Starting phenix.real_space_refine on Tue Sep 24 09:12:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/09_2024/6spe_10283.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/09_2024/6spe_10283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/09_2024/6spe_10283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/09_2024/6spe_10283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/09_2024/6spe_10283.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6spe_10283/09_2024/6spe_10283.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1525 5.49 5 S 67 5.16 5 C 26260 2.51 5 N 9608 2.21 5 O 13969 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 51429 Number of models: 1 Model: "" Number of chains: 21 Chain: "a" Number of atoms: 32744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1526, 32744 Classifications: {'RNA': 1526} Modifications used: {'5*END': 1, 'rna2p_pur': 125, 'rna2p_pyr': 83, 'rna3p_pur': 747, 'rna3p_pyr': 571} Link IDs: {'rna2p': 208, 'rna3p': 1317} Chain: "b" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1822 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 225} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1627 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 198} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1603 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 200} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "e" Number of atoms: 1145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1145 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 853 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "g" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1190 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 148} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 21 Chain: "h" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 982 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "i" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 994 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 765 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "k" Number of atoms: 838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 838 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 107} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "l" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 949 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "m" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "n" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 778 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "o" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 686 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "p" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 610 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "q" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 619 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "r" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 556 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 68} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "s" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 635 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 75} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 655 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 82} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "u" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 519 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain breaks: 1 Time building chain proxies: 23.20, per 1000 atoms: 0.45 Number of scatterers: 51429 At special positions: 0 Unit cell: (239.8, 194.7, 190.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 67 16.00 P 1525 15.00 O 13969 8.00 N 9608 7.00 C 26260 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS d 9 " - pdb=" SG CYS d 32 " distance=2.03 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: 8.83 Conformation dependent library (CDL) restraints added in 2.3 seconds 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4414 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 21 sheets defined 39.3% alpha, 13.5% beta 398 base pairs and 838 stacking pairs defined. Time for finding SS restraints: 18.62 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.823A pdb=" N MET b 9 " --> pdb=" O ASN b 5 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY b 13 " --> pdb=" O MET b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 34 through 38 removed outlier: 3.659A pdb=" N LYS b 37 " --> pdb=" O ALA b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 62 removed outlier: 3.881A pdb=" N MET b 49 " --> pdb=" O LYS b 45 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU b 54 " --> pdb=" O PHE b 50 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE b 56 " --> pdb=" O GLU b 52 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA b 62 " --> pdb=" O GLU b 58 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 83 Processing helix chain 'b' and resid 103 through 111 removed outlier: 3.561A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 113 through 121 removed outlier: 4.280A pdb=" N GLU b 118 " --> pdb=" O LEU b 114 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N THR b 119 " --> pdb=" O ARG b 115 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER b 121 " --> pdb=" O LEU b 117 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 139 removed outlier: 3.827A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG b 137 " --> pdb=" O GLU b 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 148 removed outlier: 3.974A pdb=" N LYS b 143 " --> pdb=" O ARG b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 178 Processing helix chain 'b' and resid 206 through 213 Processing helix chain 'b' and resid 214 through 232 removed outlier: 3.510A pdb=" N GLU b 219 " --> pdb=" O ASN b 215 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 47 removed outlier: 3.566A pdb=" N LEU c 33 " --> pdb=" O TYR c 29 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE c 34 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA c 35 " --> pdb=" O ASP c 31 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS c 38 " --> pdb=" O PHE c 34 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG c 40 " --> pdb=" O ASP c 36 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU c 41 " --> pdb=" O LEU c 37 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR c 42 " --> pdb=" O LYS c 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN c 44 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP c 45 " --> pdb=" O GLU c 41 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 77 removed outlier: 4.188A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 83 through 92 removed outlier: 3.718A pdb=" N ASP c 90 " --> pdb=" O LYS c 86 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR c 92 " --> pdb=" O ARG c 88 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 111 Processing helix chain 'c' and resid 112 through 124 removed outlier: 3.795A pdb=" N SER c 119 " --> pdb=" O LEU c 115 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA c 121 " --> pdb=" O ALA c 117 " (cutoff:3.500A) Processing helix chain 'c' and resid 131 through 144 removed outlier: 4.031A pdb=" N ARG c 136 " --> pdb=" O ARG c 132 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN c 139 " --> pdb=" O LYS c 135 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA c 141 " --> pdb=" O ALA c 137 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 3.803A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 removed outlier: 3.772A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N TYR d 65 " --> pdb=" O VAL d 61 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY d 66 " --> pdb=" O ARG d 62 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 82 removed outlier: 3.615A pdb=" N GLY d 74 " --> pdb=" O ARG d 70 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG d 82 " --> pdb=" O GLU d 78 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 96 removed outlier: 3.591A pdb=" N LEU d 94 " --> pdb=" O LEU d 90 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS d 96 " --> pdb=" O GLN d 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 106 removed outlier: 3.671A pdb=" N TYR d 103 " --> pdb=" O ASP d 99 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 120 removed outlier: 3.791A pdb=" N SER d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN d 116 " --> pdb=" O SER d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 147 through 150 removed outlier: 3.847A pdb=" N LYS d 150 " --> pdb=" O GLU d 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 147 through 150' Processing helix chain 'd' and resid 152 through 159 removed outlier: 3.740A pdb=" N ALA d 158 " --> pdb=" O ARG d 154 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU d 159 " --> pdb=" O ILE d 155 " (cutoff:3.500A) Processing helix chain 'd' and resid 199 through 204 removed outlier: 3.541A pdb=" N TYR d 204 " --> pdb=" O ILE d 200 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 69 removed outlier: 4.143A pdb=" N GLN e 62 " --> pdb=" O PRO e 58 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG e 69 " --> pdb=" O MET e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 111 through 119 removed outlier: 3.846A pdb=" N VAL e 115 " --> pdb=" O ALA e 111 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL e 118 " --> pdb=" O ALA e 114 " (cutoff:3.500A) Processing helix chain 'e' and resid 136 through 146 removed outlier: 3.589A pdb=" N ALA e 140 " --> pdb=" O ASN e 136 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY e 144 " --> pdb=" O ALA e 140 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 16 removed outlier: 3.703A pdb=" N SER f 15 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU f 16 " --> pdb=" O ASP f 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 12 through 16' Processing helix chain 'f' and resid 17 through 33 removed outlier: 3.536A pdb=" N MET f 21 " --> pdb=" O GLN f 17 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU f 23 " --> pdb=" O GLY f 19 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR f 25 " --> pdb=" O MET f 21 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE f 29 " --> pdb=" O TYR f 25 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 78 removed outlier: 3.544A pdb=" N LEU f 71 " --> pdb=" O SER f 67 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA f 72 " --> pdb=" O ALA f 68 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASP f 76 " --> pdb=" O ALA f 72 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE f 78 " --> pdb=" O LEU f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 101 through 106 Processing helix chain 'g' and resid 21 through 29 removed outlier: 3.669A pdb=" N LYS g 25 " --> pdb=" O GLN g 21 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 44 removed outlier: 3.675A pdb=" N ARG g 41 " --> pdb=" O ALA g 37 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE g 42 " --> pdb=" O VAL g 38 " (cutoff:3.500A) Processing helix chain 'g' and resid 47 through 54 Processing helix chain 'g' and resid 57 through 67 removed outlier: 3.726A pdb=" N THR g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) Processing helix chain 'g' and resid 95 through 109 removed outlier: 3.566A pdb=" N LEU g 99 " --> pdb=" O ARG g 95 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA g 100 " --> pdb=" O ARG g 96 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL g 105 " --> pdb=" O MET g 101 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP g 106 " --> pdb=" O ARG g 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 127 removed outlier: 3.633A pdb=" N LEU g 120 " --> pdb=" O MET g 116 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 removed outlier: 3.744A pdb=" N VAL g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA g 145 " --> pdb=" O VAL g 141 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU g 146 " --> pdb=" O HIS g 142 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 152 Processing helix chain 'h' and resid 6 through 18 removed outlier: 3.536A pdb=" N LEU h 11 " --> pdb=" O LEU h 7 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR h 12 " --> pdb=" O ALA h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 44 removed outlier: 4.120A pdb=" N LYS h 38 " --> pdb=" O ALA h 34 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 113 through 120 removed outlier: 3.693A pdb=" N ALA h 118 " --> pdb=" O ARG h 114 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 39 removed outlier: 3.571A pdb=" N PHE i 39 " --> pdb=" O LEU i 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 35 through 39' Processing helix chain 'i' and resid 43 through 48 removed outlier: 3.706A pdb=" N VAL i 47 " --> pdb=" O THR i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 55 Processing helix chain 'i' and resid 71 through 88 removed outlier: 3.798A pdb=" N ALA i 76 " --> pdb=" O VAL i 72 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY i 77 " --> pdb=" O SER i 73 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR i 84 " --> pdb=" O ARG i 80 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG i 85 " --> pdb=" O HIS i 81 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE i 88 " --> pdb=" O THR i 84 " (cutoff:3.500A) Processing helix chain 'i' and resid 95 through 100 Processing helix chain 'j' and resid 17 through 21 removed outlier: 3.614A pdb=" N SER j 21 " --> pdb=" O ILE j 18 " (cutoff:3.500A) Processing helix chain 'j' and resid 22 through 31 removed outlier: 4.327A pdb=" N THR j 28 " --> pdb=" O GLU j 24 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 87 removed outlier: 3.506A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 92 removed outlier: 3.650A pdb=" N ASP j 91 " --> pdb=" O LEU j 87 " (cutoff:3.500A) Processing helix chain 'k' and resid 55 through 59 removed outlier: 3.678A pdb=" N SER k 58 " --> pdb=" O SER k 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR k 59 " --> pdb=" O ARG k 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 55 through 59' Processing helix chain 'k' and resid 61 through 71 removed outlier: 3.923A pdb=" N ALA k 67 " --> pdb=" O ALA k 63 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 removed outlier: 3.517A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 Processing helix chain 'm' and resid 20 through 23 removed outlier: 3.726A pdb=" N TYR m 23 " --> pdb=" O THR m 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 20 through 23' Processing helix chain 'm' and resid 28 through 38 removed outlier: 3.613A pdb=" N SER m 32 " --> pdb=" O THR m 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS m 34 " --> pdb=" O ALA m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 61 removed outlier: 3.502A pdb=" N GLU m 59 " --> pdb=" O GLN m 55 " (cutoff:3.500A) Processing helix chain 'm' and resid 65 through 83 removed outlier: 4.435A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU m 80 " --> pdb=" O ASN m 76 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.738A pdb=" N HIS m 91 " --> pdb=" O ARG m 87 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) Processing helix chain 'n' and resid 4 through 10 removed outlier: 3.683A pdb=" N ARG n 9 " --> pdb=" O SER n 5 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 21 removed outlier: 3.506A pdb=" N LEU n 15 " --> pdb=" O LEU n 11 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR n 20 " --> pdb=" O THR n 16 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA n 21 " --> pdb=" O VAL n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 22 through 32 removed outlier: 3.625A pdb=" N ILE n 31 " --> pdb=" O LEU n 27 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA n 32 " --> pdb=" O LYS n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 50 removed outlier: 3.651A pdb=" N ASN n 43 " --> pdb=" O GLU n 39 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA n 44 " --> pdb=" O GLU n 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL n 46 " --> pdb=" O TRP n 42 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA n 47 " --> pdb=" O ASN n 43 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN n 49 " --> pdb=" O GLN n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 60 Processing helix chain 'n' and resid 83 through 89 Processing helix chain 'o' and resid 4 through 15 removed outlier: 3.544A pdb=" N LYS o 8 " --> pdb=" O SER o 4 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE o 11 " --> pdb=" O GLU o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 40 removed outlier: 3.925A pdb=" N ALA o 30 " --> pdb=" O GLU o 26 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN o 35 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN o 37 " --> pdb=" O SER o 33 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS o 38 " --> pdb=" O ALA o 34 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU o 39 " --> pdb=" O ASN o 35 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) Processing helix chain 'o' and resid 41 through 46 removed outlier: 3.610A pdb=" N ALA o 45 " --> pdb=" O ASP o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 52 through 72 removed outlier: 3.794A pdb=" N LEU o 56 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE o 57 " --> pdb=" O ARG o 53 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG o 58 " --> pdb=" O ARG o 54 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP o 68 " --> pdb=" O ARG o 64 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.563A pdb=" N LEU o 81 " --> pdb=" O ARG o 77 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG o 84 " --> pdb=" O ALA o 80 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 62 removed outlier: 3.801A pdb=" N ALA p 57 " --> pdb=" O ASP p 53 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU p 61 " --> pdb=" O ALA p 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY p 62 " --> pdb=" O THR p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 70 through 75 Processing helix chain 'r' and resid 5 through 9 removed outlier: 3.568A pdb=" N ARG r 9 " --> pdb=" O PHE r 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 5 through 9' Processing helix chain 'r' and resid 10 through 15 Processing helix chain 'r' and resid 25 through 30 Processing helix chain 'r' and resid 31 through 33 No H-bonds generated for 'chain 'r' and resid 31 through 33' Processing helix chain 'r' and resid 48 through 65 removed outlier: 3.723A pdb=" N ARG r 53 " --> pdb=" O ALA r 49 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR r 57 " --> pdb=" O ARG r 53 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA r 58 " --> pdb=" O GLN r 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR r 64 " --> pdb=" O LYS r 60 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 25 removed outlier: 3.650A pdb=" N VAL s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ALA s 22 " --> pdb=" O LYS s 18 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS s 25 " --> pdb=" O VAL s 21 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 74 removed outlier: 3.627A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 40 removed outlier: 3.629A pdb=" N LYS t 12 " --> pdb=" O LYS t 8 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA t 14 " --> pdb=" O ARG t 10 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU t 15 " --> pdb=" O ALA t 11 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS t 16 " --> pdb=" O LYS t 12 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG t 17 " --> pdb=" O GLN t 13 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS t 20 " --> pdb=" O LYS t 16 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER t 23 " --> pdb=" O SER t 19 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL t 28 " --> pdb=" O LEU t 24 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG t 29 " --> pdb=" O ARG t 25 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 4.430A pdb=" N VAL t 35 " --> pdb=" O TYR t 31 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP t 40 " --> pdb=" O VAL t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 53 removed outlier: 3.866A pdb=" N ALA t 47 " --> pdb=" O ASP t 43 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA t 53 " --> pdb=" O ALA t 49 " (cutoff:3.500A) Processing helix chain 't' and resid 54 through 64 removed outlier: 3.606A pdb=" N ASP t 63 " --> pdb=" O ASP t 59 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS t 64 " --> pdb=" O ARG t 60 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 84 removed outlier: 3.673A pdb=" N ARG t 74 " --> pdb=" O ASN t 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS t 75 " --> pdb=" O LYS t 71 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS t 76 " --> pdb=" O ALA t 72 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER t 77 " --> pdb=" O ALA t 73 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 4.034A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG u 21 " --> pdb=" O ARG u 17 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER u 22 " --> pdb=" O ARG u 18 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU u 24 " --> pdb=" O LYS u 20 " (cutoff:3.500A) Processing helix chain 'u' and resid 29 through 34 removed outlier: 3.685A pdb=" N ARG u 33 " --> pdb=" O LEU u 29 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 57 removed outlier: 3.692A pdb=" N ARG u 47 " --> pdb=" O ALA u 43 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS u 48 " --> pdb=" O GLU u 44 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA u 52 " --> pdb=" O LYS u 48 " (cutoff:3.500A) Processing helix chain 'u' and resid 57 through 66 removed outlier: 4.278A pdb=" N GLU u 63 " --> pdb=" O LYS u 59 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN u 64 " --> pdb=" O VAL u 60 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG u 65 " --> pdb=" O GLN u 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 31 through 33 removed outlier: 6.538A pdb=" N ILE b 40 " --> pdb=" O PHE b 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 68 through 69 removed outlier: 6.442A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU b 161 " --> pdb=" O ILE b 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'c' and resid 20 through 21 removed outlier: 4.434A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE c 66 " --> pdb=" O ASN c 102 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU c 104 " --> pdb=" O ILE c 66 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE c 68 " --> pdb=" O GLU c 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 165 through 166 Processing sheet with id=AA5, first strand: chain 'c' and resid 165 through 166 removed outlier: 3.531A pdb=" N TYR c 187 " --> pdb=" O VAL c 198 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA c 185 " --> pdb=" O VAL c 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'd' and resid 123 through 124 Processing sheet with id=AA7, first strand: chain 'e' and resid 13 through 19 removed outlier: 6.735A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL e 19 " --> pdb=" O THR e 35 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR e 35 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 13 through 19 removed outlier: 6.735A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL e 19 " --> pdb=" O THR e 35 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR e 35 " --> pdb=" O VAL e 19 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 86 through 89 Processing sheet with id=AB1, first strand: chain 'f' and resid 36 through 43 removed outlier: 3.824A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS f 58 " --> pdb=" O VAL f 10 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'g' and resid 73 through 74 Processing sheet with id=AB3, first strand: chain 'h' and resid 24 through 28 removed outlier: 6.335A pdb=" N SER h 60 " --> pdb=" O PHE h 49 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE h 49 " --> pdb=" O SER h 60 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU h 62 " --> pdb=" O ALA h 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'h' and resid 86 through 87 removed outlier: 6.108A pdb=" N VAL h 125 " --> pdb=" O SER h 105 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N SER h 105 " --> pdb=" O VAL h 125 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N CYS h 127 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY h 109 " --> pdb=" O THR h 106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 6 through 10 removed outlier: 3.657A pdb=" N GLY i 10 " --> pdb=" O ALA i 17 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N SER i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N VAL i 67 " --> pdb=" O SER i 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 40 through 41 Processing sheet with id=AB7, first strand: chain 'j' and resid 45 through 52 Processing sheet with id=AB8, first strand: chain 'k' and resid 41 through 46 removed outlier: 8.114A pdb=" N LEU k 82 " --> pdb=" O ALA k 108 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE k 110 " --> pdb=" O LEU k 82 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL k 84 " --> pdb=" O ILE k 110 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP k 112 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL k 86 " --> pdb=" O ASP k 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 62 through 66 removed outlier: 3.526A pdb=" N CYS l 53 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ARG l 50 " --> pdb=" O THR l 39 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR l 39 " --> pdb=" O ARG l 50 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL l 52 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N VAL l 37 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG l 83 " --> pdb=" O HIS l 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'p' and resid 34 through 35 removed outlier: 3.693A pdb=" N GLU p 34 " --> pdb=" O VAL p 21 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL p 2 " --> pdb=" O GLN p 66 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'q' and resid 46 through 47 removed outlier: 3.619A pdb=" N LEU q 47 " --> pdb=" O VAL q 26 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL q 26 " --> pdb=" O LEU q 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR q 25 " --> pdb=" O VAL q 16 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N LEU q 61 " --> pdb=" O ILE q 81 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE q 81 " --> pdb=" O LEU q 61 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N THR q 63 " --> pdb=" O VAL q 79 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG q 65 " --> pdb=" O THR q 77 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA q 75 " --> pdb=" O THR q 67 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU q 78 " --> pdb=" O HIS q 50 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 's' and resid 31 through 33 removed outlier: 6.523A pdb=" N ILE s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N HIS s 52 " --> pdb=" O ILE s 31 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR s 33 " --> pdb=" O HIS s 52 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 961 hydrogen bonds 1592 hydrogen bond angles 0 basepair planarities 398 basepair parallelities 838 stacking parallelities Total time for adding SS restraints: 35.30 Time building geometry restraints manager: 10.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6499 1.32 - 1.45: 23029 1.45 - 1.57: 22923 1.57 - 1.69: 3050 1.69 - 1.81: 115 Bond restraints: 55616 Sorted by residual: bond pdb=" CG LEU l 24 " pdb=" CD2 LEU l 24 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" C5 A a 383 " pdb=" C6 A a 383 " ideal model delta sigma weight residual 1.406 1.366 0.040 2.00e-02 2.50e+03 4.07e+00 bond pdb=" CA ARG q 31 " pdb=" CB ARG q 31 " ideal model delta sigma weight residual 1.526 1.497 0.029 1.53e-02 4.27e+03 3.64e+00 bond pdb=" C5 A a 810 " pdb=" C6 A a 810 " ideal model delta sigma weight residual 1.406 1.370 0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" N1 C a 873 " pdb=" C2 C a 873 " ideal model delta sigma weight residual 1.397 1.365 0.032 2.00e-02 2.50e+03 2.60e+00 ... (remaining 55611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 81800 3.00 - 6.00: 757 6.00 - 9.00: 83 9.00 - 12.00: 9 12.00 - 15.00: 1 Bond angle restraints: 82650 Sorted by residual: angle pdb=" C3' A a 963 " pdb=" O3' A a 963 " pdb=" P C a 964 " ideal model delta sigma weight residual 120.20 127.96 -7.76 1.50e+00 4.44e-01 2.68e+01 angle pdb=" C3' A a1195 " pdb=" O3' A a1195 " pdb=" P U a1196 " ideal model delta sigma weight residual 120.20 127.57 -7.37 1.50e+00 4.44e-01 2.42e+01 angle pdb=" C4' A a 963 " pdb=" C3' A a 963 " pdb=" O3' A a 963 " ideal model delta sigma weight residual 109.40 116.63 -7.23 1.50e+00 4.44e-01 2.32e+01 angle pdb=" C3' G a1341 " pdb=" O3' G a1341 " pdb=" P U a1342 " ideal model delta sigma weight residual 120.20 127.34 -7.14 1.50e+00 4.44e-01 2.26e+01 angle pdb=" C3' C a 893 " pdb=" O3' C a 893 " pdb=" P A a 894 " ideal model delta sigma weight residual 120.20 126.84 -6.64 1.50e+00 4.44e-01 1.96e+01 ... (remaining 82645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 31696 35.88 - 71.76: 3423 71.76 - 107.63: 419 107.63 - 143.51: 12 143.51 - 179.39: 18 Dihedral angle restraints: 35568 sinusoidal: 28715 harmonic: 6853 Sorted by residual: dihedral pdb=" O4' U a 975 " pdb=" C1' U a 975 " pdb=" N1 U a 975 " pdb=" C2 U a 975 " ideal model delta sinusoidal sigma weight residual -160.00 12.62 -172.62 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C a 104 " pdb=" C1' C a 104 " pdb=" N1 C a 104 " pdb=" C2 C a 104 " ideal model delta sinusoidal sigma weight residual -160.00 7.96 -167.96 1 1.50e+01 4.44e-03 8.44e+01 dihedral pdb=" O4' U a1024 " pdb=" C1' U a1024 " pdb=" N1 U a1024 " pdb=" C2 U a1024 " ideal model delta sinusoidal sigma weight residual 200.00 37.95 162.05 1 1.50e+01 4.44e-03 8.33e+01 ... (remaining 35565 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 9342 0.069 - 0.139: 1020 0.139 - 0.208: 84 0.208 - 0.277: 12 0.277 - 0.346: 8 Chirality restraints: 10466 Sorted by residual: chirality pdb=" C3' G a1341 " pdb=" C4' G a1341 " pdb=" O3' G a1341 " pdb=" C2' G a1341 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" C3' A a 709 " pdb=" C4' A a 709 " pdb=" O3' A a 709 " pdb=" C2' A a 709 " both_signs ideal model delta sigma weight residual False -2.48 -2.13 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C3' C a 87 " pdb=" C4' C a 87 " pdb=" O3' C a 87 " pdb=" C2' C a 87 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 10463 not shown) Planarity restraints: 4829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE c 106 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C ILE c 106 " 0.059 2.00e-02 2.50e+03 pdb=" O ILE c 106 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG c 107 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G a 829 " 0.036 2.00e-02 2.50e+03 1.69e-02 8.61e+00 pdb=" N9 G a 829 " -0.043 2.00e-02 2.50e+03 pdb=" C8 G a 829 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G a 829 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G a 829 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G a 829 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G a 829 " 0.015 2.00e-02 2.50e+03 pdb=" N1 G a 829 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G a 829 " -0.002 2.00e-02 2.50e+03 pdb=" N2 G a 829 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G a 829 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G a 829 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR c 63 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR c 63 " -0.049 2.00e-02 2.50e+03 pdb=" O THR c 63 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA c 64 " 0.017 2.00e-02 2.50e+03 ... (remaining 4826 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 13057 2.80 - 3.33: 41658 3.33 - 3.85: 100069 3.85 - 4.38: 119722 4.38 - 4.90: 164809 Nonbonded interactions: 439315 Sorted by model distance: nonbonded pdb=" OP2 U a 20 " pdb=" OG SER e 131 " model vdw 2.277 3.040 nonbonded pdb=" O2' U a1046 " pdb=" OP2 A a1049 " model vdw 2.288 3.040 nonbonded pdb=" O2' C a 853 " pdb=" O4' A a 854 " model vdw 2.289 3.040 nonbonded pdb=" O2' G a1047 " pdb=" OP2 U a1193 " model vdw 2.296 3.040 nonbonded pdb=" N6 A a 445 " pdb=" O2' U a 474 " model vdw 2.297 3.120 ... (remaining 439310 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.660 Check model and map are aligned: 0.300 Set scattering table: 0.390 Process input model: 113.580 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 55616 Z= 0.432 Angle : 0.851 15.004 82650 Z= 0.434 Chirality : 0.045 0.346 10466 Planarity : 0.005 0.061 4829 Dihedral : 22.600 179.390 31151 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.10 % Allowed : 2.84 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.99 (0.13), residues: 2348 helix: -4.24 (0.09), residues: 802 sheet: -2.71 (0.24), residues: 391 loop : -2.74 (0.15), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP n 42 HIS 0.017 0.002 HIS f 37 PHE 0.022 0.003 PHE p 38 TYR 0.026 0.003 TYR e 12 ARG 0.016 0.001 ARG d 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 832 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 830 time to evaluate : 2.502 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 9 MET cc_start: 0.7682 (mmm) cc_final: 0.7336 (ttt) REVERT: b 42 ASN cc_start: 0.7709 (t0) cc_final: 0.6723 (t0) REVERT: b 65 ASN cc_start: 0.7336 (p0) cc_final: 0.7104 (p0) REVERT: b 136 MET cc_start: 0.8062 (mtp) cc_final: 0.7753 (mtm) REVERT: b 216 SER cc_start: 0.8437 (m) cc_final: 0.8114 (m) REVERT: d 20 PHE cc_start: 0.8307 (m-80) cc_final: 0.8080 (m-80) REVERT: e 15 LYS cc_start: 0.8794 (tptt) cc_final: 0.8495 (ttmt) REVERT: e 55 ARG cc_start: 0.8475 (mmm-85) cc_final: 0.8251 (tpp-160) REVERT: e 66 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7596 (tm-30) REVERT: e 88 SER cc_start: 0.9050 (m) cc_final: 0.8842 (p) REVERT: e 164 GLU cc_start: 0.6823 (pp20) cc_final: 0.6232 (pp20) REVERT: f 4 TYR cc_start: 0.8845 (m-80) cc_final: 0.8579 (m-80) REVERT: f 13 ASP cc_start: 0.9197 (m-30) cc_final: 0.8893 (p0) REVERT: f 18 VAL cc_start: 0.9137 (p) cc_final: 0.8627 (p) REVERT: f 21 MET cc_start: 0.8534 (mtp) cc_final: 0.8218 (mtt) REVERT: f 22 VAL cc_start: 0.9469 (t) cc_final: 0.9267 (p) REVERT: f 42 TRP cc_start: 0.8900 (m-10) cc_final: 0.7995 (m-10) REVERT: f 47 LEU cc_start: 0.8862 (mt) cc_final: 0.8394 (mt) REVERT: f 77 ASN cc_start: 0.9169 (m-40) cc_final: 0.8958 (p0) REVERT: f 85 ILE cc_start: 0.9017 (tt) cc_final: 0.8797 (tp) REVERT: g 97 ASN cc_start: 0.8531 (m110) cc_final: 0.8214 (m-40) REVERT: h 23 THR cc_start: 0.9230 (m) cc_final: 0.8898 (t) REVERT: h 113 ASP cc_start: 0.7914 (p0) cc_final: 0.7709 (p0) REVERT: i 54 LEU cc_start: 0.9141 (tp) cc_final: 0.8932 (tt) REVERT: j 54 SER cc_start: 0.9370 (t) cc_final: 0.9168 (t) REVERT: j 77 VAL cc_start: 0.9126 (t) cc_final: 0.7980 (t) REVERT: j 88 MET cc_start: 0.7478 (ttt) cc_final: 0.6813 (tmm) REVERT: k 30 THR cc_start: 0.9582 (m) cc_final: 0.9100 (p) REVERT: k 47 SER cc_start: 0.9494 (m) cc_final: 0.8949 (m) REVERT: k 65 VAL cc_start: 0.9442 (t) cc_final: 0.9039 (p) REVERT: k 93 ARG cc_start: 0.7993 (ttt90) cc_final: 0.7662 (ttt90) REVERT: k 100 LEU cc_start: 0.9044 (mt) cc_final: 0.8631 (mt) REVERT: k 122 ARG cc_start: 0.8975 (ptm160) cc_final: 0.8547 (ptm160) REVERT: l 15 MET cc_start: 0.6532 (pmt) cc_final: 0.6056 (ptt) REVERT: l 38 TYR cc_start: 0.6751 (m-80) cc_final: 0.5753 (m-80) REVERT: l 78 SER cc_start: 0.9143 (m) cc_final: 0.8776 (p) REVERT: l 88 LYS cc_start: 0.8658 (tttm) cc_final: 0.8437 (ttmt) REVERT: m 47 ASP cc_start: 0.8355 (m-30) cc_final: 0.8086 (m-30) REVERT: m 97 VAL cc_start: 0.9404 (t) cc_final: 0.9112 (p) REVERT: m 110 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7992 (mtpp) REVERT: n 23 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8282 (mtmm) REVERT: o 10 GLN cc_start: 0.9153 (tp40) cc_final: 0.8844 (tm-30) REVERT: o 11 ILE cc_start: 0.9603 (mt) cc_final: 0.9137 (mt) REVERT: o 16 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8948 (ttmt) REVERT: p 53 ASP cc_start: 0.8323 (m-30) cc_final: 0.7944 (p0) REVERT: p 77 ASP cc_start: 0.7992 (m-30) cc_final: 0.7654 (m-30) REVERT: q 57 ARG cc_start: 0.8044 (mmp80) cc_final: 0.7062 (ptt180) REVERT: q 58 ILE cc_start: 0.9277 (mt) cc_final: 0.8623 (mt) REVERT: q 60 ASP cc_start: 0.7431 (m-30) cc_final: 0.6742 (m-30) REVERT: r 7 ARG cc_start: 0.7773 (mtt90) cc_final: 0.7501 (mtt-85) REVERT: r 73 SER cc_start: 0.8227 (t) cc_final: 0.7934 (m) REVERT: s 60 VAL cc_start: 0.8931 (t) cc_final: 0.8633 (p) REVERT: t 25 ARG cc_start: 0.8839 (ttm170) cc_final: 0.8635 (ttm-80) REVERT: u 10 GLU cc_start: 0.6706 (mm-30) cc_final: 0.5989 (mp0) REVERT: u 21 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7583 (mmm-85) REVERT: u 45 ARG cc_start: 0.8350 (mpp80) cc_final: 0.8024 (mtm180) REVERT: u 58 LYS cc_start: 0.8178 (tptm) cc_final: 0.7936 (tttt) outliers start: 2 outliers final: 1 residues processed: 831 average time/residue: 0.6723 time to fit residues: 881.5966 Evaluate side-chains 573 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 572 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t residue 27 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 322 optimal weight: 9.9990 chunk 289 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 195 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 299 optimal weight: 0.0670 chunk 115 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 222 optimal weight: 4.9990 chunk 346 optimal weight: 7.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 6 HIS c 69 HIS c 190 HIS d 100 ASN e 20 ASN e 98 GLN f 17 GLN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 58 GLN i 6 ASN ** i 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 81 ASN k 85 ASN ** k 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS m 40 ASN m 91 HIS m 105 ASN o 42 HIS o 46 ASN p 54 GLN p 73 GLN q 34 HIS s 52 HIS ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 68 HIS u 56 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 55616 Z= 0.207 Angle : 0.667 9.239 82650 Z= 0.341 Chirality : 0.038 0.258 10466 Planarity : 0.005 0.052 4829 Dihedral : 23.686 179.936 26508 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.25 % Allowed : 13.87 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.77 (0.15), residues: 2348 helix: -2.69 (0.13), residues: 865 sheet: -2.15 (0.26), residues: 391 loop : -2.35 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP d 170 HIS 0.006 0.001 HIS t 82 PHE 0.017 0.001 PHE p 38 TYR 0.019 0.002 TYR l 117 ARG 0.006 0.001 ARG q 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 626 time to evaluate : 2.564 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: c 123 GLN cc_start: 0.8517 (mt0) cc_final: 0.8196 (mt0) REVERT: e 15 LYS cc_start: 0.8731 (tptt) cc_final: 0.8267 (ttmt) REVERT: e 66 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7916 (tm-30) REVERT: e 88 SER cc_start: 0.9259 (m) cc_final: 0.8840 (p) REVERT: f 13 ASP cc_start: 0.9097 (m-30) cc_final: 0.8822 (p0) REVERT: f 14 GLN cc_start: 0.9000 (mm110) cc_final: 0.8530 (mm110) REVERT: f 42 TRP cc_start: 0.8706 (m-10) cc_final: 0.8320 (m-10) REVERT: f 56 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8844 (mmmt) REVERT: f 61 LEU cc_start: 0.8814 (tt) cc_final: 0.8518 (tt) REVERT: f 77 ASN cc_start: 0.9008 (m-40) cc_final: 0.8655 (p0) REVERT: g 27 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7504 (tpp) REVERT: g 97 ASN cc_start: 0.8686 (m110) cc_final: 0.8378 (m-40) REVERT: g 143 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8533 (ttp80) REVERT: h 23 THR cc_start: 0.9142 (m) cc_final: 0.8842 (t) REVERT: h 66 PHE cc_start: 0.8156 (t80) cc_final: 0.7826 (t80) REVERT: j 88 MET cc_start: 0.7525 (ttt) cc_final: 0.6766 (tmm) REVERT: k 68 GLU cc_start: 0.8379 (pp20) cc_final: 0.7599 (pp20) REVERT: k 100 LEU cc_start: 0.9050 (mt) cc_final: 0.8590 (mt) REVERT: l 15 MET cc_start: 0.6407 (pmt) cc_final: 0.5707 (ptt) REVERT: l 73 ASN cc_start: 0.9014 (p0) cc_final: 0.8797 (p0) REVERT: l 78 SER cc_start: 0.9233 (m) cc_final: 0.8787 (p) REVERT: l 88 LYS cc_start: 0.8770 (tttm) cc_final: 0.8520 (ttpt) REVERT: n 4 GLU cc_start: 0.8429 (tp30) cc_final: 0.8118 (tp30) REVERT: n 7 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8871 (ptmt) REVERT: n 54 ASP cc_start: 0.8509 (p0) cc_final: 0.7566 (p0) REVERT: o 26 GLU cc_start: 0.9188 (mp0) cc_final: 0.8816 (mp0) REVERT: o 54 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.8042 (mmm160) REVERT: p 53 ASP cc_start: 0.8153 (m-30) cc_final: 0.7798 (p0) REVERT: q 22 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8473 (mtpp) REVERT: q 52 GLU cc_start: 0.7668 (tp30) cc_final: 0.7389 (tp30) REVERT: r 7 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7499 (mtt-85) REVERT: t 20 HIS cc_start: 0.8940 (t70) cc_final: 0.8739 (t-170) REVERT: t 25 ARG cc_start: 0.8944 (ttm170) cc_final: 0.8565 (ttm-80) REVERT: u 10 GLU cc_start: 0.6627 (mm-30) cc_final: 0.5804 (mp0) REVERT: u 12 PHE cc_start: 0.8082 (t80) cc_final: 0.7852 (t80) REVERT: u 24 GLU cc_start: 0.7589 (pt0) cc_final: 0.7382 (pt0) REVERT: u 58 LYS cc_start: 0.8043 (tptm) cc_final: 0.7766 (tttt) outliers start: 63 outliers final: 35 residues processed: 653 average time/residue: 0.6414 time to fit residues: 695.4747 Evaluate side-chains 591 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 554 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 GLU Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain g residue 27 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 115 SER Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 7 LYS Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 16 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 192 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 288 optimal weight: 7.9990 chunk 236 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 347 optimal weight: 8.9990 chunk 375 optimal weight: 10.0000 chunk 309 optimal weight: 0.8980 chunk 344 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 278 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 3 GLN ** g 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN i 126 GLN j 56 HIS k 38 GLN k 85 ASN l 77 HIS m 55 GLN p 54 GLN q 48 HIS ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 55616 Z= 0.272 Angle : 0.645 8.875 82650 Z= 0.330 Chirality : 0.037 0.264 10466 Planarity : 0.005 0.052 4829 Dihedral : 23.586 179.097 26505 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.71 % Allowed : 17.23 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.90 (0.16), residues: 2348 helix: -1.71 (0.16), residues: 864 sheet: -1.70 (0.27), residues: 375 loop : -2.10 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 23 HIS 0.007 0.001 HIS s 57 PHE 0.017 0.001 PHE p 38 TYR 0.015 0.002 TYR l 117 ARG 0.006 0.001 ARG c 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 579 time to evaluate : 2.529 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 74 ARG cc_start: 0.6092 (mtt180) cc_final: 0.5677 (mpt180) REVERT: c 118 GLN cc_start: 0.8904 (mt0) cc_final: 0.8574 (mt0) REVERT: e 66 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8121 (tm-30) REVERT: e 88 SER cc_start: 0.9286 (m) cc_final: 0.8872 (p) REVERT: e 133 ASN cc_start: 0.9002 (t0) cc_final: 0.8645 (t0) REVERT: f 5 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7701 (tm-30) REVERT: f 13 ASP cc_start: 0.9289 (m-30) cc_final: 0.9036 (p0) REVERT: f 27 LYS cc_start: 0.9129 (mmtp) cc_final: 0.8764 (mmtp) REVERT: f 56 LYS cc_start: 0.9215 (mmtm) cc_final: 0.8928 (mmmt) REVERT: h 23 THR cc_start: 0.9129 (m) cc_final: 0.8856 (t) REVERT: j 9 ARG cc_start: 0.8877 (ptp-170) cc_final: 0.8553 (ptp-110) REVERT: j 58 ASN cc_start: 0.8449 (t0) cc_final: 0.8244 (t0) REVERT: j 88 MET cc_start: 0.7165 (ttt) cc_final: 0.6714 (tmm) REVERT: k 68 GLU cc_start: 0.8443 (pp20) cc_final: 0.7766 (pp20) REVERT: l 15 MET cc_start: 0.6328 (pmt) cc_final: 0.5721 (ptt) REVERT: l 73 ASN cc_start: 0.9073 (p0) cc_final: 0.8854 (p0) REVERT: l 78 SER cc_start: 0.9363 (m) cc_final: 0.8716 (p) REVERT: l 88 LYS cc_start: 0.8828 (tttm) cc_final: 0.8590 (ttpt) REVERT: m 37 THR cc_start: 0.7625 (m) cc_final: 0.7197 (p) REVERT: n 10 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8510 (tm-30) REVERT: n 54 ASP cc_start: 0.8311 (p0) cc_final: 0.7511 (p0) REVERT: p 53 ASP cc_start: 0.8132 (m-30) cc_final: 0.7765 (p0) REVERT: p 73 GLN cc_start: 0.8205 (pt0) cc_final: 0.7971 (pt0) REVERT: q 22 LYS cc_start: 0.9001 (mtmt) cc_final: 0.8525 (mtpp) REVERT: r 4 PHE cc_start: 0.6039 (m-80) cc_final: 0.5295 (m-80) REVERT: r 7 ARG cc_start: 0.7791 (mtt90) cc_final: 0.7489 (mtp85) REVERT: t 25 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8760 (ttm-80) REVERT: t 48 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8647 (mm-40) REVERT: u 58 LYS cc_start: 0.8015 (tptm) cc_final: 0.7726 (tttt) outliers start: 72 outliers final: 53 residues processed: 611 average time/residue: 0.5356 time to fit residues: 540.0315 Evaluate side-chains 579 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 526 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 44 GLU Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain f residue 46 GLN Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 58 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 16 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 343 optimal weight: 0.0670 chunk 261 optimal weight: 0.0370 chunk 180 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 348 optimal weight: 3.9990 chunk 369 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 330 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 overall best weight: 1.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 139 GLN c 190 HIS f 37 HIS ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 ASN g 97 ASN g 148 ASN ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN i 126 GLN l 77 HIS m 55 GLN m 74 ASN p 54 GLN q 34 HIS r 52 GLN ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 55616 Z= 0.174 Angle : 0.582 11.296 82650 Z= 0.299 Chirality : 0.034 0.251 10466 Planarity : 0.004 0.046 4829 Dihedral : 23.470 178.912 26505 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.13 % Allowed : 18.51 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.45 (0.17), residues: 2348 helix: -1.18 (0.16), residues: 872 sheet: -1.41 (0.27), residues: 385 loop : -2.01 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP b 23 HIS 0.005 0.001 HIS f 3 PHE 0.014 0.001 PHE p 38 TYR 0.016 0.001 TYR m 86 ARG 0.006 0.001 ARG k 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 569 time to evaluate : 2.541 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: b 74 ARG cc_start: 0.6068 (mtt180) cc_final: 0.5524 (mpt180) REVERT: e 15 LYS cc_start: 0.8834 (tptt) cc_final: 0.8633 (tppt) REVERT: e 25 THR cc_start: 0.9027 (m) cc_final: 0.8764 (p) REVERT: e 88 SER cc_start: 0.9300 (m) cc_final: 0.8911 (p) REVERT: e 117 GLU cc_start: 0.8428 (pt0) cc_final: 0.8075 (pt0) REVERT: e 133 ASN cc_start: 0.8935 (t0) cc_final: 0.8590 (t0) REVERT: f 5 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7425 (tm-30) REVERT: f 56 LYS cc_start: 0.9102 (mmtm) cc_final: 0.8819 (mmmt) REVERT: g 67 ASP cc_start: 0.8188 (m-30) cc_final: 0.7714 (p0) REVERT: h 23 THR cc_start: 0.9099 (m) cc_final: 0.8793 (t) REVERT: h 80 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8089 (ptm-80) REVERT: i 91 ASP cc_start: 0.6183 (p0) cc_final: 0.5966 (p0) REVERT: j 9 ARG cc_start: 0.8890 (ptp-170) cc_final: 0.8574 (ptp-110) REVERT: j 88 MET cc_start: 0.7066 (ttt) cc_final: 0.6631 (tmm) REVERT: l 15 MET cc_start: 0.6325 (pmt) cc_final: 0.5688 (ptt) REVERT: l 73 ASN cc_start: 0.9054 (p0) cc_final: 0.8787 (p0) REVERT: l 78 SER cc_start: 0.9339 (m) cc_final: 0.8694 (p) REVERT: m 37 THR cc_start: 0.7269 (m) cc_final: 0.7039 (p) REVERT: m 46 LYS cc_start: 0.8717 (ptmm) cc_final: 0.8411 (ptpp) REVERT: n 6 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7887 (tpp) REVERT: n 10 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8511 (tm-30) REVERT: n 14 GLN cc_start: 0.8207 (pm20) cc_final: 0.7841 (pm20) REVERT: n 54 ASP cc_start: 0.8342 (p0) cc_final: 0.7590 (p0) REVERT: n 80 SER cc_start: 0.9335 (t) cc_final: 0.9063 (p) REVERT: o 7 GLU cc_start: 0.9304 (tp30) cc_final: 0.8985 (tp30) REVERT: p 53 ASP cc_start: 0.8084 (m-30) cc_final: 0.7694 (p0) REVERT: q 22 LYS cc_start: 0.8900 (mtmt) cc_final: 0.8572 (mtpp) REVERT: q 52 GLU cc_start: 0.7585 (tp30) cc_final: 0.7372 (mm-30) REVERT: r 4 PHE cc_start: 0.5930 (m-80) cc_final: 0.5451 (m-80) REVERT: r 25 ASP cc_start: 0.8412 (t0) cc_final: 0.7953 (t70) REVERT: r 27 ASN cc_start: 0.9037 (m-40) cc_final: 0.8593 (p0) REVERT: s 44 MET cc_start: 0.8149 (mtm) cc_final: 0.7806 (ptp) REVERT: t 24 LEU cc_start: 0.9531 (tp) cc_final: 0.9303 (tp) REVERT: t 25 ARG cc_start: 0.8963 (ttm170) cc_final: 0.8635 (ttm-80) REVERT: t 48 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8530 (mm-40) REVERT: u 58 LYS cc_start: 0.7942 (tptm) cc_final: 0.7651 (tttt) outliers start: 80 outliers final: 59 residues processed: 599 average time/residue: 0.5233 time to fit residues: 517.6138 Evaluate side-chains 589 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 528 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 216 SER Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 109 SER Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 63 ILE Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain u residue 16 LEU Chi-restraints excluded: chain u residue 32 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 307 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 315 optimal weight: 0.0870 chunk 255 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 188 optimal weight: 0.9990 chunk 331 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 HIS e 98 GLN f 58 HIS ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 91 GLN i 50 GLN ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS m 76 ASN n 45 GLN p 54 GLN ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 55616 Z= 0.229 Angle : 0.602 10.759 82650 Z= 0.307 Chirality : 0.035 0.391 10466 Planarity : 0.004 0.051 4829 Dihedral : 23.431 179.469 26505 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 4.54 % Allowed : 21.14 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.20 (0.17), residues: 2348 helix: -0.89 (0.17), residues: 877 sheet: -1.37 (0.27), residues: 393 loop : -1.92 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP b 23 HIS 0.005 0.001 HIS s 57 PHE 0.015 0.001 PHE p 38 TYR 0.019 0.002 TYR h 65 ARG 0.006 0.001 ARG j 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 534 time to evaluate : 2.501 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 74 ARG cc_start: 0.6085 (mtt180) cc_final: 0.5577 (mmt180) REVERT: c 32 TYR cc_start: 0.8615 (m-10) cc_final: 0.8374 (m-10) REVERT: e 88 SER cc_start: 0.9312 (m) cc_final: 0.8948 (p) REVERT: e 117 GLU cc_start: 0.8460 (pt0) cc_final: 0.8131 (pt0) REVERT: e 133 ASN cc_start: 0.8997 (t0) cc_final: 0.8664 (t0) REVERT: f 5 GLU cc_start: 0.8071 (tm-30) cc_final: 0.7402 (tm-30) REVERT: f 56 LYS cc_start: 0.9098 (mmtm) cc_final: 0.8763 (mmmt) REVERT: g 67 ASP cc_start: 0.8173 (m-30) cc_final: 0.7666 (p0) REVERT: h 23 THR cc_start: 0.9071 (m) cc_final: 0.8766 (t) REVERT: h 80 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8069 (ptm-80) REVERT: i 91 ASP cc_start: 0.6150 (p0) cc_final: 0.5910 (p0) REVERT: j 9 ARG cc_start: 0.8908 (ptp-170) cc_final: 0.8569 (ptp-110) REVERT: j 23 GLN cc_start: 0.9163 (mp10) cc_final: 0.8817 (mp10) REVERT: j 76 ILE cc_start: 0.5190 (OUTLIER) cc_final: 0.4966 (pp) REVERT: j 88 MET cc_start: 0.7155 (ttt) cc_final: 0.6702 (tmm) REVERT: l 15 MET cc_start: 0.6331 (pmt) cc_final: 0.5574 (ptm) REVERT: l 73 ASN cc_start: 0.9058 (p0) cc_final: 0.8790 (p0) REVERT: l 78 SER cc_start: 0.9346 (m) cc_final: 0.8672 (p) REVERT: m 37 THR cc_start: 0.7412 (m) cc_final: 0.7126 (p) REVERT: m 46 LYS cc_start: 0.8740 (ptmm) cc_final: 0.8394 (ptpp) REVERT: m 72 GLU cc_start: 0.8459 (pp20) cc_final: 0.8219 (pp20) REVERT: n 10 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8501 (tm-30) REVERT: n 14 GLN cc_start: 0.8259 (pm20) cc_final: 0.7898 (pm20) REVERT: n 54 ASP cc_start: 0.8350 (p0) cc_final: 0.7670 (p0) REVERT: o 7 GLU cc_start: 0.9283 (tp30) cc_final: 0.8961 (tp30) REVERT: p 53 ASP cc_start: 0.8058 (m-30) cc_final: 0.7746 (p0) REVERT: q 22 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8593 (mtpp) REVERT: q 52 GLU cc_start: 0.7637 (tp30) cc_final: 0.7419 (mm-30) REVERT: q 57 ARG cc_start: 0.8234 (mmm160) cc_final: 0.7752 (ptm-80) REVERT: r 4 PHE cc_start: 0.5921 (m-80) cc_final: 0.5492 (m-80) REVERT: r 52 GLN cc_start: 0.9123 (tp40) cc_final: 0.8768 (tt0) REVERT: s 44 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.7752 (ptp) REVERT: t 25 ARG cc_start: 0.8995 (ttm170) cc_final: 0.8666 (ttm-80) REVERT: t 48 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8557 (mm-40) REVERT: t 61 MET cc_start: 0.8739 (mmm) cc_final: 0.8336 (mmm) REVERT: u 58 LYS cc_start: 0.7915 (tptm) cc_final: 0.7628 (tttt) outliers start: 88 outliers final: 75 residues processed: 569 average time/residue: 0.5212 time to fit residues: 490.7386 Evaluate side-chains 607 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 529 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 62 MET Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 17 LEU Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 76 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 110 ILE Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 39 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 55 GLU Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain q residue 58 ILE Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 44 MET Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 16 LEU Chi-restraints excluded: chain u residue 32 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 124 optimal weight: 10.0000 chunk 332 optimal weight: 0.0030 chunk 72 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 369 optimal weight: 0.3980 chunk 306 optimal weight: 4.9990 chunk 171 optimal weight: 0.0050 chunk 30 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 overall best weight: 1.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 190 HIS e 98 GLN ** f 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS m 74 ASN n 45 GLN p 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 55616 Z= 0.151 Angle : 0.562 10.355 82650 Z= 0.289 Chirality : 0.033 0.255 10466 Planarity : 0.004 0.074 4829 Dihedral : 23.376 178.855 26505 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.38 % Allowed : 21.56 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.17), residues: 2348 helix: -0.60 (0.17), residues: 878 sheet: -1.23 (0.27), residues: 404 loop : -1.81 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP b 23 HIS 0.004 0.001 HIS s 14 PHE 0.012 0.001 PHE p 38 TYR 0.017 0.001 TYR l 117 ARG 0.005 0.000 ARG m 79 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 559 time to evaluate : 2.555 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 74 ARG cc_start: 0.6005 (mtt180) cc_final: 0.5661 (mpt180) REVERT: c 44 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8770 (mm-40) REVERT: d 20 PHE cc_start: 0.8084 (m-80) cc_final: 0.7884 (m-10) REVERT: e 88 SER cc_start: 0.9303 (m) cc_final: 0.8925 (p) REVERT: e 133 ASN cc_start: 0.8979 (t0) cc_final: 0.8629 (t0) REVERT: f 27 LYS cc_start: 0.9304 (mmmm) cc_final: 0.9031 (mmtp) REVERT: f 56 LYS cc_start: 0.9042 (mmtm) cc_final: 0.8745 (mmmt) REVERT: g 67 ASP cc_start: 0.8057 (m-30) cc_final: 0.7665 (p0) REVERT: h 23 THR cc_start: 0.9066 (m) cc_final: 0.8703 (t) REVERT: h 80 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8126 (ptm-80) REVERT: i 91 ASP cc_start: 0.6281 (p0) cc_final: 0.6067 (p0) REVERT: j 20 GLN cc_start: 0.9235 (tm-30) cc_final: 0.8818 (tm-30) REVERT: j 23 GLN cc_start: 0.9181 (mp10) cc_final: 0.8691 (mp10) REVERT: j 88 MET cc_start: 0.7217 (ttt) cc_final: 0.6738 (tmm) REVERT: k 30 THR cc_start: 0.9590 (m) cc_final: 0.9221 (p) REVERT: l 15 MET cc_start: 0.6370 (pmt) cc_final: 0.5578 (ptm) REVERT: l 73 ASN cc_start: 0.9030 (p0) cc_final: 0.8730 (p0) REVERT: l 78 SER cc_start: 0.9303 (m) cc_final: 0.8640 (p) REVERT: m 37 THR cc_start: 0.7291 (m) cc_final: 0.7053 (p) REVERT: m 46 LYS cc_start: 0.8766 (ptmm) cc_final: 0.8421 (ptpp) REVERT: n 10 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8471 (tm-30) REVERT: n 14 GLN cc_start: 0.8297 (pm20) cc_final: 0.7921 (pm20) REVERT: n 54 ASP cc_start: 0.8291 (p0) cc_final: 0.7589 (p0) REVERT: n 80 SER cc_start: 0.9326 (t) cc_final: 0.8995 (p) REVERT: o 7 GLU cc_start: 0.9276 (tp30) cc_final: 0.8868 (tp30) REVERT: p 53 ASP cc_start: 0.8043 (m-30) cc_final: 0.7577 (p0) REVERT: q 22 LYS cc_start: 0.8919 (mtmt) cc_final: 0.8592 (mtpp) REVERT: q 52 GLU cc_start: 0.7650 (tp30) cc_final: 0.7429 (mm-30) REVERT: q 57 ARG cc_start: 0.8192 (mmm160) cc_final: 0.7680 (ptm-80) REVERT: r 25 ASP cc_start: 0.8502 (t0) cc_final: 0.8098 (t70) REVERT: r 27 ASN cc_start: 0.8952 (m-40) cc_final: 0.8436 (p0) REVERT: r 52 GLN cc_start: 0.9162 (tp40) cc_final: 0.8821 (tt0) REVERT: t 25 ARG cc_start: 0.8976 (ttm170) cc_final: 0.8615 (ttm-80) REVERT: t 61 MET cc_start: 0.8822 (mmm) cc_final: 0.8406 (mmm) REVERT: u 58 LYS cc_start: 0.7981 (tptm) cc_final: 0.7643 (tttt) outliers start: 85 outliers final: 65 residues processed: 592 average time/residue: 0.5562 time to fit residues: 547.9806 Evaluate side-chains 599 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 533 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain c residue 94 GLN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 98 GLN Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 115 SER Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 7 LEU Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 59 ASN Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain r residue 26 LEU Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain u residue 16 LEU Chi-restraints excluded: chain u residue 32 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 356 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 210 optimal weight: 0.0470 chunk 269 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 311 optimal weight: 0.0050 chunk 206 optimal weight: 1.9990 chunk 368 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 overall best weight: 0.7694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN i 126 GLN ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS n 45 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 55616 Z= 0.134 Angle : 0.547 10.794 82650 Z= 0.280 Chirality : 0.032 0.220 10466 Planarity : 0.004 0.071 4829 Dihedral : 23.311 178.752 26505 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.56 % Allowed : 22.54 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.63 (0.18), residues: 2348 helix: -0.35 (0.18), residues: 871 sheet: -0.95 (0.27), residues: 392 loop : -1.70 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP d 170 HIS 0.004 0.001 HIS k 22 PHE 0.018 0.001 PHE u 37 TYR 0.018 0.001 TYR l 117 ARG 0.008 0.000 ARG k 37 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 568 time to evaluate : 2.540 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 74 ARG cc_start: 0.5936 (mtt180) cc_final: 0.5610 (mpt180) REVERT: c 44 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8749 (mm-40) REVERT: e 88 SER cc_start: 0.9256 (m) cc_final: 0.8922 (p) REVERT: e 133 ASN cc_start: 0.8903 (t0) cc_final: 0.8553 (t0) REVERT: f 5 GLU cc_start: 0.7981 (tm-30) cc_final: 0.6988 (tm-30) REVERT: f 56 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8646 (mmmt) REVERT: f 74 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8714 (mm) REVERT: g 67 ASP cc_start: 0.7969 (m-30) cc_final: 0.7668 (p0) REVERT: h 23 THR cc_start: 0.9046 (m) cc_final: 0.8828 (p) REVERT: h 80 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8135 (ptm-80) REVERT: j 20 GLN cc_start: 0.9270 (tm-30) cc_final: 0.8784 (pp30) REVERT: j 23 GLN cc_start: 0.9228 (mp10) cc_final: 0.8626 (mp10) REVERT: j 88 MET cc_start: 0.7203 (ttt) cc_final: 0.6745 (tmm) REVERT: k 30 THR cc_start: 0.9581 (m) cc_final: 0.9216 (p) REVERT: k 38 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8801 (mp10) REVERT: l 15 MET cc_start: 0.6272 (pmt) cc_final: 0.5535 (ptm) REVERT: l 62 GLU cc_start: 0.7852 (tp30) cc_final: 0.6978 (tp30) REVERT: l 73 ASN cc_start: 0.8985 (p0) cc_final: 0.8644 (p0) REVERT: l 78 SER cc_start: 0.9259 (m) cc_final: 0.8603 (p) REVERT: m 37 THR cc_start: 0.7332 (m) cc_final: 0.7088 (p) REVERT: m 46 LYS cc_start: 0.8789 (ptmm) cc_final: 0.8422 (ptpp) REVERT: n 10 GLU cc_start: 0.8714 (tm-30) cc_final: 0.7967 (tm-30) REVERT: n 14 GLN cc_start: 0.8288 (pm20) cc_final: 0.7513 (pm20) REVERT: n 54 ASP cc_start: 0.8236 (p0) cc_final: 0.7586 (p0) REVERT: n 80 SER cc_start: 0.9338 (t) cc_final: 0.8991 (p) REVERT: o 7 GLU cc_start: 0.9248 (tp30) cc_final: 0.8980 (tp30) REVERT: p 53 ASP cc_start: 0.8041 (m-30) cc_final: 0.7601 (p0) REVERT: q 22 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8565 (mtpp) REVERT: q 52 GLU cc_start: 0.7616 (tp30) cc_final: 0.7404 (mm-30) REVERT: q 57 ARG cc_start: 0.8310 (mmm160) cc_final: 0.7795 (ptm-80) REVERT: r 25 ASP cc_start: 0.8325 (t0) cc_final: 0.7819 (t70) REVERT: r 27 ASN cc_start: 0.8955 (m-40) cc_final: 0.8442 (p0) REVERT: r 52 GLN cc_start: 0.9162 (tp40) cc_final: 0.8947 (tt0) REVERT: t 20 HIS cc_start: 0.9007 (t70) cc_final: 0.8795 (t-170) REVERT: t 25 ARG cc_start: 0.8924 (ttm170) cc_final: 0.8613 (ttm-80) REVERT: t 61 MET cc_start: 0.8842 (mmm) cc_final: 0.8603 (mmm) REVERT: u 58 LYS cc_start: 0.7980 (tptm) cc_final: 0.7639 (tttt) outliers start: 69 outliers final: 55 residues processed: 594 average time/residue: 0.5210 time to fit residues: 512.4753 Evaluate side-chains 594 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 537 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 44 GLU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 115 SER Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 30 LYS Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 74 LEU Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain u residue 16 LEU Chi-restraints excluded: chain u residue 32 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 227 optimal weight: 0.6980 chunk 147 optimal weight: 8.9990 chunk 219 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 250 optimal weight: 6.9990 chunk 182 optimal weight: 0.0670 chunk 34 optimal weight: 7.9990 chunk 289 optimal weight: 8.9990 overall best weight: 3.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS e 98 GLN ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN j 70 HIS ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS n 45 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN t 13 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 55616 Z= 0.334 Angle : 0.662 11.454 82650 Z= 0.334 Chirality : 0.037 0.246 10466 Planarity : 0.005 0.063 4829 Dihedral : 23.347 179.634 26505 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.49 % Allowed : 22.74 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.74 (0.17), residues: 2348 helix: -0.43 (0.17), residues: 874 sheet: -1.11 (0.27), residues: 387 loop : -1.72 (0.19), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP d 170 HIS 0.005 0.001 HIS s 57 PHE 0.033 0.002 PHE h 66 TYR 0.027 0.002 TYR o 78 ARG 0.013 0.001 ARG s 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 528 time to evaluate : 2.569 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 74 ARG cc_start: 0.6021 (mtt180) cc_final: 0.5673 (mpt180) REVERT: e 88 SER cc_start: 0.9322 (m) cc_final: 0.8967 (p) REVERT: e 133 ASN cc_start: 0.9011 (t0) cc_final: 0.8628 (t0) REVERT: f 5 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7378 (tm-30) REVERT: f 56 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8847 (mmmt) REVERT: f 74 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8798 (mm) REVERT: f 88 LEU cc_start: 0.9108 (tp) cc_final: 0.8900 (tt) REVERT: g 67 ASP cc_start: 0.8097 (m-30) cc_final: 0.7698 (p0) REVERT: h 18 GLN cc_start: 0.8988 (tt0) cc_final: 0.8702 (tt0) REVERT: h 23 THR cc_start: 0.9076 (m) cc_final: 0.8745 (t) REVERT: h 80 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8347 (ptm-80) REVERT: j 88 MET cc_start: 0.7312 (ttt) cc_final: 0.6791 (tmm) REVERT: k 38 GLN cc_start: 0.9071 (mm-40) cc_final: 0.8822 (mp10) REVERT: k 68 GLU cc_start: 0.8355 (pp20) cc_final: 0.8050 (pp20) REVERT: l 62 GLU cc_start: 0.7861 (tp30) cc_final: 0.6926 (tp30) REVERT: l 78 SER cc_start: 0.9314 (m) cc_final: 0.8610 (p) REVERT: m 37 THR cc_start: 0.7476 (m) cc_final: 0.7160 (p) REVERT: m 46 LYS cc_start: 0.8793 (ptmm) cc_final: 0.8423 (ptpp) REVERT: m 78 LYS cc_start: 0.9227 (mmmm) cc_final: 0.8927 (mmmt) REVERT: n 10 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8466 (tm-30) REVERT: n 14 GLN cc_start: 0.8284 (pm20) cc_final: 0.7872 (pm20) REVERT: n 54 ASP cc_start: 0.8373 (p0) cc_final: 0.7717 (p0) REVERT: o 7 GLU cc_start: 0.9340 (tp30) cc_final: 0.8904 (tp30) REVERT: p 53 ASP cc_start: 0.8393 (m-30) cc_final: 0.7620 (p0) REVERT: q 57 ARG cc_start: 0.8415 (mmm160) cc_final: 0.7927 (ptt-90) REVERT: r 4 PHE cc_start: 0.6316 (m-80) cc_final: 0.5782 (m-80) REVERT: r 7 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7754 (mtp85) REVERT: r 25 ASP cc_start: 0.8479 (t0) cc_final: 0.8061 (t70) REVERT: r 27 ASN cc_start: 0.9026 (m-40) cc_final: 0.8437 (p0) REVERT: t 25 ARG cc_start: 0.8957 (ttm170) cc_final: 0.8617 (ttm-80) REVERT: u 58 LYS cc_start: 0.7986 (tptm) cc_final: 0.7647 (tttt) outliers start: 87 outliers final: 75 residues processed: 564 average time/residue: 0.5360 time to fit residues: 500.4285 Evaluate side-chains 591 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 514 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 202 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain d residue 174 ASP Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 85 ILE Chi-restraints excluded: chain f residue 103 LEU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain h residue 91 GLN Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 25 ILE Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 33 LYS Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 44 SER Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 41 LEU Chi-restraints excluded: chain s residue 61 LEU Chi-restraints excluded: chain t residue 4 THR Chi-restraints excluded: chain t residue 27 MET Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain u residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 334 optimal weight: 0.9980 chunk 352 optimal weight: 0.9980 chunk 321 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 149 optimal weight: 6.9990 chunk 269 optimal weight: 0.0470 chunk 105 optimal weight: 7.9990 chunk 310 optimal weight: 6.9990 chunk 324 optimal weight: 9.9990 chunk 341 optimal weight: 1.9990 overall best weight: 1.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS m 74 ASN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55616 Z= 0.178 Angle : 0.591 12.471 82650 Z= 0.302 Chirality : 0.033 0.274 10466 Planarity : 0.004 0.069 4829 Dihedral : 23.298 179.663 26505 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.71 % Allowed : 23.93 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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 (0.18), residues: 2348 helix: -0.33 (0.17), residues: 887 sheet: -1.06 (0.27), residues: 407 loop : -1.63 (0.20), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP d 170 HIS 0.004 0.001 HIS s 57 PHE 0.041 0.001 PHE b 30 TYR 0.025 0.002 TYR o 78 ARG 0.010 0.000 ARG e 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 535 time to evaluate : 2.550 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 74 ARG cc_start: 0.5903 (mtt180) cc_final: 0.5584 (mpt180) REVERT: e 69 ARG cc_start: 0.7892 (ptp90) cc_final: 0.7679 (ptp-110) REVERT: e 88 SER cc_start: 0.9324 (m) cc_final: 0.8942 (p) REVERT: e 133 ASN cc_start: 0.8977 (t0) cc_final: 0.8630 (t0) REVERT: f 5 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7284 (tm-30) REVERT: f 40 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8563 (mt-10) REVERT: f 56 LYS cc_start: 0.9104 (mmtm) cc_final: 0.8802 (mmmt) REVERT: f 74 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8812 (mm) REVERT: f 88 LEU cc_start: 0.9032 (tp) cc_final: 0.8820 (tt) REVERT: g 67 ASP cc_start: 0.8026 (m-30) cc_final: 0.7694 (p0) REVERT: h 80 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8139 (ptm-80) REVERT: j 88 MET cc_start: 0.7266 (ttt) cc_final: 0.6773 (tmm) REVERT: k 30 THR cc_start: 0.9591 (m) cc_final: 0.9222 (p) REVERT: l 15 MET cc_start: 0.6370 (pmt) cc_final: 0.5839 (ptt) REVERT: l 62 GLU cc_start: 0.7832 (tp30) cc_final: 0.6937 (tp30) REVERT: l 78 SER cc_start: 0.9280 (m) cc_final: 0.8602 (p) REVERT: m 37 THR cc_start: 0.7333 (m) cc_final: 0.7098 (p) REVERT: m 46 LYS cc_start: 0.8786 (ptmm) cc_final: 0.8427 (ptpp) REVERT: m 78 LYS cc_start: 0.9173 (mmmm) cc_final: 0.8737 (mmmm) REVERT: n 10 GLU cc_start: 0.8715 (tm-30) cc_final: 0.7936 (tm-30) REVERT: n 14 GLN cc_start: 0.8326 (pm20) cc_final: 0.7526 (pm20) REVERT: n 54 ASP cc_start: 0.8284 (p0) cc_final: 0.7655 (p0) REVERT: p 53 ASP cc_start: 0.8083 (m-30) cc_final: 0.7625 (p0) REVERT: q 57 ARG cc_start: 0.8434 (mmm160) cc_final: 0.7917 (ptt-90) REVERT: r 7 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7618 (mtt180) REVERT: r 25 ASP cc_start: 0.8421 (t0) cc_final: 0.8064 (t0) REVERT: r 27 ASN cc_start: 0.9024 (m-40) cc_final: 0.8455 (p0) REVERT: r 52 GLN cc_start: 0.9152 (tp40) cc_final: 0.8777 (tt0) REVERT: t 25 ARG cc_start: 0.8857 (ttm170) cc_final: 0.8503 (ttm-80) REVERT: u 58 LYS cc_start: 0.7971 (tptm) cc_final: 0.7639 (tttt) outliers start: 72 outliers final: 63 residues processed: 563 average time/residue: 0.5799 time to fit residues: 548.4583 Evaluate side-chains 588 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 523 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 102 THR Chi-restraints excluded: chain b residue 147 SER Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain h residue 83 LEU Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 27 LEU Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 33 THR Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 41 LEU Chi-restraints excluded: chain s residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 225 optimal weight: 2.9990 chunk 362 optimal weight: 9.9990 chunk 221 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 252 optimal weight: 0.9980 chunk 380 optimal weight: 1.9990 chunk 350 optimal weight: 6.9990 chunk 303 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 234 optimal weight: 9.9990 chunk 185 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN i 126 GLN ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS n 45 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55616 Z= 0.178 Angle : 0.589 13.527 82650 Z= 0.300 Chirality : 0.033 0.294 10466 Planarity : 0.004 0.062 4829 Dihedral : 23.264 179.706 26505 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 3.25 % Allowed : 24.08 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.53 (0.18), residues: 2348 helix: -0.23 (0.17), residues: 884 sheet: -0.91 (0.27), residues: 396 loop : -1.68 (0.20), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP c 167 HIS 0.004 0.001 HIS s 14 PHE 0.038 0.001 PHE b 30 TYR 0.026 0.002 TYR o 78 ARG 0.011 0.000 ARG g 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4696 Ramachandran restraints generated. 2348 Oldfield, 0 Emsley, 2348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 525 time to evaluate : 2.507 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 TARDY: cannot create tardy model for: "MET t 27 " (corrupted residue). Skipping it. REVERT: b 74 ARG cc_start: 0.5896 (mtt180) cc_final: 0.5575 (mpt180) REVERT: e 88 SER cc_start: 0.9283 (m) cc_final: 0.8971 (p) REVERT: e 133 ASN cc_start: 0.8981 (t0) cc_final: 0.8628 (t0) REVERT: f 5 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7246 (tm-30) REVERT: f 56 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8838 (mmmt) REVERT: f 74 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8850 (mm) REVERT: f 88 LEU cc_start: 0.9045 (tp) cc_final: 0.8839 (tt) REVERT: g 67 ASP cc_start: 0.8018 (m-30) cc_final: 0.7706 (p0) REVERT: g 107 PHE cc_start: 0.8128 (m-80) cc_final: 0.7869 (m-80) REVERT: h 80 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8175 (ptm-80) REVERT: j 88 MET cc_start: 0.7258 (ttt) cc_final: 0.6767 (tmm) REVERT: k 30 THR cc_start: 0.9582 (m) cc_final: 0.9220 (p) REVERT: l 15 MET cc_start: 0.6147 (pmt) cc_final: 0.5726 (ptt) REVERT: l 62 GLU cc_start: 0.7780 (tp30) cc_final: 0.6865 (tp30) REVERT: l 78 SER cc_start: 0.9281 (m) cc_final: 0.8592 (p) REVERT: m 37 THR cc_start: 0.7283 (m) cc_final: 0.7066 (p) REVERT: m 46 LYS cc_start: 0.8780 (ptmm) cc_final: 0.8431 (ptpp) REVERT: n 10 GLU cc_start: 0.8722 (tm-30) cc_final: 0.7939 (tm-30) REVERT: n 14 GLN cc_start: 0.8329 (pm20) cc_final: 0.7531 (pm20) REVERT: n 54 ASP cc_start: 0.8253 (p0) cc_final: 0.7649 (p0) REVERT: o 7 GLU cc_start: 0.9301 (tp30) cc_final: 0.8935 (tp30) REVERT: o 71 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8780 (ttmm) REVERT: o 78 TYR cc_start: 0.9052 (t80) cc_final: 0.8821 (t80) REVERT: p 53 ASP cc_start: 0.8366 (m-30) cc_final: 0.7555 (p0) REVERT: q 57 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7948 (ptt-90) REVERT: r 7 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7689 (mtt180) REVERT: r 25 ASP cc_start: 0.8411 (t0) cc_final: 0.8084 (t0) REVERT: r 27 ASN cc_start: 0.9018 (m-40) cc_final: 0.8443 (p0) REVERT: r 52 GLN cc_start: 0.9177 (tp40) cc_final: 0.8954 (tt0) REVERT: u 58 LYS cc_start: 0.7979 (tptm) cc_final: 0.7643 (tttt) outliers start: 63 outliers final: 58 residues processed: 549 average time/residue: 0.5342 time to fit residues: 483.8358 Evaluate side-chains 574 residues out of total 1977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 514 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 39 HIS Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 67 ILE Chi-restraints excluded: chain b residue 72 THR Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain c residue 144 ILE Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain d residue 9 CYS Chi-restraints excluded: chain d residue 32 CYS Chi-restraints excluded: chain d residue 86 THR Chi-restraints excluded: chain d residue 124 THR Chi-restraints excluded: chain e residue 16 LEU Chi-restraints excluded: chain e residue 31 ILE Chi-restraints excluded: chain e residue 73 ILE Chi-restraints excluded: chain e residue 142 PHE Chi-restraints excluded: chain f residue 47 LEU Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 48 ASP Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 101 MET Chi-restraints excluded: chain g residue 153 HIS Chi-restraints excluded: chain h residue 75 VAL Chi-restraints excluded: chain h residue 80 ARG Chi-restraints excluded: chain i residue 28 ILE Chi-restraints excluded: chain i residue 62 ASP Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 15 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 17 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 47 SER Chi-restraints excluded: chain k residue 58 SER Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain k residue 113 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 41 THR Chi-restraints excluded: chain l residue 67 ILE Chi-restraints excluded: chain l residue 104 THR Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 51 GLU Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 26 GLU Chi-restraints excluded: chain n residue 60 LEU Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 68 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain q residue 32 VAL Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 24 GLU Chi-restraints excluded: chain s residue 38 SER Chi-restraints excluded: chain s residue 41 LEU Chi-restraints excluded: chain s residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 240 optimal weight: 1.9990 chunk 322 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 279 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 303 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 311 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 190 HIS ** f 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN ** j 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 77 HIS p 73 GLN r 54 GLN ** s 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.069025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.055955 restraints weight = 228385.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.057238 restraints weight = 88611.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.057979 restraints weight = 53861.064| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 55616 Z= 0.264 Angle : 0.634 13.478 82650 Z= 0.322 Chirality : 0.035 0.308 10466 Planarity : 0.005 0.061 4829 Dihedral : 23.280 178.929 26505 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.76 % Allowed : 24.55 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -1.56 (0.18), residues: 2348 helix: -0.25 (0.17), residues: 881 sheet: -0.97 (0.27), residues: 404 loop : -1.68 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP c 167 HIS 0.004 0.001 HIS j 56 PHE 0.037 0.001 PHE b 30 TYR 0.025 0.002 TYR o 78 ARG 0.010 0.001 ARG g 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9845.64 seconds wall clock time: 171 minutes 53.41 seconds (10313.41 seconds total)