: h 48 LEU cc_start: 0.7012 (tp) cc_final: 0.6809 (mt) REVERT: j 34 THR cc_start: 0.6267 (p) cc_final: 0.6062 (p) REVERT: N 65 ILE cc_start: 0.4020 (tp) cc_final: 0.3797 (tp) REVERT: 1 97 THR cc_start: 0.4943 (t) cc_final: 0.4633 (t) REVERT: 8 105 PRO cc_start: 0.5040 (Cg_exo) cc_final: 0.4784 (Cg_endo) REVERT: m 44 ASN cc_start: 0.4974 (p0) cc_final: 0.4161 (p0) REVERT: o 84 THR cc_start: 0.7503 (p) cc_final: 0.6469 (p) REVERT: x 124 VAL cc_start: 0.5630 (p) cc_final: 0.5231 (p) REVERT: AD 126 ASP cc_start: 0.4444 (t0) cc_final: 0.3204 (t0) outliers start: 9 outliers final: 1 residues processed: 770 average time/residue: 0.6040 time to fit residues: 788.0436 Evaluate side-chains 493 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 4.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 416 optimal weight: 7.9990 chunk 232 optimal weight: 0.6980 chunk 623 optimal weight: 30.0000 chunk 510 optimal weight: 6.9990 chunk 206 optimal weight: 5.9990 chunk 750 optimal weight: 10.0000 chunk 810 optimal weight: 30.0000 chunk 668 optimal weight: 6.9990 chunk 744 optimal weight: 50.0000 chunk 255 optimal weight: 7.9990 chunk 602 optimal weight: 8.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 HIS ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 GLN f 81 ASN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 ASN D 6 GLN ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 HIS ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 98 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 HIS ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 ASN ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** T 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 81 ASN U 82 GLN ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 98 HIS X 98 HIS ** Z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 82 GLN ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 79 ASN ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 69 ASN 6 61 GLN ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 109 ASN 8 81 ASN ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 82 GLN ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 81 ASN ** o 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN ** z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 33 HIS AD 82 GLN ** AD 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AF 6 GLN AG 12 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4255 moved from start: 0.4276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 63735 Z= 0.206 Angle : 0.655 13.357 87560 Z= 0.340 Chirality : 0.042 0.347 10405 Planarity : 0.005 0.069 11555 Dihedral : 4.381 22.108 9210 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 1.86 % Allowed : 6.55 % Favored : 91.59 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.16 (0.09), residues: 8005 helix: 1.65 (0.20), residues: 650 sheet: 1.15 (0.14), residues: 1305 loop : -1.64 (0.07), residues: 6050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP p 51 HIS 0.008 0.002 HIS T 98 PHE 0.018 0.002 PHE C 86 TYR 0.027 0.002 TYR 6 85 ARG 0.010 0.001 ARG L 120 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 695 time to evaluate : 4.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.7060 (t0) cc_final: 0.6798 (t0) REVERT: c 36 ASP cc_start: 0.6514 (t0) cc_final: 0.6250 (t0) REVERT: f 36 ASP cc_start: 0.6955 (t0) cc_final: 0.6733 (t0) REVERT: h 48 LEU cc_start: 0.7366 (tp) cc_final: 0.7077 (mt) REVERT: j 7 TYR cc_start: 0.6965 (t80) cc_final: 0.6763 (t80) REVERT: N 65 ILE cc_start: 0.4933 (tp) cc_final: 0.4693 (tp) REVERT: S 36 ASP cc_start: 0.6617 (t0) cc_final: 0.6389 (t0) REVERT: Y 36 ASP cc_start: 0.7038 (t0) cc_final: 0.6646 (t0) REVERT: 1 14 ASN cc_start: 0.7353 (m-40) cc_final: 0.6614 (m110) REVERT: 8 105 PRO cc_start: 0.5235 (Cg_exo) cc_final: 0.4957 (Cg_endo) REVERT: v 36 ASP cc_start: 0.6942 (t0) cc_final: 0.6486 (t0) REVERT: w 44 ASN cc_start: 0.5025 (p0) cc_final: 0.4808 (p0) REVERT: AA 7 TYR cc_start: 0.5119 (t80) cc_final: 0.4698 (t80) REVERT: AH 73 THR cc_start: 0.5790 (m) cc_final: 0.5457 (t) outliers start: 0 outliers final: 0 residues processed: 695 average time/residue: 0.5890 time to fit residues: 696.4120 Evaluate side-chains 465 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 4.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 741 optimal weight: 8.9990 chunk 564 optimal weight: 40.0000 chunk 389 optimal weight: 40.0000 chunk 83 optimal weight: 30.0000 chunk 358 optimal weight: 7.9990 chunk 503 optimal weight: 0.4980 chunk 753 optimal weight: 7.9990 chunk 797 optimal weight: 50.0000 chunk 393 optimal weight: 9.9990 chunk 713 optimal weight: 50.0000 chunk 214 optimal weight: 20.0000 overall best weight: 7.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 138 GLN ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN f 81 ASN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 GLN ** K 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 ASN ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 GLN ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 GLN ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 82 GLN ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 10 ASN ** Z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 76 GLN ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 10 ASN ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 11 ASN ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4569 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 63735 Z= 0.230 Angle : 0.673 12.065 87560 Z= 0.350 Chirality : 0.042 0.348 10405 Planarity : 0.005 0.092 11555 Dihedral : 4.507 22.095 9210 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 1.86 % Allowed : 6.78 % Favored : 91.36 % Rotamer: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.21 (0.09), residues: 8005 helix: 1.47 (0.20), residues: 650 sheet: 1.17 (0.14), residues: 1205 loop : -1.62 (0.07), residues: 6150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 22 HIS 0.014 0.002 HIS L 98 PHE 0.023 0.002 PHE Z 112 TYR 0.026 0.002 TYR E 85 ARG 0.041 0.001 ARG i 57 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 645 time to evaluate : 5.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: f 36 ASP cc_start: 0.7037 (t0) cc_final: 0.6581 (t0) REVERT: E 36 ASP cc_start: 0.7187 (t0) cc_final: 0.6829 (t0) REVERT: N 65 ILE cc_start: 0.4670 (tp) cc_final: 0.4455 (tp) REVERT: n 36 ASP cc_start: 0.6955 (t0) cc_final: 0.6685 (t0) REVERT: v 36 ASP cc_start: 0.6519 (t0) cc_final: 0.6188 (t0) REVERT: AA 7 TYR cc_start: 0.5088 (t80) cc_final: 0.4679 (t80) REVERT: AB 71 PRO cc_start: 0.7037 (Cg_exo) cc_final: 0.6779 (Cg_endo) outliers start: 1 outliers final: 1 residues processed: 646 average time/residue: 0.6337 time to fit residues: 704.9079 Evaluate side-chains 453 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 4.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 664 optimal weight: 9.9990 chunk 452 optimal weight: 8.9990 chunk 11 optimal weight: 30.0000 chunk 593 optimal weight: 50.0000 chunk 329 optimal weight: 50.0000 chunk 680 optimal weight: 30.0000 chunk 551 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 407 optimal weight: 0.3980 chunk 715 optimal weight: 40.0000 chunk 201 optimal weight: 30.0000 overall best weight: 11.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN f 81 ASN ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 138 GLN ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 44 ASN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 138 GLN ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 98 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** Q 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 138 GLN 1 10 ASN ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 138 GLN ** p 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 44 ASN z 76 GLN ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 89 ASN ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5028 moved from start: 0.8833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.115 63735 Z= 0.320 Angle : 0.750 14.433 87560 Z= 0.392 Chirality : 0.044 0.202 10405 Planarity : 0.006 0.072 11555 Dihedral : 5.086 31.766 9210 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 25.10 Ramachandran Plot: Outliers : 1.95 % Allowed : 7.61 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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 (0.09), residues: 8005 helix: 1.00 (0.20), residues: 650 sheet: 0.60 (0.14), residues: 1290 loop : -1.65 (0.07), residues: 6065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 22 HIS 0.015 0.003 HIS N 33 PHE 0.035 0.002 PHE 0 102 TYR 0.039 0.003 TYR 0 7 ARG 0.032 0.001 ARGAA 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 4.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 36 ASP cc_start: 0.7364 (t0) cc_final: 0.7098 (t0) REVERT: e 106 THR cc_start: 0.6488 (p) cc_final: 0.6256 (p) REVERT: f 36 ASP cc_start: 0.7332 (t0) cc_final: 0.6610 (t0) REVERT: i 69 TRP cc_start: 0.2000 (m-90) cc_final: 0.1697 (m-90) REVERT: G 44 ASN cc_start: 0.4717 (p0) cc_final: 0.4267 (p0) REVERT: N 65 ILE cc_start: 0.4426 (tp) cc_final: 0.4044 (tp) REVERT: U 36 ASP cc_start: 0.6884 (t70) cc_final: 0.6406 (t0) REVERT: Y 36 ASP cc_start: 0.7370 (t0) cc_final: 0.7137 (t70) REVERT: 1 65 ILE cc_start: 0.4842 (tp) cc_final: 0.4413 (tp) REVERT: l 36 ASP cc_start: 0.6665 (t0) cc_final: 0.6076 (t0) REVERT: n 36 ASP cc_start: 0.7264 (t0) cc_final: 0.6977 (t0) REVERT: p 121 THR cc_start: 0.7232 (t) cc_final: 0.6935 (t) REVERT: v 36 ASP cc_start: 0.7578 (t0) cc_final: 0.7079 (t0) REVERT: AA 7 TYR cc_start: 0.5678 (t80) cc_final: 0.5380 (t80) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.6065 time to fit residues: 637.0562 Evaluate side-chains 401 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 5.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 268 optimal weight: 8.9990 chunk 718 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 468 optimal weight: 50.0000 chunk 196 optimal weight: 20.0000 chunk 798 optimal weight: 50.0000 chunk 662 optimal weight: 9.9990 chunk 369 optimal weight: 30.0000 chunk 66 optimal weight: 20.0000 chunk 264 optimal weight: 50.0000 chunk 419 optimal weight: 40.0000 overall best weight: 12.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 138 GLN ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 98 HIS ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 138 GLN ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 ASN ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 HIS ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 GLN ** Z 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 14 ASN ** 1 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 138 GLN ** k 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 44 ASN ** m 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 138 GLN ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 50 ASN ** y 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 76 GLN ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 109 ASN ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5181 moved from start: 1.0225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 63735 Z= 0.296 Angle : 0.702 15.274 87560 Z= 0.364 Chirality : 0.043 0.199 10405 Planarity : 0.006 0.204 11555 Dihedral : 5.014 23.689 9210 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 23.70 Ramachandran Plot: Outliers : 1.92 % Allowed : 7.96 % Favored : 90.12 % Rotamer: Outliers : 0.03 % Allowed : 2.28 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.54 (0.09), residues: 8005 helix: 1.03 (0.21), residues: 650 sheet: 0.40 (0.14), residues: 1260 loop : -1.72 (0.07), residues: 6095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 69 HIS 0.016 0.003 HIS U 98 PHE 0.021 0.002 PHE x 128 TYR 0.026 0.002 TYR l 85 ARG 0.019 0.001 ARGAA 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 571 time to evaluate : 5.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.6848 (t70) cc_final: 0.6597 (t70) REVERT: e 36 ASP cc_start: 0.7243 (t0) cc_final: 0.6858 (t0) REVERT: e 106 THR cc_start: 0.6815 (p) cc_final: 0.6543 (p) REVERT: G 44 ASN cc_start: 0.4687 (p0) cc_final: 0.4309 (p0) REVERT: I 106 THR cc_start: 0.6452 (p) cc_final: 0.6201 (p) REVERT: J 36 ASP cc_start: 0.6688 (t0) cc_final: 0.5946 (t0) REVERT: P 25 ASP cc_start: 0.5139 (p0) cc_final: 0.4782 (p0) REVERT: S 36 ASP cc_start: 0.7491 (t70) cc_final: 0.7020 (t0) REVERT: V 39 VAL cc_start: 0.5891 (t) cc_final: 0.5671 (p) REVERT: 1 36 ASP cc_start: 0.8416 (t0) cc_final: 0.8169 (t0) REVERT: 1 65 ILE cc_start: 0.5202 (tp) cc_final: 0.4740 (tp) REVERT: l 36 ASP cc_start: 0.7392 (t0) cc_final: 0.6848 (t0) REVERT: v 36 ASP cc_start: 0.7572 (t0) cc_final: 0.6940 (t0) REVERT: z 36 ASP cc_start: 0.6698 (t0) cc_final: 0.6461 (t0) REVERT: AA 7 TYR cc_start: 0.5918 (t80) cc_final: 0.5639 (t80) outliers start: 2 outliers final: 0 residues processed: 573 average time/residue: 0.5727 time to fit residues: 572.6423 Evaluate side-chains 410 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 4.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 769 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 454 optimal weight: 50.0000 chunk 582 optimal weight: 50.0000 chunk 451 optimal weight: 10.0000 chunk 671 optimal weight: 40.0000 chunk 445 optimal weight: 40.0000 chunk 795 optimal weight: 50.0000 chunk 497 optimal weight: 4.9990 chunk 484 optimal weight: 50.0000 chunk 367 optimal weight: 7.9990 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 81 ASN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 81 ASN ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 138 GLN ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 HIS T 82 GLN ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 10 ASN ** Z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 76 GLN 1 82 GLN ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 81 ASN o 82 GLN ** o 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 138 GLN ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 33 HIS ** w 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AD 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5240 moved from start: 1.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 63735 Z= 0.257 Angle : 0.673 14.196 87560 Z= 0.346 Chirality : 0.042 0.301 10405 Planarity : 0.005 0.123 11555 Dihedral : 4.892 21.612 9210 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 22.43 Ramachandran Plot: Outliers : 1.80 % Allowed : 8.43 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.60 (0.09), residues: 8005 helix: 1.04 (0.21), residues: 650 sheet: 0.66 (0.15), residues: 1160 loop : -1.81 (0.07), residues: 6195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 22 HIS 0.013 0.003 HIS U 98 PHE 0.016 0.002 PHE f 128 TYR 0.029 0.002 TYR u 29 ARG 0.020 0.001 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 561 time to evaluate : 5.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 36 ASP cc_start: 0.7128 (t0) cc_final: 0.6640 (t0) REVERT: e 36 ASP cc_start: 0.7458 (t0) cc_final: 0.6792 (t0) REVERT: e 106 THR cc_start: 0.6758 (p) cc_final: 0.6489 (p) REVERT: F 36 ASP cc_start: 0.6945 (t0) cc_final: 0.6530 (t0) REVERT: I 106 THR cc_start: 0.6258 (p) cc_final: 0.5887 (p) REVERT: J 36 ASP cc_start: 0.6858 (t0) cc_final: 0.5972 (t0) REVERT: N 61 GLN cc_start: 0.5064 (mp10) cc_final: 0.4799 (pm20) REVERT: W 50 ASN cc_start: 0.5004 (p0) cc_final: 0.4619 (p0) REVERT: Y 36 ASP cc_start: 0.8061 (t70) cc_final: 0.7518 (t70) REVERT: Z 48 LEU cc_start: 0.6308 (tp) cc_final: 0.5819 (tp) REVERT: 1 36 ASP cc_start: 0.8635 (t0) cc_final: 0.8358 (t0) REVERT: 1 65 ILE cc_start: 0.5087 (tp) cc_final: 0.4839 (tp) REVERT: 9 36 ASP cc_start: 0.7454 (t0) cc_final: 0.7099 (t0) REVERT: l 36 ASP cc_start: 0.6838 (t0) cc_final: 0.6286 (t0) REVERT: m 36 ASP cc_start: 0.8345 (t70) cc_final: 0.8055 (t0) REVERT: v 36 ASP cc_start: 0.7801 (t0) cc_final: 0.7213 (t0) REVERT: z 36 ASP cc_start: 0.6821 (t0) cc_final: 0.6616 (t0) REVERT: AA 7 TYR cc_start: 0.6055 (t80) cc_final: 0.5785 (t80) REVERT: AA 36 ASP cc_start: 0.8086 (t70) cc_final: 0.7607 (t0) outliers start: 0 outliers final: 0 residues processed: 561 average time/residue: 0.5604 time to fit residues: 552.6104 Evaluate side-chains 407 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 4.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 491 optimal weight: 8.9990 chunk 317 optimal weight: 30.0000 chunk 474 optimal weight: 8.9990 chunk 239 optimal weight: 30.0000 chunk 156 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 505 optimal weight: 10.0000 chunk 541 optimal weight: 0.0670 chunk 393 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 625 optimal weight: 50.0000 overall best weight: 7.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 10 ASN ** i 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 138 GLN ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 ASN ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 138 GLN U 82 GLN ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 89 ASN 1 10 ASN 1 82 GLN ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 11 ASN ** m 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 89 ASN o 138 GLN ** p 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AD 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AD 89 ASN ** AD 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5226 moved from start: 1.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 63735 Z= 0.213 Angle : 0.647 13.037 87560 Z= 0.332 Chirality : 0.042 0.287 10405 Planarity : 0.005 0.104 11555 Dihedral : 4.749 24.202 9210 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 1.75 % Allowed : 8.01 % Favored : 90.24 % Rotamer: Outliers : 0.02 % Allowed : 1.28 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.61 (0.09), residues: 8005 helix: 1.07 (0.21), residues: 650 sheet: 0.67 (0.15), residues: 1160 loop : -1.83 (0.07), residues: 6195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 22 HIS 0.013 0.002 HIS X 98 PHE 0.014 0.002 PHE C 86 TYR 0.025 0.002 TYR u 29 ARG 0.009 0.001 ARG X 120 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 569 time to evaluate : 5.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.6362 (t70) cc_final: 0.6024 (t70) REVERT: c 36 ASP cc_start: 0.6989 (t0) cc_final: 0.6437 (t0) REVERT: c 44 ASN cc_start: 0.4342 (m110) cc_final: 0.4035 (m110) REVERT: d 36 ASP cc_start: 0.7166 (t0) cc_final: 0.6933 (t0) REVERT: e 36 ASP cc_start: 0.7345 (t0) cc_final: 0.6875 (t0) REVERT: e 106 THR cc_start: 0.6752 (p) cc_final: 0.6522 (p) REVERT: F 36 ASP cc_start: 0.6864 (t0) cc_final: 0.6318 (t0) REVERT: I 106 THR cc_start: 0.6378 (p) cc_final: 0.6047 (p) REVERT: J 36 ASP cc_start: 0.6640 (t0) cc_final: 0.5831 (t0) REVERT: N 36 ASP cc_start: 0.7756 (t70) cc_final: 0.6899 (t0) REVERT: N 61 GLN cc_start: 0.5079 (mp10) cc_final: 0.4830 (pm20) REVERT: P 25 ASP cc_start: 0.4627 (p0) cc_final: 0.4278 (p0) REVERT: W 36 ASP cc_start: 0.8002 (t70) cc_final: 0.7732 (t70) REVERT: X 36 ASP cc_start: 0.7685 (t0) cc_final: 0.7313 (t0) REVERT: Y 36 ASP cc_start: 0.8047 (t70) cc_final: 0.7495 (t70) REVERT: 1 36 ASP cc_start: 0.8689 (t0) cc_final: 0.8417 (t0) REVERT: 1 65 ILE cc_start: 0.5097 (tp) cc_final: 0.4869 (tp) REVERT: 9 36 ASP cc_start: 0.7503 (t0) cc_final: 0.7143 (t0) REVERT: l 36 ASP cc_start: 0.7166 (t0) cc_final: 0.6653 (t0) REVERT: m 36 ASP cc_start: 0.8262 (t70) cc_final: 0.7933 (t0) REVERT: o 6 THR cc_start: 0.7735 (p) cc_final: 0.7348 (p) REVERT: v 36 ASP cc_start: 0.7679 (t0) cc_final: 0.7013 (t0) REVERT: y 106 THR cc_start: 0.6021 (p) cc_final: 0.5818 (p) REVERT: z 36 ASP cc_start: 0.6816 (t0) cc_final: 0.6547 (t0) REVERT: AA 7 TYR cc_start: 0.5727 (t80) cc_final: 0.5076 (t80) REVERT: AA 36 ASP cc_start: 0.8318 (t70) cc_final: 0.7754 (t0) outliers start: 1 outliers final: 0 residues processed: 569 average time/residue: 0.5548 time to fit residues: 559.4489 Evaluate side-chains 402 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 402 time to evaluate : 4.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 723 optimal weight: 7.9990 chunk 761 optimal weight: 20.0000 chunk 695 optimal weight: 5.9990 chunk 740 optimal weight: 10.0000 chunk 445 optimal weight: 10.0000 chunk 322 optimal weight: 0.5980 chunk 581 optimal weight: 10.0000 chunk 227 optimal weight: 0.4980 chunk 669 optimal weight: 30.0000 chunk 700 optimal weight: 9.9990 chunk 738 optimal weight: 50.0000 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 138 GLN ** d 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 61 GLN ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 138 GLN ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN F 82 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 89 ASN ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 76 GLN ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 11 ASN m 61 GLN ** m 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 138 GLN ** p 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AC 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5193 moved from start: 1.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 63735 Z= 0.182 Angle : 0.624 12.113 87560 Z= 0.320 Chirality : 0.042 0.272 10405 Planarity : 0.005 0.093 11555 Dihedral : 4.508 22.258 9210 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 1.71 % Allowed : 7.90 % Favored : 90.39 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.60 (0.09), residues: 8005 helix: 1.06 (0.21), residues: 650 sheet: 0.71 (0.15), residues: 1160 loop : -1.82 (0.07), residues: 6195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 22 HIS 0.010 0.002 HIS X 98 PHE 0.015 0.002 PHE 1 128 TYR 0.021 0.002 TYR K 7 ARG 0.007 0.001 ARG a 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 573 time to evaluate : 5.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 36 ASP cc_start: 0.6212 (t70) cc_final: 0.5912 (t70) REVERT: c 36 ASP cc_start: 0.7273 (t0) cc_final: 0.6789 (t0) REVERT: d 36 ASP cc_start: 0.7132 (t0) cc_final: 0.6909 (t0) REVERT: e 36 ASP cc_start: 0.7361 (t0) cc_final: 0.6926 (t0) REVERT: e 106 THR cc_start: 0.6665 (p) cc_final: 0.6414 (p) REVERT: f 36 ASP cc_start: 0.7105 (t0) cc_final: 0.6318 (t0) REVERT: F 36 ASP cc_start: 0.6936 (t0) cc_final: 0.6404 (t0) REVERT: I 106 THR cc_start: 0.6520 (p) cc_final: 0.6164 (p) REVERT: J 36 ASP cc_start: 0.7042 (t0) cc_final: 0.6307 (t0) REVERT: N 61 GLN cc_start: 0.5125 (mp10) cc_final: 0.4852 (pm20) REVERT: X 36 ASP cc_start: 0.7614 (t0) cc_final: 0.7209 (t0) REVERT: Y 36 ASP cc_start: 0.8054 (t70) cc_final: 0.7604 (t70) REVERT: 1 36 ASP cc_start: 0.8451 (t0) cc_final: 0.8115 (t0) REVERT: 1 65 ILE cc_start: 0.5008 (tp) cc_final: 0.4750 (tp) REVERT: 6 36 ASP cc_start: 0.7468 (t70) cc_final: 0.7020 (t70) REVERT: 9 36 ASP cc_start: 0.7420 (t0) cc_final: 0.7049 (t0) REVERT: k 36 ASP cc_start: 0.8137 (t0) cc_final: 0.7456 (t0) REVERT: l 36 ASP cc_start: 0.7131 (t0) cc_final: 0.6635 (t0) REVERT: m 36 ASP cc_start: 0.8223 (t70) cc_final: 0.7755 (t0) REVERT: o 6 THR cc_start: 0.7686 (p) cc_final: 0.7313 (p) REVERT: o 84 THR cc_start: 0.7041 (p) cc_final: 0.6167 (p) REVERT: v 36 ASP cc_start: 0.7479 (t0) cc_final: 0.6864 (t0) REVERT: z 36 ASP cc_start: 0.6841 (t0) cc_final: 0.6547 (t0) REVERT: AA 36 ASP cc_start: 0.8303 (t70) cc_final: 0.7820 (t0) outliers start: 2 outliers final: 0 residues processed: 574 average time/residue: 0.5465 time to fit residues: 554.7561 Evaluate side-chains 417 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 4.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 486 optimal weight: 40.0000 chunk 783 optimal weight: 20.0000 chunk 478 optimal weight: 50.0000 chunk 371 optimal weight: 10.0000 chunk 544 optimal weight: 3.9990 chunk 821 optimal weight: 30.0000 chunk 756 optimal weight: 40.0000 chunk 654 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 505 optimal weight: 30.0000 chunk 401 optimal weight: 40.0000 overall best weight: 12.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 50 ASN ** f 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 138 GLN ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN ** K 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 138 GLN ** N 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 44 ASN ** Z 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 76 GLN ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 11 ASN m 44 ASN ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 109 ASN o 138 GLN ** p 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AA 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AD 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AF 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 1.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 63735 Z= 0.294 Angle : 0.699 14.737 87560 Z= 0.359 Chirality : 0.043 0.324 10405 Planarity : 0.005 0.106 11555 Dihedral : 4.935 23.157 9210 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 1.75 % Allowed : 8.96 % Favored : 89.29 % Rotamer: Outliers : 0.02 % Allowed : 0.48 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.80 (0.09), residues: 8005 helix: 0.82 (0.21), residues: 650 sheet: 0.21 (0.15), residues: 1195 loop : -1.88 (0.07), residues: 6160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 22 HIS 0.015 0.003 HIS X 98 PHE 0.021 0.002 PHE p 128 TYR 0.035 0.003 TYR u 29 ARG 0.015 0.001 ARG e 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16010 Ramachandran restraints generated. 8005 Oldfield, 0 Emsley, 8005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 537 time to evaluate : 5.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 36 ASP cc_start: 0.6896 (t0) cc_final: 0.6487 (t0) REVERT: c 36 ASP cc_start: 0.7206 (t0) cc_final: 0.6962 (t0) REVERT: e 36 ASP cc_start: 0.7500 (t0) cc_final: 0.7098 (t0) REVERT: e 106 THR cc_start: 0.6917 (p) cc_final: 0.6682 (p) REVERT: j 65 ILE cc_start: 0.4995 (tp) cc_final: 0.4710 (tp) REVERT: F 36 ASP cc_start: 0.7348 (t0) cc_final: 0.6989 (t0) REVERT: G 36 ASP cc_start: 0.6972 (t0) cc_final: 0.6550 (t0) REVERT: I 106 THR cc_start: 0.6811 (p) cc_final: 0.6371 (p) REVERT: J 36 ASP cc_start: 0.6598 (t0) cc_final: 0.6125 (t0) REVERT: N 36 ASP cc_start: 0.8118 (t70) cc_final: 0.7188 (t0) REVERT: T 36 ASP cc_start: 0.7309 (t0) cc_final: 0.6675 (t0) REVERT: U 36 ASP cc_start: 0.7564 (t0) cc_final: 0.7203 (t0) REVERT: X 36 ASP cc_start: 0.7039 (t0) cc_final: 0.6776 (t0) REVERT: 1 36 ASP cc_start: 0.8885 (t0) cc_final: 0.8558 (t0) REVERT: 9 36 ASP cc_start: 0.7624 (t0) cc_final: 0.7175 (t0) REVERT: l 36 ASP cc_start: 0.6655 (t0) cc_final: 0.6435 (t0) REVERT: m 36 ASP cc_start: 0.8372 (t70) cc_final: 0.7958 (t0) REVERT: o 6 THR cc_start: 0.7586 (p) cc_final: 0.7199 (p) REVERT: v 36 ASP cc_start: 0.7663 (t0) cc_final: 0.6994 (t0) REVERT: y 106 THR cc_start: 0.6385 (p) cc_final: 0.6173 (p) REVERT: z 36 ASP cc_start: 0.7188 (t0) cc_final: 0.6911 (t0) REVERT: AA 36 ASP cc_start: 0.8474 (t70) cc_final: 0.7953 (t0) REVERT: AD 120 ARG cc_start: 0.3321 (ttt90) cc_final: 0.2751 (ttt90) outliers start: 1 outliers final: 0 residues processed: 537 average time/residue: 0.5629 time to fit residues: 538.8160 Evaluate side-chains 390 residues out of total 6100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 5.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 825 random chunks: chunk 519 optimal weight: 5.9990 chunk 697 optimal weight: 10.0000 chunk 200 optimal weight: 2.9990 chunk 603 optimal weight: 50.0000 chunk 96 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 655 optimal weight: 0.4980 chunk 274 optimal weight: 9.9990 chunk 673 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 89 ASN ** h 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 138 GLN ** j 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN ** J 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN L 44 ASN ** L 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 10 ASN ** N 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 123 GLN ** U 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 76 GLN ** Z 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 123 GLN ** 8 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 89 ASN ** k 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 11 ASN m 44 ASN ** n 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 138 GLN ** p 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 82 GLN ** AB 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AC 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AC 11 ASN ** AC 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AD 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.055747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.045104 restraints weight = 997070.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.044144 restraints weight = 824503.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.044314 restraints weight = 584675.861| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 1.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 63735 Z= 0.186 Angle : 0.635 12.878 87560 Z= 0.324 Chirality : 0.042 0.291 10405 Planarity : 0.005 0.074 11555 Dihedral : 4.636 24.329 9210 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 1.69 % Allowed : 8.04 % Favored : 90.27 % Rotamer: Outliers : 0.05 % Allowed : 0.26 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.66 % 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: -1.72 (0.09), residues: 8005 helix: 0.92 (0.21), residues: 650 sheet: 0.47 (0.15), residues: 1160 loop : -1.87 (0.07), residues: 6195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 22 HIS 0.010 0.002 HIS X 98 PHE 0.034 0.002 PHEAC 102 TYR 0.022 0.002 TYR u 29 ARG 0.018 0.001 ARG 1 57 =============================================================================== Job complete usr+sys time: 14931.03 seconds wall clock time: 262 minutes 22.10 seconds (15742.10 seconds total)