Starting phenix.real_space_refine on Tue Mar 19 20:05:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd9_3625/03_2024/5nd9_3625.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd9_3625/03_2024/5nd9_3625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd9_3625/03_2024/5nd9_3625.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd9_3625/03_2024/5nd9_3625.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd9_3625/03_2024/5nd9_3625.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd9_3625/03_2024/5nd9_3625.pdb" } resolution = 3.7 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= 0.017 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 4569 5.49 5 S 114 5.16 5 C 70709 2.51 5 N 26039 2.21 5 O 39620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c ARG 203": "NH1" <-> "NH2" Residue "g PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 53": "NH1" <-> "NH2" Residue "v ARG 30": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "v ARG 90": "NH1" <-> "NH2" Residue "v ARG 98": "NH1" <-> "NH2" Residue "v ARG 101": "NH1" <-> "NH2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 107": "NH1" <-> "NH2" Residue "F ARG 168": "NH1" <-> "NH2" Residue "G ARG 78": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "G ARG 92": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 110": "NH1" <-> "NH2" Residue "G ARG 112": "NH1" <-> "NH2" Residue "G ARG 125": "NH1" <-> "NH2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 167": "NH1" <-> "NH2" Residue "M ARG 144": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 41": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 10": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 134": "NH1" <-> "NH2" Residue "Q ARG 96": "NH1" <-> "NH2" Residue "S ARG 23": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S ARG 39": "NH1" <-> "NH2" Residue "T ARG 48": "NH1" <-> "NH2" Residue "U TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 84": "NH1" <-> "NH2" Residue "V ARG 11": "NH1" <-> "NH2" Residue "W ARG 4": "NH1" <-> "NH2" Residue "W ARG 9": "NH1" <-> "NH2" Residue "W ARG 64": "NH1" <-> "NH2" Residue "X ARG 32": "NH1" <-> "NH2" Residue "X ARG 92": "NH1" <-> "NH2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "Z GLU 25": "OE1" <-> "OE2" Residue "Z ARG 79": "NH1" <-> "NH2" Residue "Z ARG 82": "NH1" <-> "NH2" Residue "0 ARG 17": "NH1" <-> "NH2" Residue "0 ARG 27": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 ARG 52": "NH1" <-> "NH2" Residue "1 ARG 7": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "1 ARG 58": "NH1" <-> "NH2" Residue "1 ARG 60": "NH1" <-> "NH2" Residue "4 ARG 35": "NH1" <-> "NH2" Residue "4 ARG 42": "NH1" <-> "NH2" Residue "6 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 16": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "7 ARG 45": "NH1" <-> "NH2" Residue "7 ARG 48": "NH1" <-> "NH2" Residue "7 ARG 57": "NH1" <-> "NH2" Residue "8 ARG 19": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 141051 Number of models: 1 Model: "" Number of chains: 52 Chain: "a" Number of atoms: 33006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 33006 Classifications: {'RNA': 1541} Modifications used: {'rna2p_pur': 123, 'rna2p_pyr': 88, 'rna3p_pur': 744, 'rna3p_pyr': 586} Link IDs: {'rna2p': 211, 'rna3p': 1329} Chain: "b" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "c" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1600 Classifications: {'peptide': 203} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 197} Chain: "d" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1600 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 8, 'TRANS': 185} Chain breaks: 1 Chain: "e" Number of atoms: 1194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1194 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain: "f" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 781 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "g" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1142 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 124} Chain: "i" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1017 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'CIS': 4, 'PTRANS': 7, 'TRANS': 116} Chain: "j" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 791 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 92} Chain: "k" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 851 Classifications: {'peptide': 115} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 105} Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1058 Classifications: {'peptide': 135} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 121} Chain: "m" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 877 Classifications: {'peptide': 110} Link IDs: {'CIS': 5, 'PTRANS': 2, 'TRANS': 102} Chain: "n" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 502 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 2, 'TRANS': 54} Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 85} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 83} Chain: "q" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 698 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "r" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 466 Classifications: {'peptide': 56} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 51} Chain: "s" Number of atoms: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 677 Classifications: {'peptide': 84} Link IDs: {'CIS': 3, 'PTRANS': 4, 'TRANS': 76} Chain: "t" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'CIS': 2, 'TRANS': 77} Chain: "u" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 377 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "v" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 831 Classifications: {'peptide': 101} Link IDs: {'CIS': 5, 'PTRANS': 2, 'TRANS': 93} Chain: "A" Number of atoms: 62480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2914, 62480 Classifications: {'RNA': 2914} Modifications used: {'rna2p_pur': 302, 'rna2p_pyr': 167, 'rna3p_pur': 1366, 'rna3p_pyr': 1079} Link IDs: {'rna2p': 469, 'rna3p': 2444} Chain breaks: 4 Chain: "B" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2430 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 98} Chain: "D" Number of atoms: 2103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2103 Classifications: {'peptide': 275} Link IDs: {'CIS': 2, 'PTRANS': 17, 'TRANS': 255} Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1649 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 8, 'TRANS': 209} Chain: "F" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1524 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "G" Number of atoms: 1311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1311 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "H" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "M" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1151 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 138} Chain: "N" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 116} Chain: "O" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 997 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "P" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1065 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "Q" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain: "R" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 922 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'CIS': 3, 'PTRANS': 1, 'TRANS': 114} Chain: "S" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 862 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "T" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "U" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 799 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "V" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "W" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 725 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "X" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 668 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 3, 'TRANS': 83} Chain breaks: 2 Chain: "Y" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "Z" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 591 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "0" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 373 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "1" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 536 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "2" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 441 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 663 Classifications: {'peptide': 81} Link IDs: {'CIS': 5, 'PTRANS': 3, 'TRANS': 72} Chain: "4" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 3, 'TRANS': 40} Chain: "5" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 229 Classifications: {'peptide': 28} Link IDs: {'CIS': 1, 'TRANS': 26} Chain breaks: 1 Chain: "6" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "7" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 487 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "8" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Time building chain proxies: 53.85, per 1000 atoms: 0.38 Number of scatterers: 141051 At special positions: 0 Unit cell: (250.8, 269.5, 232.1, 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 114 16.00 P 4569 15.00 O 39620 8.00 N 26039 7.00 C 70709 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 66.46 Conformation dependent library (CDL) restraints added in 6.5 seconds 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10048 Finding SS restraints... Secondary structure from input PDB file: 158 helices and 68 sheets defined 30.7% alpha, 10.6% beta 1442 base pairs and 2220 stacking pairs defined. Time for finding SS restraints: 49.48 Creating SS restraints... Processing helix chain 'b' and resid 8 through 15 removed outlier: 4.211A pdb=" N HIS b 15 " --> pdb=" O GLU b 11 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 31 removed outlier: 3.698A pdb=" N MET b 27 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS b 29 " --> pdb=" O LYS b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 44 No H-bonds generated for 'chain 'b' and resid 42 through 44' Processing helix chain 'b' and resid 45 through 64 Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.677A pdb=" N LYS b 81 " --> pdb=" O GLN b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 120 removed outlier: 4.215A pdb=" N ILE b 107 " --> pdb=" O ASN b 103 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 149 removed outlier: 3.559A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 180 Processing helix chain 'b' and resid 192 through 196 removed outlier: 3.526A pdb=" N GLU b 195 " --> pdb=" O ASP b 192 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 7 through 12 removed outlier: 3.594A pdb=" N VAL c 12 " --> pdb=" O ILE c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 42 removed outlier: 3.646A pdb=" N LEU c 31 " --> pdb=" O ASP c 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE c 38 " --> pdb=" O GLU c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 50 removed outlier: 4.250A pdb=" N GLU c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER c 50 " --> pdb=" O LEU c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 76 Processing helix chain 'c' and resid 82 through 95 Processing helix chain 'c' and resid 111 through 124 Processing helix chain 'c' and resid 128 through 139 Processing helix chain 'c' and resid 139 through 144 removed outlier: 3.649A pdb=" N LEU c 143 " --> pdb=" O ARG c 139 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 16 Processing helix chain 'd' and resid 45 through 62 removed outlier: 4.084A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 removed outlier: 3.800A pdb=" N ASN d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 74 through 77 Processing helix chain 'd' and resid 82 through 93 removed outlier: 3.672A pdb=" N PHE d 86 " --> pdb=" O HIS d 82 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA d 91 " --> pdb=" O MET d 87 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER d 92 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 102 removed outlier: 3.579A pdb=" N VAL d 98 " --> pdb=" O LEU d 94 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 117 removed outlier: 3.899A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN d 112 " --> pdb=" O ARG d 108 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU d 113 " --> pdb=" O GLN d 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 146 Processing helix chain 'd' and resid 148 through 155 Processing helix chain 'd' and resid 181 through 185 Processing helix chain 'd' and resid 193 through 198 removed outlier: 3.596A pdb=" N TYR d 197 " --> pdb=" O LEU d 193 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR d 198 " --> pdb=" O ILE d 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 193 through 198' Processing helix chain 'e' and resid 55 through 69 removed outlier: 3.872A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 117 removed outlier: 3.875A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 146 Processing helix chain 'e' and resid 149 through 155 removed outlier: 3.801A pdb=" N LYS e 155 " --> pdb=" O GLU e 151 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.731A pdb=" N LYS f 19 " --> pdb=" O GLU f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 72 through 80 removed outlier: 4.538A pdb=" N ARG f 78 " --> pdb=" O ASP f 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 31 removed outlier: 4.026A pdb=" N LYS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 32 through 34 No H-bonds generated for 'chain 'g' and resid 32 through 34' Processing helix chain 'g' and resid 35 through 53 Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.648A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 110 through 112 No H-bonds generated for 'chain 'g' and resid 110 through 112' Processing helix chain 'g' and resid 117 through 129 removed outlier: 3.660A pdb=" N ASN g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 145 Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.671A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 32 through 44 Processing helix chain 'h' and resid 96 through 100 removed outlier: 3.513A pdb=" N ASN h 99 " --> pdb=" O LYS h 96 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 Processing helix chain 'i' and resid 48 through 50 No H-bonds generated for 'chain 'i' and resid 48 through 50' Processing helix chain 'i' and resid 51 through 57 Processing helix chain 'i' and resid 73 through 78 Processing helix chain 'i' and resid 79 through 93 removed outlier: 3.676A pdb=" N HIS i 83 " --> pdb=" O GLN i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 96 through 101 Processing helix chain 'j' and resid 16 through 32 removed outlier: 4.226A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.253A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 47 through 51 Processing helix chain 'k' and resid 59 through 76 removed outlier: 4.076A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET k 65 " --> pdb=" O PHE k 61 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 94 removed outlier: 3.748A pdb=" N GLU k 94 " --> pdb=" O PRO k 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 91 through 94' Processing helix chain 'k' and resid 95 through 101 Processing helix chain 'k' and resid 102 through 104 No H-bonds generated for 'chain 'k' and resid 102 through 104' Processing helix chain 'l' and resid 3 through 9 removed outlier: 3.606A 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 27 through 36 removed outlier: 3.575A pdb=" N GLN m 31 " --> pdb=" O THR m 27 " (cutoff:3.500A) Processing helix chain 'm' and resid 52 through 61 removed outlier: 3.578A pdb=" N VAL m 60 " --> pdb=" O ILE m 56 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP m 61 " --> pdb=" O ARG m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 67 through 83 removed outlier: 3.672A pdb=" N ILE m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) Processing helix chain 'm' and resid 89 through 94 removed outlier: 3.710A pdb=" N ARG m 93 " --> pdb=" O ILE m 89 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 89 through 94' Processing helix chain 'n' and resid 3 through 12 removed outlier: 3.916A pdb=" N ALA n 8 " --> pdb=" O THR n 4 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN n 11 " --> pdb=" O VAL n 7 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 49 removed outlier: 3.758A pdb=" N PHE n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 4.082A pdb=" N ILE o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N LYS o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLU o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR o 15 " --> pdb=" O ILE o 11 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.886A pdb=" N GLN o 28 " --> pdb=" O SER o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 74 removed outlier: 3.541A pdb=" N LYS o 73 " --> pdb=" O TYR o 69 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 56 through 62 removed outlier: 4.028A pdb=" N ASN p 62 " --> pdb=" O LEU p 58 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 Processing helix chain 'p' and resid 80 through 88 removed outlier: 4.601A pdb=" N GLU p 86 " --> pdb=" O LYS p 82 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 38 Processing helix chain 'r' and resid 46 through 51 removed outlier: 3.630A pdb=" N THR r 50 " --> pdb=" O PRO r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 70 removed outlier: 3.613A pdb=" N GLN r 57 " --> pdb=" O SER r 53 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR r 62 " --> pdb=" O ARG r 58 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET r 70 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 15 through 23 removed outlier: 3.805A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) Processing helix chain 't' and resid 6 through 41 removed outlier: 3.694A pdb=" N ARG t 10 " --> pdb=" O SER t 6 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER t 40 " --> pdb=" O LYS t 36 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN t 41 " --> pdb=" O THR t 37 " (cutoff:3.500A) Processing helix chain 't' and resid 46 through 62 Processing helix chain 't' and resid 68 through 80 Processing helix chain 'u' and resid 13 through 27 removed outlier: 3.633A pdb=" N ARG u 17 " --> pdb=" O GLU u 13 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE u 19 " --> pdb=" O ALA u 15 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS u 20 " --> pdb=" O LEU u 16 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER u 26 " --> pdb=" O SER u 22 " (cutoff:3.500A) Processing helix chain 'u' and resid 27 through 34 Processing helix chain 'u' and resid 40 through 50 Processing helix chain 'v' and resid 15 through 27 Processing helix chain 'v' and resid 28 through 31 Processing helix chain 'v' and resid 73 through 93 removed outlier: 3.732A pdb=" N LEU v 80 " --> pdb=" O ALA v 76 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE v 81 " --> pdb=" O GLY v 77 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU v 85 " --> pdb=" O ILE v 81 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ARG v 87 " --> pdb=" O ASN v 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 134 No H-bonds generated for 'chain 'D' and resid 132 through 134' Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'E' and resid 70 through 79 removed outlier: 3.537A pdb=" N GLU E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 29 through 43 removed outlier: 3.835A pdb=" N LEU F 33 " --> pdb=" O ASN F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 119 Processing helix chain 'F' and resid 134 through 142 removed outlier: 3.597A pdb=" N ASN F 141 " --> pdb=" O GLU F 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL F 142 " --> pdb=" O PHE F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 192 through 201 removed outlier: 3.728A pdb=" N GLU F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 18 removed outlier: 3.701A pdb=" N GLU G 14 " --> pdb=" O THR G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 28 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 97 through 99 No H-bonds generated for 'chain 'G' and resid 97 through 99' Processing helix chain 'G' and resid 154 through 165 removed outlier: 3.787A pdb=" N THR G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 81 Processing helix chain 'H' and resid 137 through 152 removed outlier: 3.904A pdb=" N GLY H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ARG H 152 " --> pdb=" O ILE H 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 60 through 63 removed outlier: 3.850A pdb=" N ILE M 63 " --> pdb=" O ALA M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 60 through 63' Processing helix chain 'M' and resid 90 through 95 Processing helix chain 'M' and resid 98 through 104 removed outlier: 3.506A pdb=" N ILE M 102 " --> pdb=" O PRO M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 119 removed outlier: 3.887A pdb=" N LYS M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 132 through 137 removed outlier: 3.791A pdb=" N ALA M 135 " --> pdb=" O PRO M 132 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 110 Processing helix chain 'N' and resid 111 through 116 Processing helix chain 'O' and resid 115 through 125 Processing helix chain 'P' and resid 43 through 56 removed outlier: 4.354A pdb=" N ILE P 47 " --> pdb=" O THR P 43 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU P 48 " --> pdb=" O SER P 44 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 123 Processing helix chain 'Q' and resid 9 through 23 removed outlier: 3.650A pdb=" N LYS Q 14 " --> pdb=" O SER Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 51 Processing helix chain 'Q' and resid 56 through 63 Processing helix chain 'Q' and resid 84 through 93 removed outlier: 5.717A pdb=" N ALA Q 90 " --> pdb=" O PHE Q 86 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU Q 91 " --> pdb=" O GLY Q 87 " (cutoff:3.500A) Processing helix chain 'Q' and resid 94 through 96 No H-bonds generated for 'chain 'Q' and resid 94 through 96' Processing helix chain 'R' and resid 6 through 22 removed outlier: 3.613A pdb=" N VAL R 10 " --> pdb=" O ASP R 6 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG R 19 " --> pdb=" O HIS R 15 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN R 21 " --> pdb=" O ARG R 17 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU R 22 " --> pdb=" O VAL R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 62 Processing helix chain 'R' and resid 71 through 84 Processing helix chain 'R' and resid 85 through 87 No H-bonds generated for 'chain 'R' and resid 85 through 87' Processing helix chain 'R' and resid 104 through 113 Processing helix chain 'S' and resid 7 through 12 Processing helix chain 'S' and resid 55 through 58 Processing helix chain 'S' and resid 66 through 70 Processing helix chain 'T' and resid 8 through 19 removed outlier: 3.607A pdb=" N ALA T 12 " --> pdb=" O THR T 8 " (cutoff:3.500A) Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.874A pdb=" N LYS T 28 " --> pdb=" O PHE T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 70 removed outlier: 4.713A pdb=" N ARG T 51 " --> pdb=" O PHE T 47 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG T 70 " --> pdb=" O ASN T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 73 No H-bonds generated for 'chain 'T' and resid 71 through 73' Processing helix chain 'T' and resid 75 through 85 Processing helix chain 'T' and resid 94 through 102 Processing helix chain 'T' and resid 102 through 115 Processing helix chain 'V' and resid 13 through 25 removed outlier: 3.859A pdb=" N VAL V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL V 20 " --> pdb=" O LYS V 16 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE V 24 " --> pdb=" O VAL V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 37 Processing helix chain 'V' and resid 43 through 63 Processing helix chain 'W' and resid 3 through 7 removed outlier: 3.741A pdb=" N LEU W 7 " --> pdb=" O ALA W 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 3 through 7' Processing helix chain 'W' and resid 13 through 20 Processing helix chain 'W' and resid 37 through 47 removed outlier: 3.680A pdb=" N ALA W 41 " --> pdb=" O GLN W 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 25 Processing helix chain 'Y' and resid 45 through 56 removed outlier: 3.811A pdb=" N ARG Y 53 " --> pdb=" O ILE Y 49 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU Y 54 " --> pdb=" O LYS Y 50 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 7 Processing helix chain '1' and resid 12 through 33 removed outlier: 4.040A pdb=" N GLU 1 16 " --> pdb=" O SER 1 12 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ALA 1 33 " --> pdb=" O ARG 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 66 removed outlier: 4.087A pdb=" N THR 1 45 " --> pdb=" O ALA 1 41 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 25 Processing helix chain '2' and resid 40 through 49 Processing helix chain '2' and resid 50 through 52 No H-bonds generated for 'chain '2' and resid 50 through 52' Processing helix chain '4' and resid 9 through 16 Processing helix chain '6' and resid 9 through 15 Processing helix chain '6' and resid 19 through 24 Processing helix chain '6' and resid 25 through 38 removed outlier: 3.748A pdb=" N LYS 6 38 " --> pdb=" O ARG 6 34 " (cutoff:3.500A) Processing helix chain '7' and resid 9 through 13 removed outlier: 3.832A pdb=" N ARG 7 13 " --> pdb=" O ALA 7 10 " (cutoff:3.500A) Processing helix chain '8' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'b' and resid 184 through 186 removed outlier: 6.452A pdb=" N GLY b 185 " --> pdb=" O ILE b 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'c' and resid 53 through 54 removed outlier: 3.542A pdb=" N HIS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 57 through 58 Processing sheet with id=AA4, first strand: chain 'c' and resid 165 through 168 removed outlier: 3.560A pdb=" N LYS c 149 " --> pdb=" O TRP c 200 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP c 200 " --> pdb=" O LYS c 149 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL c 199 " --> pdb=" O ALA c 184 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA c 184 " --> pdb=" O VAL c 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'd' and resid 165 through 168 removed outlier: 3.506A pdb=" N ASN d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'e' and resid 20 through 21 removed outlier: 3.807A pdb=" N VAL e 39 " --> pdb=" O GLY e 47 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY e 47 " --> pdb=" O VAL e 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 92 through 93 Processing sheet with id=AA8, first strand: chain 'e' and resid 96 through 98 Processing sheet with id=AA9, first strand: chain 'f' and resid 36 through 42 removed outlier: 3.588A pdb=" N GLU f 36 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS f 66 " --> pdb=" O GLU f 36 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG f 64 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA f 40 " --> pdb=" O ILE f 62 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE f 62 " --> pdb=" O ALA f 40 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP f 42 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N TYR f 60 " --> pdb=" O ASP f 42 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL f 65 " --> pdb=" O TYR f 4 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 46 through 47 removed outlier: 3.844A pdb=" N ARG f 46 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY f 58 " --> pdb=" O ARG f 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'g' and resid 73 through 76 Processing sheet with id=AB3, first strand: chain 'h' and resid 48 through 51 Processing sheet with id=AB4, first strand: chain 'h' and resid 76 through 79 removed outlier: 3.538A pdb=" N TRP h 132 " --> pdb=" O GLY h 76 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR h 130 " --> pdb=" O LYS h 78 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE h 103 " --> pdb=" O VAL h 131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'i' and resid 9 through 14 Processing sheet with id=AB6, first strand: chain 'j' and resid 40 through 41 removed outlier: 3.540A pdb=" N ARG j 7 " --> pdb=" O LYS j 101 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'j' and resid 45 through 52 removed outlier: 3.964A pdb=" N GLN j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'k' and resid 41 through 43 removed outlier: 3.912A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN k 29 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ARG k 24 " --> pdb=" O ILE k 31 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER k 25 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VAL k 82 " --> pdb=" O THR k 108 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE k 110 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL k 84 " --> pdb=" O ILE k 110 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ASP k 112 " --> pdb=" O VAL k 84 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N VAL k 86 " --> pdb=" O ASP k 112 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'l' and resid 43 through 47 removed outlier: 3.591A pdb=" N GLY l 45 " --> pdb=" O VAL l 93 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER l 91 " --> pdb=" O CYS l 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'l' and resid 51 through 53 Processing sheet with id=AC2, first strand: chain 'l' and resid 68 through 69 Processing sheet with id=AC3, first strand: chain 'p' and resid 3 through 7 removed outlier: 4.015A pdb=" N ALA p 23 " --> pdb=" O LYS p 4 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE p 20 " --> pdb=" O ILE p 37 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE p 37 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'q' and resid 12 through 16 removed outlier: 6.287A pdb=" N THR q 24 " --> pdb=" O VAL q 15 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR q 48 " --> pdb=" O ILE q 23 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN q 64 " --> pdb=" O ARG q 76 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL q 78 " --> pdb=" O LYS q 62 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N ILE q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ILE q 60 " --> pdb=" O ILE q 80 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 's' and resid 32 through 33 removed outlier: 7.937A pdb=" N THR s 33 " --> pdb=" O TYR s 52 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL s 51 " --> pdb=" O VAL s 58 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'v' and resid 6 through 8 removed outlier: 7.312A pdb=" N HIS v 7 " --> pdb=" O VAL v 42 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AC8, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AC9, first strand: chain 'D' and resid 80 through 82 Processing sheet with id=AD1, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AD2, first strand: chain 'D' and resid 171 through 174 removed outlier: 3.524A pdb=" N ARG D 181 " --> pdb=" O ILE D 173 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 6 through 7 Processing sheet with id=AD4, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.232A pdb=" N LYS E 198 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 185 " --> pdb=" O LYS E 198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 34 through 39 removed outlier: 6.736A pdb=" N GLN E 50 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS E 38 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ALA E 48 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 127 through 128 removed outlier: 4.285A pdb=" N GLY E 171 " --> pdb=" O GLN E 128 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 6 through 8 removed outlier: 4.645A pdb=" N GLY F 15 " --> pdb=" O LEU F 7 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 85 through 86 removed outlier: 3.569A pdb=" N VAL G 36 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 147 " --> pdb=" O VAL G 35 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AE1, first strand: chain 'H' and resid 125 through 127 removed outlier: 4.656A pdb=" N VAL H 125 " --> pdb=" O LYS H 132 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS H 132 " --> pdb=" O VAL H 125 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ARG H 163 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 96 through 99 Processing sheet with id=AE3, first strand: chain 'M' and resid 123 through 126 removed outlier: 6.225A pdb=" N VAL M 55 " --> pdb=" O PHE M 124 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N TYR M 126 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL M 57 " --> pdb=" O TYR M 126 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR M 17 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N ILE M 58 " --> pdb=" O TYR M 17 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE M 19 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP M 16 " --> pdb=" O GLU M 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AE5, first strand: chain 'N' and resid 40 through 42 removed outlier: 3.881A pdb=" N VAL N 63 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 76 through 77 removed outlier: 3.569A pdb=" N TYR N 76 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR S 75 " --> pdb=" O TYR N 76 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS S 65 " --> pdb=" O VAL S 72 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE S 61 " --> pdb=" O PHE S 76 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR S 60 " --> pdb=" O ARG S 52 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ARG S 52 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR S 62 " --> pdb=" O ILE S 50 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 64 through 66 removed outlier: 4.317A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL P 106 " --> pdb=" O PHE P 32 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE P 32 " --> pdb=" O VAL P 106 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY P 33 " --> pdb=" O VAL P 132 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 40 through 42 Processing sheet with id=AE9, first strand: chain 'P' and resid 75 through 76 removed outlier: 4.247A pdb=" N ALA P 89 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 103 through 108 removed outlier: 5.277A pdb=" N LYS Q 105 " --> pdb=" O ILE Q 118 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ILE Q 118 " --> pdb=" O LYS Q 105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'R' and resid 30 through 31 Processing sheet with id=AF3, first strand: chain 'R' and resid 30 through 31 removed outlier: 4.069A pdb=" N ALA R 54 " --> pdb=" O ILE R 44 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASP R 46 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR R 52 " --> pdb=" O ASP R 46 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 42 through 45 removed outlier: 3.543A pdb=" N HIS S 31 " --> pdb=" O LYS S 85 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS S 85 " --> pdb=" O HIS S 31 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG S 33 " --> pdb=" O ILE S 83 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE S 83 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 3 through 4 Processing sheet with id=AF6, first strand: chain 'U' and resid 19 through 22 removed outlier: 3.556A pdb=" N ILE U 20 " --> pdb=" O LEU U 95 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR U 96 " --> pdb=" O VAL U 62 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N VAL U 62 " --> pdb=" O THR U 96 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ASP U 98 " --> pdb=" O ALA U 60 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA U 60 " --> pdb=" O ASP U 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U' and resid 71 through 76 removed outlier: 3.888A pdb=" N LYS U 86 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR U 75 " --> pdb=" O ARG U 84 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG U 84 " --> pdb=" O THR U 75 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'V' and resid 4 through 10 removed outlier: 3.689A pdb=" N ALA V 7 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N SER V 101 " --> pdb=" O THR V 9 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU V 73 " --> pdb=" O VAL V 106 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N SER V 108 " --> pdb=" O VAL V 71 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL V 71 " --> pdb=" O SER V 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 81 through 87 removed outlier: 3.515A pdb=" N ARG V 86 " --> pdb=" O SER V 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER V 94 " --> pdb=" O ARG V 86 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'W' and resid 9 through 10 removed outlier: 4.785A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG W 75 " --> pdb=" O TYR W 58 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 62 through 63 removed outlier: 3.994A pdb=" N GLY W 70 " --> pdb=" O LYS W 63 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'X' and resid 9 through 10 removed outlier: 3.838A pdb=" N GLY X 21 " --> pdb=" O VAL X 9 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 23 through 24 removed outlier: 4.114A pdb=" N VAL X 34 " --> pdb=" O ILE X 24 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 80 through 81 removed outlier: 3.873A pdb=" N ARG X 80 " --> pdb=" O ALA X 94 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA X 94 " --> pdb=" O ARG X 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'Y' and resid 39 through 44 removed outlier: 11.734A pdb=" N LYS Y 26 " --> pdb=" O GLN Y 85 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N THR Y 87 " --> pdb=" O LYS Y 26 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE Y 89 " --> pdb=" O PRO Y 28 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL Y 30 " --> pdb=" O ILE Y 89 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE Y 91 " --> pdb=" O VAL Y 30 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR Y 32 " --> pdb=" O PHE Y 91 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE Y 89 " --> pdb=" O ASP Y 76 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP Y 76 " --> pdb=" O ILE Y 89 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Z' and resid 30 through 31 removed outlier: 3.595A pdb=" N GLY Z 30 " --> pdb=" O ARG Z 47 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG Z 47 " --> pdb=" O GLY Z 30 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU Z 67 " --> pdb=" O LEU Z 45 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Z' and resid 74 through 77 Processing sheet with id=AG9, first strand: chain '0' and resid 18 through 19 Processing sheet with id=AH1, first strand: chain '0' and resid 36 through 39 removed outlier: 3.646A pdb=" N VAL 0 47 " --> pdb=" O ILE 0 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '2' and resid 34 through 38 removed outlier: 3.643A pdb=" N THR 2 55 " --> pdb=" O THR 2 7 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '3' and resid 28 through 29 removed outlier: 6.193A pdb=" N ILE 3 46 " --> pdb=" O LYS 3 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain '4' and resid 28 through 29 Processing sheet with id=AH5, first strand: chain '8' and resid 15 through 17 1257 hydrogen bonds defined for protein. 3471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3597 hydrogen bonds 5866 hydrogen bond angles 0 basepair planarities 1442 basepair parallelities 2220 stacking parallelities Total time for adding SS restraints: 210.20 Time building geometry restraints manager: 71.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 13306 1.30 - 1.43: 68060 1.43 - 1.56: 62608 1.56 - 1.69: 9169 1.69 - 1.82: 210 Bond restraints: 153353 Sorted by residual: bond pdb=" C GLY Y 25 " pdb=" N LYS Y 26 " ideal model delta sigma weight residual 1.329 1.736 -0.407 1.44e-02 4.82e+03 7.99e+02 bond pdb=" CA LEU H 87 " pdb=" CB LEU H 87 " ideal model delta sigma weight residual 1.532 1.416 0.116 1.58e-02 4.01e+03 5.38e+01 bond pdb=" CA ALA 7 10 " pdb=" C ALA 7 10 " ideal model delta sigma weight residual 1.523 1.420 0.103 1.41e-02 5.03e+03 5.29e+01 bond pdb=" CA PHE E 147 " pdb=" CB PHE E 147 " ideal model delta sigma weight residual 1.527 1.358 0.169 2.48e-02 1.63e+03 4.65e+01 bond pdb=" CA LEU W 7 " pdb=" CB LEU W 7 " ideal model delta sigma weight residual 1.523 1.451 0.073 1.27e-02 6.20e+03 3.28e+01 ... (remaining 153348 not shown) Histogram of bond angle deviations from ideal: 58.73 - 79.67: 2 79.67 - 100.61: 575 100.61 - 121.55: 190067 121.55 - 142.49: 38900 142.49 - 163.43: 1 Bond angle restraints: 229545 Sorted by residual: angle pdb=" O GLY Y 25 " pdb=" C GLY Y 25 " pdb=" N LYS Y 26 " ideal model delta sigma weight residual 122.70 163.43 -40.73 1.30e+00 5.92e-01 9.82e+02 angle pdb=" C GLY Y 25 " pdb=" N LYS Y 26 " pdb=" CA LYS Y 26 " ideal model delta sigma weight residual 122.03 63.28 58.75 2.01e+00 2.48e-01 8.54e+02 angle pdb=" CA GLY Y 25 " pdb=" C GLY Y 25 " pdb=" N LYS Y 26 " ideal model delta sigma weight residual 116.69 58.73 57.96 2.04e+00 2.40e-01 8.07e+02 angle pdb=" C5' A A 260 " pdb=" C4' A A 260 " pdb=" C3' A A 260 " ideal model delta sigma weight residual 116.00 92.23 23.77 1.50e+00 4.44e-01 2.51e+02 angle pdb=" N GLY O 100 " pdb=" CA GLY O 100 " pdb=" C GLY O 100 " ideal model delta sigma weight residual 112.08 103.28 8.80 1.01e+00 9.80e-01 7.59e+01 ... (remaining 229540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 86430 35.85 - 71.70: 10482 71.70 - 107.54: 1072 107.54 - 143.39: 20 143.39 - 179.24: 12 Dihedral angle restraints: 98016 sinusoidal: 82417 harmonic: 15599 Sorted by residual: dihedral pdb=" CA ILE R 89 " pdb=" C ILE R 89 " pdb=" N LYS R 90 " pdb=" CA LYS R 90 " ideal model delta harmonic sigma weight residual -180.00 -48.85 -131.15 0 5.00e+00 4.00e-02 6.88e+02 dihedral pdb=" CA SER v 50 " pdb=" C SER v 50 " pdb=" N ALA v 51 " pdb=" CA ALA v 51 " ideal model delta harmonic sigma weight residual 180.00 127.60 52.40 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" O4' C B 114 " pdb=" C1' C B 114 " pdb=" N1 C B 114 " pdb=" C2 C B 114 " ideal model delta sinusoidal sigma weight residual -160.00 17.83 -177.83 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 98013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 29381 0.344 - 0.689: 3 0.689 - 1.033: 1 1.033 - 1.377: 0 1.377 - 1.722: 2 Chirality restraints: 29387 Sorted by residual: chirality pdb=" CB THR b 214 " pdb=" CA THR b 214 " pdb=" OG1 THR b 214 " pdb=" CG2 THR b 214 " both_signs ideal model delta sigma weight residual False 2.55 0.83 1.72 2.00e-01 2.50e+01 7.41e+01 chirality pdb=" CB VAL S 94 " pdb=" CA VAL S 94 " pdb=" CG1 VAL S 94 " pdb=" CG2 VAL S 94 " both_signs ideal model delta sigma weight residual False -2.63 -1.16 -1.47 2.00e-01 2.50e+01 5.41e+01 chirality pdb=" C3' C a1474 " pdb=" C4' C a1474 " pdb=" O3' C a1474 " pdb=" C2' C a1474 " both_signs ideal model delta sigma weight residual False -2.48 -1.74 -0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 29384 not shown) Planarity restraints: 12106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG v 66 " -0.851 9.50e-02 1.11e+02 3.81e-01 8.88e+01 pdb=" NE ARG v 66 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG v 66 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG v 66 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG v 66 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY Y 25 " 0.001 2.00e-02 2.50e+03 8.43e-02 7.11e+01 pdb=" C GLY Y 25 " -0.137 2.00e-02 2.50e+03 pdb=" O GLY Y 25 " 0.080 2.00e-02 2.50e+03 pdb=" N LYS Y 26 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG v 98 " 0.578 9.50e-02 1.11e+02 2.59e-01 4.11e+01 pdb=" NE ARG v 98 " -0.034 2.00e-02 2.50e+03 pdb=" CZ ARG v 98 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG v 98 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG v 98 " 0.019 2.00e-02 2.50e+03 ... (remaining 12103 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.69: 9 1.69 - 2.49: 1367 2.49 - 3.30: 163665 3.30 - 4.10: 445165 4.10 - 4.90: 664158 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1274364 Sorted by model distance: nonbonded pdb=" NH2 ARG g 78 " pdb=" NH2 ARG v 103 " model vdw 0.889 3.200 nonbonded pdb=" O GLU r 40 " pdb=" O LYS r 77 " model vdw 1.029 3.040 nonbonded pdb=" CZ ARG g 78 " pdb=" NH2 ARG v 103 " model vdw 1.053 3.350 nonbonded pdb=" N GLY Y 25 " pdb=" N LYS Y 26 " model vdw 1.214 2.560 nonbonded pdb=" CD2 TYR g 85 " pdb=" NH1 ARG v 103 " model vdw 1.258 3.420 ... (remaining 1274359 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.99 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: 2.030 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: 0.100 Extract box with map and model: 14.000 Check model and map are aligned: 1.490 Set scattering table: 0.980 Process input model: 482.290 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.400 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: 0.040 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 506.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 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 : 0.011 0.407 153353 Z= 0.682 Angle : 1.188 58.746 229545 Z= 0.596 Chirality : 0.059 1.722 29387 Planarity : 0.009 0.381 12106 Dihedral : 23.175 179.238 87968 Min Nonbonded Distance : 0.889 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.64 % Allowed : 19.26 % Favored : 80.10 % Rotamer: Outliers : 1.12 % Allowed : 5.78 % Favored : 93.10 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.94 % Twisted Proline : 2.17 % Twisted General : 1.09 % 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: -5.81 (0.09), residues: 5353 helix: -3.64 (0.09), residues: 1386 sheet: -4.04 (0.14), residues: 744 loop : -4.12 (0.09), residues: 3223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP 0 29 HIS 0.022 0.004 HIS O 35 PHE 0.034 0.004 PHE D 66 TYR 0.044 0.004 TYR G 143 ARG 0.022 0.003 ARG 7 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1512 time to evaluate : 6.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 54 TYR cc_start: 0.6573 (t80) cc_final: 0.6176 (t80) REVERT: b 217 MET cc_start: 0.7221 (mpp) cc_final: 0.6987 (ppp) REVERT: b 219 ASP cc_start: 0.7524 (p0) cc_final: 0.7133 (t0) REVERT: c 35 ASP cc_start: 0.7813 (t0) cc_final: 0.7484 (t0) REVERT: c 106 LYS cc_start: 0.4595 (mptt) cc_final: 0.3290 (tttp) REVERT: c 175 HIS cc_start: 0.5019 (t-90) cc_final: 0.4788 (m170) REVERT: d 151 ILE cc_start: 0.7156 (mp) cc_final: 0.6905 (tp) REVERT: f 9 ILE cc_start: 0.7877 (mt) cc_final: 0.7557 (mt) REVERT: f 64 ARG cc_start: 0.6890 (mtp-110) cc_final: 0.6407 (mtm110) REVERT: g 86 GLN cc_start: 0.4832 (mp10) cc_final: 0.4419 (mt0) REVERT: g 116 MET cc_start: 0.5562 (ptp) cc_final: 0.5240 (ptp) REVERT: g 149 LYS cc_start: 0.7227 (ttmt) cc_final: 0.7019 (ttmm) REVERT: j 63 GLU cc_start: 0.7531 (pp20) cc_final: 0.6849 (pp20) REVERT: j 65 PHE cc_start: 0.6455 (m-80) cc_final: 0.6244 (m-10) REVERT: l 29 ASN cc_start: 0.6528 (m110) cc_final: 0.6111 (m-40) REVERT: m 3 ARG cc_start: 0.4022 (tmt-80) cc_final: 0.3732 (tpp80) REVERT: n 47 LEU cc_start: 0.8206 (mt) cc_final: 0.7772 (mt) REVERT: o 45 THR cc_start: 0.7871 (m) cc_final: 0.7659 (p) REVERT: o 76 GLN cc_start: 0.6769 (tm130) cc_final: 0.6564 (tm-30) REVERT: o 81 LEU cc_start: 0.8294 (pt) cc_final: 0.7996 (pp) REVERT: p 35 GLU cc_start: 0.7397 (pp20) cc_final: 0.6616 (pm20) REVERT: q 72 THR cc_start: 0.7228 (m) cc_final: 0.6909 (p) REVERT: s 6 LYS cc_start: 0.3189 (mttp) cc_final: 0.2409 (mmmt) REVERT: t 8 ILE cc_start: 0.8036 (mt) cc_final: 0.7176 (mp) REVERT: t 33 LYS cc_start: 0.7775 (tttt) cc_final: 0.7390 (ttpt) REVERT: v 32 PHE cc_start: 0.5714 (t80) cc_final: 0.5110 (t80) REVERT: v 82 ASN cc_start: 0.7166 (OUTLIER) cc_final: 0.6850 (t0) REVERT: v 101 ARG cc_start: 0.1913 (OUTLIER) cc_final: -0.0792 (mmt180) REVERT: D 77 VAL cc_start: 0.8108 (p) cc_final: 0.7841 (t) REVERT: E 122 SER cc_start: 0.8798 (p) cc_final: 0.8531 (m) REVERT: F 17 ILE cc_start: 0.6220 (pp) cc_final: 0.5849 (mp) REVERT: M 32 GLU cc_start: 0.7024 (tt0) cc_final: 0.6700 (tt0) REVERT: M 103 GLU cc_start: 0.7121 (tt0) cc_final: 0.6531 (tt0) REVERT: O 99 SER cc_start: 0.7230 (m) cc_final: 0.6828 (m) REVERT: P 37 THR cc_start: 0.7786 (p) cc_final: 0.7526 (p) REVERT: P 65 TRP cc_start: 0.7364 (m-90) cc_final: 0.7105 (m-90) REVERT: P 112 GLU cc_start: 0.6794 (pm20) cc_final: 0.6476 (pm20) REVERT: R 94 PHE cc_start: 0.6200 (t80) cc_final: 0.5213 (t80) REVERT: T 41 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8105 (mmtm) REVERT: T 94 MET cc_start: 0.7276 (mmt) cc_final: 0.6475 (mmt) REVERT: U 16 GLU cc_start: 0.6026 (tp30) cc_final: 0.5234 (tm-30) REVERT: U 99 LYS cc_start: 0.8430 (tppt) cc_final: 0.8207 (tppt) REVERT: V 48 GLU cc_start: 0.7319 (pt0) cc_final: 0.7091 (pt0) REVERT: V 90 GLN cc_start: 0.8544 (mp-120) cc_final: 0.8119 (mp10) REVERT: W 71 TYR cc_start: 0.6645 (m-10) cc_final: 0.6391 (m-10) REVERT: X 34 VAL cc_start: 0.9251 (t) cc_final: 0.8867 (m) REVERT: X 39 ASN cc_start: 0.7098 (m-40) cc_final: 0.6864 (m-40) REVERT: Y 21 LEU cc_start: 0.3767 (OUTLIER) cc_final: 0.3342 (tp) REVERT: Z 54 TYR cc_start: 0.7626 (m-80) cc_final: 0.6882 (m-80) REVERT: 2 21 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8550 (mtpt) REVERT: 3 11 GLN cc_start: 0.2646 (tm-30) cc_final: 0.2133 (tm-30) REVERT: 8 18 LYS cc_start: 0.6952 (mttt) cc_final: 0.6537 (mttp) outliers start: 52 outliers final: 18 residues processed: 1559 average time/residue: 1.2996 time to fit residues: 3401.4057 Evaluate side-chains 1055 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1034 time to evaluate : 5.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 8 THR Chi-restraints excluded: chain j residue 5 LYS Chi-restraints excluded: chain l residue 101 LYS Chi-restraints excluded: chain u residue 25 LYS Chi-restraints excluded: chain u residue 54 LYS Chi-restraints excluded: chain v residue 30 ARG Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 80 LEU Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain v residue 83 ASN Chi-restraints excluded: chain v residue 94 THR Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain v residue 103 ARG Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain N residue 63 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain P residue 136 GLU Chi-restraints excluded: chain Y residue 21 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 827 optimal weight: 5.9990 chunk 742 optimal weight: 3.9990 chunk 412 optimal weight: 10.0000 chunk 253 optimal weight: 0.3980 chunk 501 optimal weight: 50.0000 chunk 396 optimal weight: 10.0000 chunk 768 optimal weight: 20.0000 chunk 297 optimal weight: 20.0000 chunk 467 optimal weight: 0.9990 chunk 571 optimal weight: 0.9990 chunk 889 optimal weight: 9.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN b 159 GLN c 33 HIS c 61 ASN c 68 HIS c 88 ASN e 54 GLN e 145 GLN e 146 ASN e 149 ASN g 19 ASN h 31 ASN i 33 ASN j 64 GLN l 39 ASN l 73 ASN ** l 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 76 ASN o 37 ASN p 36 GLN p 87 GLN ** q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 41 ASN t 45 ASN t 62 GLN t 67 HIS t 69 ASN v 19 ASN ** v 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 ASN D 53 HIS D 132 GLN D 142 ASN D 152 GLN ** D 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN E 128 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN F 82 GLN H 81 GLN H 106 ASN ** M 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 ASN O 17 ASN O 114 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 61 ASN R 15 HIS S 31 HIS T 38 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 ASN Z 37 GLN 0 32 ASN 0 34 GLN 1 31 GLN 2 40 ASN 3 3 GLN 3 75 ASN 6 13 HIS ** 7 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 153353 Z= 0.180 Angle : 0.685 12.126 229545 Z= 0.347 Chirality : 0.036 0.319 29387 Planarity : 0.006 0.112 12106 Dihedral : 23.462 179.531 76881 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.15 % Favored : 88.68 % Rotamer: Outliers : 3.52 % Allowed : 13.94 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.23 % 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: -4.43 (0.10), residues: 5353 helix: -1.90 (0.12), residues: 1466 sheet: -3.16 (0.15), residues: 797 loop : -3.57 (0.09), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP g 103 HIS 0.010 0.001 HIS E 134 PHE 0.024 0.002 PHE H 123 TYR 0.031 0.002 TYR Z 90 ARG 0.010 0.001 ARG O 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1484 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1321 time to evaluate : 6.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 19 GLN cc_start: 0.4811 (mp-120) cc_final: 0.4500 (tt0) REVERT: b 26 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7324 (mmtt) REVERT: b 27 MET cc_start: 0.6876 (ptp) cc_final: 0.6443 (ptp) REVERT: b 130 PRO cc_start: 0.5827 (Cg_endo) cc_final: 0.4539 (Cg_exo) REVERT: b 133 GLU cc_start: 0.7515 (tp30) cc_final: 0.7235 (mp0) REVERT: b 219 ASP cc_start: 0.7663 (p0) cc_final: 0.7384 (t0) REVERT: b 223 GLU cc_start: 0.7414 (pt0) cc_final: 0.6854 (mm-30) REVERT: c 35 ASP cc_start: 0.7152 (t0) cc_final: 0.6780 (t0) REVERT: c 68 HIS cc_start: 0.6112 (OUTLIER) cc_final: 0.5812 (t-170) REVERT: c 106 LYS cc_start: 0.4820 (mptt) cc_final: 0.3666 (ttpt) REVERT: e 152 ASP cc_start: 0.6685 (t70) cc_final: 0.6340 (t70) REVERT: g 63 GLU cc_start: 0.5759 (mm-30) cc_final: 0.4108 (pp20) REVERT: h 5 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6485 (t70) REVERT: i 101 LYS cc_start: 0.6578 (tttm) cc_final: 0.5579 (mmtm) REVERT: j 88 MET cc_start: 0.3039 (ptm) cc_final: 0.2296 (ptt) REVERT: m 81 MET cc_start: 0.5178 (ptm) cc_final: 0.4959 (mmm) REVERT: o 41 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7410 (pp20) REVERT: p 35 GLU cc_start: 0.7416 (pp20) cc_final: 0.6468 (pm20) REVERT: p 56 LEU cc_start: 0.7068 (pt) cc_final: 0.6582 (pp) REVERT: p 59 LYS cc_start: 0.7889 (ttpp) cc_final: 0.7579 (tttt) REVERT: s 6 LYS cc_start: 0.3615 (mttp) cc_final: 0.3349 (mmmt) REVERT: v 30 ARG cc_start: 0.6276 (OUTLIER) cc_final: 0.6057 (mpt180) REVERT: v 47 TYR cc_start: 0.2070 (OUTLIER) cc_final: 0.1401 (t80) REVERT: D 24 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7434 (m) REVERT: D 144 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6935 (mt-10) REVERT: E 119 THR cc_start: 0.8614 (t) cc_final: 0.7926 (p) REVERT: E 122 SER cc_start: 0.8891 (p) cc_final: 0.8671 (m) REVERT: E 161 SER cc_start: 0.8460 (t) cc_final: 0.8008 (p) REVERT: F 37 ILE cc_start: 0.9042 (mm) cc_final: 0.8601 (tp) REVERT: H 23 HIS cc_start: 0.6564 (t70) cc_final: 0.6357 (t70) REVERT: M 5 PHE cc_start: 0.7194 (t80) cc_final: 0.6924 (t80) REVERT: N 45 ASN cc_start: 0.7239 (p0) cc_final: 0.6860 (p0) REVERT: P 39 THR cc_start: 0.8475 (OUTLIER) cc_final: 0.8240 (m) REVERT: T 91 ASN cc_start: 0.7997 (m110) cc_final: 0.6649 (t0) REVERT: U 74 PHE cc_start: 0.7937 (t80) cc_final: 0.7646 (t80) REVERT: V 4 LYS cc_start: 0.8154 (pttp) cc_final: 0.7926 (pttp) REVERT: V 11 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7224 (tmm160) REVERT: V 90 GLN cc_start: 0.8654 (mp-120) cc_final: 0.8138 (mp10) REVERT: Y 21 LEU cc_start: 0.4941 (OUTLIER) cc_final: 0.4198 (tp) REVERT: Z 84 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7475 (mtpp) REVERT: 3 34 MET cc_start: 0.5315 (OUTLIER) cc_final: 0.4893 (mpp) REVERT: 6 9 ASN cc_start: 0.8807 (t0) cc_final: 0.8595 (t0) REVERT: 7 26 ARG cc_start: 0.6753 (tmt170) cc_final: 0.6420 (tmt170) REVERT: 8 18 LYS cc_start: 0.7246 (mttt) cc_final: 0.6977 (mttp) REVERT: 8 22 LYS cc_start: 0.6298 (ttpp) cc_final: 0.6013 (tttm) outliers start: 163 outliers final: 77 residues processed: 1402 average time/residue: 1.3333 time to fit residues: 3209.5093 Evaluate side-chains 1131 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1044 time to evaluate : 5.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 68 HIS Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain d residue 74 ILE Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 5 ASP Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 5 LYS Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain v residue 30 ARG Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 83 ASN Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 39 THR Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain V residue 11 ARG Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 1 residue 18 ILE Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 6 residue 17 HIS Chi-restraints excluded: chain 6 residue 19 PHE Chi-restraints excluded: chain 6 residue 24 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 494 optimal weight: 20.0000 chunk 276 optimal weight: 20.0000 chunk 740 optimal weight: 30.0000 chunk 606 optimal weight: 50.0000 chunk 245 optimal weight: 6.9990 chunk 891 optimal weight: 30.0000 chunk 963 optimal weight: 50.0000 chunk 794 optimal weight: 30.0000 chunk 884 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 715 optimal weight: 3.9990 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 125 ASN c 166 GLN d 40 GLN d 67 GLN d 109 GLN ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 ASN e 54 GLN e 145 GLN g 28 ASN g 52 GLN h 16 ASN i 62 ASN j 20 GLN j 56 HIS j 64 GLN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 ASN l 39 ASN ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 42 HIS p 36 GLN ** q 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 77 GLN D 43 ASN D 132 GLN D 142 ASN D 229 HIS D 231 HIS ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 HIS ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 HIS R 43 GLN R 102 HIS T 38 GLN T 71 GLN T 81 ASN U 63 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 27 ASN 2 46 GLN 7 7 HIS 7 31 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 153353 Z= 0.362 Angle : 0.795 12.315 229545 Z= 0.399 Chirality : 0.041 0.324 29387 Planarity : 0.006 0.112 12106 Dihedral : 23.432 179.711 76849 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.99 % Favored : 85.88 % Rotamer: Outliers : 6.08 % Allowed : 18.06 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.00 % Twisted Proline : 0.54 % Twisted General : 0.25 % 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: -3.98 (0.10), residues: 5353 helix: -1.43 (0.12), residues: 1488 sheet: -2.95 (0.16), residues: 827 loop : -3.32 (0.10), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP g 103 HIS 0.028 0.002 HIS c 68 PHE 0.024 0.002 PHE O 58 TYR 0.049 0.002 TYR Z 90 ARG 0.009 0.001 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1161 time to evaluate : 6.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7245 (ptp) cc_final: 0.7023 (ptp) REVERT: b 219 ASP cc_start: 0.7821 (p0) cc_final: 0.6893 (t0) REVERT: c 8 ILE cc_start: 0.7426 (pp) cc_final: 0.6911 (pt) REVERT: c 16 ARG cc_start: 0.3205 (ptp-170) cc_final: 0.1954 (ptm-80) REVERT: c 106 LYS cc_start: 0.4873 (mptt) cc_final: 0.3826 (ttpt) REVERT: e 10 GLU cc_start: 0.4305 (OUTLIER) cc_final: 0.3707 (pm20) REVERT: g 63 GLU cc_start: 0.5285 (mm-30) cc_final: 0.3774 (pp20) REVERT: k 68 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7548 (mt-10) REVERT: o 8 LYS cc_start: 0.7566 (ttpt) cc_final: 0.7213 (tttt) REVERT: o 31 VAL cc_start: 0.8850 (t) cc_final: 0.8516 (m) REVERT: o 41 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7597 (pp20) REVERT: p 81 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.5963 (ppp) REVERT: s 33 THR cc_start: 0.1427 (t) cc_final: 0.1121 (t) REVERT: s 71 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7704 (tt) REVERT: u 53 ARG cc_start: 0.2335 (OUTLIER) cc_final: 0.0465 (ptm-80) REVERT: v 30 ARG cc_start: 0.6480 (OUTLIER) cc_final: 0.6258 (mtt180) REVERT: v 45 LYS cc_start: 0.2186 (OUTLIER) cc_final: 0.1880 (mtpp) REVERT: v 47 TYR cc_start: 0.2931 (OUTLIER) cc_final: 0.2120 (t80) REVERT: D 4 LYS cc_start: 0.7793 (mttp) cc_final: 0.7568 (mttp) REVERT: D 142 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8271 (t0) REVERT: D 144 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7270 (mt-10) REVERT: E 122 SER cc_start: 0.9090 (p) cc_final: 0.8770 (t) REVERT: M 126 TYR cc_start: 0.7912 (m-80) cc_final: 0.7683 (m-10) REVERT: P 42 ILE cc_start: 0.9235 (pp) cc_final: 0.8869 (mt) REVERT: S 86 ILE cc_start: 0.8352 (mm) cc_final: 0.8037 (mp) REVERT: V 4 LYS cc_start: 0.8211 (pttp) cc_final: 0.7968 (pttp) REVERT: V 11 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7193 (tmm160) REVERT: V 90 GLN cc_start: 0.8668 (mp-120) cc_final: 0.7959 (mp10) REVERT: Z 76 LYS cc_start: 0.7549 (mtmm) cc_final: 0.7242 (ptpp) REVERT: 0 29 TRP cc_start: 0.5491 (p-90) cc_final: 0.4786 (p-90) REVERT: 0 52 ARG cc_start: 0.7914 (tpt170) cc_final: 0.6925 (ttp-170) REVERT: 2 18 THR cc_start: 0.9164 (p) cc_final: 0.8882 (t) REVERT: 3 1 MET cc_start: 0.4957 (tmm) cc_final: 0.4554 (tmm) REVERT: 3 34 MET cc_start: 0.6041 (tmt) cc_final: 0.5132 (mpp) REVERT: 7 26 ARG cc_start: 0.7023 (tmt170) cc_final: 0.6791 (tmt170) REVERT: 8 22 LYS cc_start: 0.6617 (ttpp) cc_final: 0.6402 (tttm) outliers start: 282 outliers final: 170 residues processed: 1307 average time/residue: 1.2578 time to fit residues: 2841.6687 Evaluate side-chains 1195 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1015 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 171 ASN Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain c residue 152 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 74 ILE Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 151 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 179 LEU Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 17 ASP Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 101 LEU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 131 THR Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 34 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain n residue 53 ILE Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 66 LYS Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 34 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 53 ARG Chi-restraints excluded: chain v residue 30 ARG Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 83 ASN Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 187 CYS Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 137 SER Chi-restraints excluded: chain E residue 169 MET Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 87 LEU Chi-restraints excluded: chain H residue 92 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 12 LEU Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 47 ASP Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 19 LYS Chi-restraints excluded: chain T residue 91 ASN Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain V residue 11 ARG Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 75 TYR Chi-restraints excluded: chain W residue 6 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 32 ARG Chi-restraints excluded: chain W residue 40 MET Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 1 residue 18 ILE Chi-restraints excluded: chain 1 residue 25 LEU Chi-restraints excluded: chain 1 residue 27 ASN Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 22 LYS Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 8 residue 3 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 880 optimal weight: 6.9990 chunk 670 optimal weight: 30.0000 chunk 462 optimal weight: 10.0000 chunk 98 optimal weight: 50.0000 chunk 425 optimal weight: 20.0000 chunk 598 optimal weight: 10.0000 chunk 894 optimal weight: 5.9990 chunk 947 optimal weight: 20.0000 chunk 467 optimal weight: 10.0000 chunk 848 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 19 GLN ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 HIS c 125 ASN ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 GLN g 28 ASN h 16 ASN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 6 GLN l 73 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 132 GLN D 142 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 GLN ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 HIS R 43 GLN ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 46 GLN 8 34 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 153353 Z= 0.276 Angle : 0.696 12.656 229545 Z= 0.352 Chirality : 0.038 0.376 29387 Planarity : 0.005 0.115 12106 Dihedral : 23.283 179.543 76845 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.92 % Favored : 87.97 % Rotamer: Outliers : 6.19 % Allowed : 21.40 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.10), residues: 5353 helix: -1.05 (0.13), residues: 1498 sheet: -2.78 (0.16), residues: 860 loop : -3.16 (0.10), residues: 2995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP g 103 HIS 0.009 0.002 HIS k 118 PHE 0.024 0.002 PHE n 44 TYR 0.030 0.002 TYR v 92 ARG 0.018 0.001 ARG S 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1407 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1120 time to evaluate : 6.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7303 (ptp) cc_final: 0.6982 (ptp) REVERT: b 173 ILE cc_start: 0.7389 (pp) cc_final: 0.7170 (pt) REVERT: b 203 ASN cc_start: 0.6284 (t0) cc_final: 0.5706 (m-40) REVERT: b 219 ASP cc_start: 0.7630 (p0) cc_final: 0.6676 (t0) REVERT: c 106 LYS cc_start: 0.4684 (mptt) cc_final: 0.3777 (ttpt) REVERT: c 130 ARG cc_start: 0.7429 (ptm-80) cc_final: 0.7038 (ttp80) REVERT: e 10 GLU cc_start: 0.4468 (OUTLIER) cc_final: 0.3781 (pm20) REVERT: e 117 LEU cc_start: 0.7508 (tp) cc_final: 0.7245 (mm) REVERT: e 138 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.8696 (mtt-85) REVERT: f 29 ILE cc_start: 0.6589 (mt) cc_final: 0.6300 (mt) REVERT: g 63 GLU cc_start: 0.5636 (mm-30) cc_final: 0.3909 (pp20) REVERT: g 102 ARG cc_start: 0.5568 (ttm170) cc_final: 0.5358 (ptm160) REVERT: h 3 MET cc_start: 0.7724 (ppp) cc_final: 0.7414 (ppp) REVERT: i 82 ARG cc_start: 0.6074 (mtp85) cc_final: 0.5631 (mtp85) REVERT: k 68 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7320 (tt0) REVERT: m 110 LYS cc_start: 0.5157 (tptm) cc_final: 0.4935 (tptt) REVERT: o 41 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: p 19 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7997 (mtp180) REVERT: s 71 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7572 (tt) REVERT: u 12 LEU cc_start: 0.3023 (OUTLIER) cc_final: 0.2385 (mp) REVERT: u 47 LYS cc_start: 0.5710 (tptt) cc_final: 0.4786 (mptt) REVERT: v 30 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6286 (mtt180) REVERT: v 47 TYR cc_start: 0.2773 (OUTLIER) cc_final: 0.2158 (t80) REVERT: D 4 LYS cc_start: 0.7849 (mttp) cc_final: 0.7584 (mttp) REVERT: E 122 SER cc_start: 0.9174 (p) cc_final: 0.8943 (t) REVERT: H 104 ILE cc_start: 0.6053 (OUTLIER) cc_final: 0.5842 (mt) REVERT: H 163 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5225 (ptm160) REVERT: M 126 TYR cc_start: 0.7929 (m-80) cc_final: 0.7693 (m-10) REVERT: P 42 ILE cc_start: 0.9173 (pp) cc_final: 0.8907 (mt) REVERT: P 72 THR cc_start: 0.8900 (m) cc_final: 0.8429 (p) REVERT: Q 24 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8669 (tt) REVERT: Q 48 ILE cc_start: 0.6266 (pt) cc_final: 0.5913 (mm) REVERT: Q 118 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8900 (tt) REVERT: S 23 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7833 (mtt90) REVERT: V 4 LYS cc_start: 0.8239 (pttp) cc_final: 0.7985 (pttp) REVERT: V 11 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7207 (tmm160) REVERT: X 24 ILE cc_start: 0.8445 (mm) cc_final: 0.8055 (mt) REVERT: Y 87 THR cc_start: 0.8099 (m) cc_final: 0.7602 (p) REVERT: Z 27 LYS cc_start: 0.8562 (tppt) cc_final: 0.8315 (tppt) REVERT: 0 29 TRP cc_start: 0.5443 (p-90) cc_final: 0.4643 (p-90) REVERT: 0 52 ARG cc_start: 0.7783 (tpt170) cc_final: 0.6872 (ttp-170) REVERT: 2 18 THR cc_start: 0.9043 (p) cc_final: 0.8653 (t) REVERT: 3 34 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5191 (mpp) outliers start: 287 outliers final: 188 residues processed: 1278 average time/residue: 1.2488 time to fit residues: 2766.1067 Evaluate side-chains 1210 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1009 time to evaluate : 6.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 171 ASN Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 68 HIS Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 85 ASN Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 138 ARG Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 36 ILE Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 34 ASN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 14 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 118 SER Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 36 GLN Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain q residue 80 ILE Chi-restraints excluded: chain q residue 81 VAL Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 21 ASN Chi-restraints excluded: chain t residue 34 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain u residue 12 LEU Chi-restraints excluded: chain u residue 42 SER Chi-restraints excluded: chain v residue 30 ARG Chi-restraints excluded: chain v residue 45 LYS Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 81 ILE Chi-restraints excluded: chain v residue 83 ASN Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 104 ILE Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 163 ARG Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 84 CYS Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 91 ASN Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain V residue 11 ARG Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 75 TYR Chi-restraints excluded: chain V residue 96 ILE Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 32 ARG Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 17 GLU Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 2 residue 55 THR Chi-restraints excluded: chain 3 residue 22 LYS Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 7 residue 29 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 788 optimal weight: 30.0000 chunk 537 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 705 optimal weight: 4.9990 chunk 390 optimal weight: 10.0000 chunk 808 optimal weight: 4.9990 chunk 654 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 483 optimal weight: 20.0000 chunk 850 optimal weight: 6.9990 chunk 239 optimal weight: 0.0770 overall best weight: 5.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 226 GLN c 133 GLN ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 GLN h 16 ASN j 20 GLN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN l 86 ASN ** m 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN D 132 GLN D 142 ASN E 33 ASN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 48 HIS ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 114 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN ** R 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 46 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 153353 Z= 0.222 Angle : 0.646 13.400 229545 Z= 0.328 Chirality : 0.035 0.393 29387 Planarity : 0.005 0.118 12106 Dihedral : 23.191 179.530 76845 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.11 % Favored : 87.82 % Rotamer: Outliers : 6.02 % Allowed : 22.78 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.11), residues: 5353 helix: -0.76 (0.13), residues: 1494 sheet: -2.61 (0.16), residues: 879 loop : -2.96 (0.10), residues: 2980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP g 103 HIS 0.027 0.001 HIS c 68 PHE 0.020 0.002 PHE n 44 TYR 0.026 0.002 TYR G 143 ARG 0.007 0.001 ARG n 57 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1401 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1122 time to evaluate : 6.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.7269 (ptp) cc_final: 0.7055 (ptp) REVERT: b 154 MET cc_start: 0.4455 (tpt) cc_final: 0.4163 (tpt) REVERT: b 219 ASP cc_start: 0.7566 (p0) cc_final: 0.6772 (t0) REVERT: c 106 LYS cc_start: 0.4895 (mptt) cc_final: 0.3970 (ttpt) REVERT: c 166 GLN cc_start: 0.7685 (mm110) cc_final: 0.7400 (mm-40) REVERT: c 167 TYR cc_start: 0.7064 (m-80) cc_final: 0.6384 (m-80) REVERT: e 10 GLU cc_start: 0.4333 (OUTLIER) cc_final: 0.3724 (pm20) REVERT: e 117 LEU cc_start: 0.7384 (tp) cc_final: 0.7105 (mm) REVERT: e 138 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8689 (mtt-85) REVERT: f 81 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.5922 (mmtp) REVERT: g 63 GLU cc_start: 0.5383 (mm-30) cc_final: 0.3843 (pp20) REVERT: g 102 ARG cc_start: 0.5662 (ttm170) cc_final: 0.5107 (ptp-170) REVERT: h 3 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7195 (pmm) REVERT: h 63 PHE cc_start: 0.7732 (m-80) cc_final: 0.7101 (m-80) REVERT: m 69 LEU cc_start: 0.6026 (OUTLIER) cc_final: 0.5718 (tt) REVERT: m 110 LYS cc_start: 0.5160 (tptm) cc_final: 0.4902 (tptt) REVERT: o 41 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7448 (pp20) REVERT: p 18 TYR cc_start: 0.7104 (m-80) cc_final: 0.6689 (m-80) REVERT: s 71 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7583 (tt) REVERT: t 10 ARG cc_start: 0.8446 (mmm160) cc_final: 0.8029 (mmm-85) REVERT: u 12 LEU cc_start: 0.3273 (OUTLIER) cc_final: 0.2978 (tt) REVERT: u 47 LYS cc_start: 0.5743 (tptt) cc_final: 0.4810 (mptt) REVERT: v 47 TYR cc_start: 0.3060 (OUTLIER) cc_final: 0.2360 (t80) REVERT: v 83 ASN cc_start: 0.6243 (OUTLIER) cc_final: 0.5662 (m110) REVERT: D 4 LYS cc_start: 0.7893 (mttp) cc_final: 0.7584 (mttp) REVERT: H 23 HIS cc_start: 0.6949 (t70) cc_final: 0.6732 (t70) REVERT: M 1 MET cc_start: 0.4991 (mmm) cc_final: 0.4509 (mmm) REVERT: P 42 ILE cc_start: 0.9091 (pp) cc_final: 0.8752 (mt) REVERT: P 68 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8377 (pt) REVERT: P 72 THR cc_start: 0.8989 (m) cc_final: 0.8601 (p) REVERT: P 91 GLU cc_start: 0.7198 (pp20) cc_final: 0.6789 (pp20) REVERT: Q 30 ILE cc_start: 0.9227 (pt) cc_final: 0.8540 (pt) REVERT: Q 48 ILE cc_start: 0.6521 (pt) cc_final: 0.6161 (mm) REVERT: V 4 LYS cc_start: 0.8285 (pttp) cc_final: 0.8050 (pttp) REVERT: V 25 ARG cc_start: 0.8285 (ttm110) cc_final: 0.7978 (ttm170) REVERT: V 90 GLN cc_start: 0.8457 (mp-120) cc_final: 0.7990 (mp10) REVERT: X 24 ILE cc_start: 0.8474 (mm) cc_final: 0.8121 (mt) REVERT: Y 87 THR cc_start: 0.8179 (m) cc_final: 0.7888 (p) REVERT: Z 27 LYS cc_start: 0.8441 (tppt) cc_final: 0.8102 (mmtt) REVERT: 0 29 TRP cc_start: 0.5654 (p-90) cc_final: 0.4792 (p-90) REVERT: 0 52 ARG cc_start: 0.7701 (tpt170) cc_final: 0.6833 (ttp-170) REVERT: 2 18 THR cc_start: 0.9007 (p) cc_final: 0.8733 (t) REVERT: 3 11 GLN cc_start: 0.3461 (tm-30) cc_final: 0.3252 (tm-30) REVERT: 3 34 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5002 (mpp) outliers start: 279 outliers final: 191 residues processed: 1281 average time/residue: 1.2144 time to fit residues: 2700.6244 Evaluate side-chains 1223 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 1020 time to evaluate : 5.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 171 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 91 ASN Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 151 ILE Chi-restraints excluded: chain d residue 179 LEU Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 10 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 138 ARG Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 81 LYS Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 34 ASN Chi-restraints excluded: chain i residue 52 GLN Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 10 LYS Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 86 ASN Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 36 GLN Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 50 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 34 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain u residue 12 LEU Chi-restraints excluded: chain u residue 42 SER Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 81 ILE Chi-restraints excluded: chain v residue 83 ASN Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 84 CYS Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 75 TYR Chi-restraints excluded: chain W residue 32 ARG Chi-restraints excluded: chain W residue 40 MET Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain 0 residue 45 LYS Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 22 LYS Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 37 ARG Chi-restraints excluded: chain 7 residue 4 MET Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 8 residue 25 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 318 optimal weight: 10.0000 chunk 853 optimal weight: 20.0000 chunk 187 optimal weight: 8.9990 chunk 556 optimal weight: 10.0000 chunk 233 optimal weight: 10.0000 chunk 948 optimal weight: 20.0000 chunk 787 optimal weight: 0.9990 chunk 439 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 313 optimal weight: 10.0000 chunk 497 optimal weight: 40.0000 overall best weight: 7.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 103 ASN b 226 GLN c 125 ASN c 133 GLN ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 159 ASN g 28 ASN h 16 ASN i 128 GLN j 20 GLN ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN l 85 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 14 GLN ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN D 132 GLN D 142 ASN E 33 ASN E 50 GLN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 114 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 HIS R 43 GLN U 101 ASN ** X 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 46 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 153353 Z= 0.298 Angle : 0.712 12.570 229545 Z= 0.358 Chirality : 0.038 0.412 29387 Planarity : 0.005 0.122 12106 Dihedral : 23.253 179.583 76841 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 13.15 % Favored : 86.77 % Rotamer: Outliers : 7.27 % Allowed : 23.32 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.10), residues: 5353 helix: -0.88 (0.13), residues: 1518 sheet: -2.59 (0.16), residues: 866 loop : -2.97 (0.10), residues: 2969 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP g 103 HIS 0.011 0.002 HIS E 134 PHE 0.018 0.002 PHE n 44 TYR 0.027 0.002 TYR G 143 ARG 0.033 0.001 ARG r 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1422 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 337 poor density : 1085 time to evaluate : 6.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 191 CYS cc_start: 0.5722 (m) cc_final: 0.5428 (m) REVERT: b 219 ASP cc_start: 0.7506 (p0) cc_final: 0.6426 (t0) REVERT: c 106 LYS cc_start: 0.4828 (mptt) cc_final: 0.3890 (tttm) REVERT: e 7 GLU cc_start: 0.3887 (OUTLIER) cc_final: 0.3569 (mt-10) REVERT: e 117 LEU cc_start: 0.7382 (tp) cc_final: 0.7008 (mm) REVERT: e 138 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8745 (mtt-85) REVERT: f 81 LYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6354 (mmtp) REVERT: g 102 ARG cc_start: 0.5758 (ttm170) cc_final: 0.5088 (ptp-170) REVERT: g 137 LYS cc_start: 0.5514 (OUTLIER) cc_final: 0.5300 (tmtt) REVERT: h 3 MET cc_start: 0.7632 (ppp) cc_final: 0.7164 (ppp) REVERT: h 63 PHE cc_start: 0.7805 (m-80) cc_final: 0.7188 (m-80) REVERT: h 132 TRP cc_start: 0.7806 (p90) cc_final: 0.7260 (p90) REVERT: m 81 MET cc_start: 0.4050 (ptt) cc_final: 0.3523 (mtp) REVERT: o 41 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7461 (pp20) REVERT: p 18 TYR cc_start: 0.7160 (m-80) cc_final: 0.6759 (m-80) REVERT: q 46 TYR cc_start: 0.7751 (m-80) cc_final: 0.7458 (m-80) REVERT: s 71 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7695 (tt) REVERT: u 47 LYS cc_start: 0.5861 (tptt) cc_final: 0.4871 (mptt) REVERT: v 47 TYR cc_start: 0.2908 (OUTLIER) cc_final: 0.2144 (t80) REVERT: D 144 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6787 (mt-10) REVERT: D 152 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8351 (mm-40) REVERT: P 68 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8383 (pt) REVERT: P 72 THR cc_start: 0.9014 (m) cc_final: 0.8534 (p) REVERT: P 94 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8333 (tt) REVERT: Q 24 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8670 (tt) REVERT: Q 48 ILE cc_start: 0.6722 (pt) cc_final: 0.6327 (mm) REVERT: Q 118 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8862 (tt) REVERT: U 29 GLU cc_start: 0.7330 (tp30) cc_final: 0.7015 (tp30) REVERT: V 4 LYS cc_start: 0.8291 (pttp) cc_final: 0.8064 (pttp) REVERT: V 11 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7045 (tmm160) REVERT: X 24 ILE cc_start: 0.8473 (mm) cc_final: 0.8107 (mt) REVERT: Y 87 THR cc_start: 0.8264 (m) cc_final: 0.7931 (p) REVERT: 2 18 THR cc_start: 0.9082 (p) cc_final: 0.8773 (t) REVERT: 3 34 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5469 (mpp) outliers start: 337 outliers final: 238 residues processed: 1279 average time/residue: 1.1870 time to fit residues: 2650.2585 Evaluate side-chains 1273 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1022 time to evaluate : 6.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 145 ILE Chi-restraints excluded: chain b residue 157 MET Chi-restraints excluded: chain b residue 171 ASN Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 150 ILE Chi-restraints excluded: chain d residue 151 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 179 LEU Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 7 GLU Chi-restraints excluded: chain e residue 14 ARG Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 132 THR Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 138 ARG Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 81 LYS Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 90 GLU Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 34 ASN Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 36 GLN Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 60 TRP Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 34 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 42 SER Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 81 ILE Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 84 CYS Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 49 SER Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 47 ASP Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 100 LEU Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 42 ILE Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain T residue 100 ILE Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain V residue 11 ARG Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 75 TYR Chi-restraints excluded: chain W residue 32 ARG Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain X residue 91 VAL Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 0 residue 45 LYS Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 1 residue 25 LEU Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 22 LYS Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 37 ARG Chi-restraints excluded: chain 7 residue 4 MET Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 8 residue 25 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 914 optimal weight: 20.0000 chunk 106 optimal weight: 40.0000 chunk 540 optimal weight: 20.0000 chunk 692 optimal weight: 0.8980 chunk 536 optimal weight: 10.0000 chunk 798 optimal weight: 20.0000 chunk 529 optimal weight: 10.0000 chunk 944 optimal weight: 6.9990 chunk 591 optimal weight: 10.0000 chunk 575 optimal weight: 10.0000 chunk 436 optimal weight: 20.0000 overall best weight: 7.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 36 HIS ** d 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 145 GLN h 16 ASN i 128 GLN k 64 GLN k 77 HIS ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN l 85 HIS l 86 ASN ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 69 ASN D 132 GLN D 142 ASN E 128 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 HIS ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 114 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN U 101 ASN ** X 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 153353 Z= 0.283 Angle : 0.697 14.509 229545 Z= 0.351 Chirality : 0.038 0.398 29387 Planarity : 0.005 0.121 12106 Dihedral : 23.233 179.193 76839 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.96 % Favored : 86.96 % Rotamer: Outliers : 6.99 % Allowed : 24.88 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.10), residues: 5353 helix: -0.78 (0.13), residues: 1505 sheet: -2.52 (0.16), residues: 874 loop : -2.92 (0.10), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP g 103 HIS 0.009 0.001 HIS k 118 PHE 0.033 0.002 PHE E 53 TYR 0.028 0.002 TYR j 58 ARG 0.011 0.001 ARG O 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 1065 time to evaluate : 8.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 219 ASP cc_start: 0.7569 (p0) cc_final: 0.6732 (t0) REVERT: c 106 LYS cc_start: 0.5014 (mptt) cc_final: 0.3975 (tttm) REVERT: c 166 GLN cc_start: 0.7970 (tp40) cc_final: 0.7745 (mm110) REVERT: e 117 LEU cc_start: 0.7367 (tp) cc_final: 0.6984 (mm) REVERT: e 138 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8698 (mtt-85) REVERT: g 102 ARG cc_start: 0.5718 (ttm170) cc_final: 0.5115 (ptp-170) REVERT: h 3 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.7252 (ppp) REVERT: h 74 ILE cc_start: 0.3722 (OUTLIER) cc_final: 0.3205 (pt) REVERT: h 132 TRP cc_start: 0.7956 (p90) cc_final: 0.7344 (p90) REVERT: j 58 TYR cc_start: 0.6222 (m-80) cc_final: 0.5941 (m-80) REVERT: j 77 VAL cc_start: 0.3605 (OUTLIER) cc_final: 0.3321 (p) REVERT: l 10 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7661 (mttp) REVERT: m 78 LYS cc_start: 0.8503 (pttt) cc_final: 0.8196 (pttm) REVERT: m 81 MET cc_start: 0.4296 (ptt) cc_final: 0.3719 (mtp) REVERT: o 41 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7500 (pp20) REVERT: p 18 TYR cc_start: 0.7173 (m-80) cc_final: 0.6803 (m-80) REVERT: q 46 TYR cc_start: 0.7730 (m-80) cc_final: 0.7437 (m-80) REVERT: r 39 SER cc_start: 0.8165 (p) cc_final: 0.7666 (t) REVERT: s 15 LEU cc_start: 0.4477 (mt) cc_final: 0.3859 (tp) REVERT: s 71 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7750 (tt) REVERT: u 47 LYS cc_start: 0.5820 (tptt) cc_final: 0.4991 (mptt) REVERT: v 47 TYR cc_start: 0.3097 (OUTLIER) cc_final: 0.2346 (t80) REVERT: D 4 LYS cc_start: 0.7919 (mttp) cc_final: 0.7594 (mttp) REVERT: D 144 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6839 (mt-10) REVERT: D 228 ASP cc_start: 0.8474 (m-30) cc_final: 0.8268 (m-30) REVERT: M 1 MET cc_start: 0.4640 (mmm) cc_final: 0.4372 (mmm) REVERT: O 33 ARG cc_start: 0.7734 (ttm-80) cc_final: 0.7297 (ttm-80) REVERT: P 68 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8432 (pt) REVERT: P 72 THR cc_start: 0.9091 (m) cc_final: 0.8737 (p) REVERT: Q 48 ILE cc_start: 0.6677 (pt) cc_final: 0.6315 (mm) REVERT: Q 118 ILE cc_start: 0.9301 (mt) cc_final: 0.8871 (tt) REVERT: V 4 LYS cc_start: 0.8293 (pttp) cc_final: 0.8074 (pttp) REVERT: X 24 ILE cc_start: 0.8502 (mm) cc_final: 0.8143 (mt) REVERT: 2 18 THR cc_start: 0.9082 (p) cc_final: 0.8789 (t) REVERT: 3 34 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5541 (mpp) REVERT: 6 10 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8260 (mtmm) outliers start: 324 outliers final: 251 residues processed: 1260 average time/residue: 1.2314 time to fit residues: 2715.9666 Evaluate side-chains 1276 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 260 poor density : 1016 time to evaluate : 6.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 145 ILE Chi-restraints excluded: chain b residue 171 ASN Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 151 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 179 LEU Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 14 ARG Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 138 ARG Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 3 MET Chi-restraints excluded: chain h residue 16 ASN Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 34 ASN Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 46 SER Chi-restraints excluded: chain k residue 64 GLN Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 59 MET Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 GLN Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain p residue 83 LYS Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 34 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 42 SER Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 72 ASP Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 81 ILE Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 149 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 84 CYS Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 46 VAL Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 42 ILE Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 98 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 101 ASN Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 75 TYR Chi-restraints excluded: chain V residue 97 ASN Chi-restraints excluded: chain W residue 32 ARG Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 0 residue 45 LYS Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 26 LYS Chi-restraints excluded: chain 6 residue 37 ARG Chi-restraints excluded: chain 7 residue 4 MET Chi-restraints excluded: chain 7 residue 29 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 584 optimal weight: 10.0000 chunk 377 optimal weight: 0.9990 chunk 564 optimal weight: 30.0000 chunk 284 optimal weight: 40.0000 chunk 185 optimal weight: 30.0000 chunk 182 optimal weight: 9.9990 chunk 600 optimal weight: 20.0000 chunk 643 optimal weight: 10.0000 chunk 467 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 742 optimal weight: 6.9990 overall best weight: 7.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 128 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 39 ASN l 73 ASN l 85 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 64 ASN D 132 GLN D 142 ASN E 50 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 42 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 153353 Z= 0.285 Angle : 0.706 13.276 229545 Z= 0.355 Chirality : 0.038 0.381 29387 Planarity : 0.005 0.123 12106 Dihedral : 23.247 178.870 76839 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.26 % Favored : 86.68 % Rotamer: Outliers : 6.73 % Allowed : 25.76 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.10), residues: 5353 helix: -0.79 (0.13), residues: 1508 sheet: -2.39 (0.16), residues: 868 loop : -2.92 (0.10), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP g 103 HIS 0.013 0.002 HIS d 118 PHE 0.028 0.002 PHE E 53 TYR 0.027 0.002 TYR j 58 ARG 0.010 0.001 ARG O 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1051 time to evaluate : 6.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.6914 (ptp) cc_final: 0.6502 (ptp) REVERT: b 219 ASP cc_start: 0.7554 (p0) cc_final: 0.6689 (t0) REVERT: c 106 LYS cc_start: 0.5153 (mptt) cc_final: 0.4122 (tttm) REVERT: e 117 LEU cc_start: 0.7363 (tp) cc_final: 0.6948 (mm) REVERT: e 138 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8727 (mtt-85) REVERT: f 81 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6399 (mmtp) REVERT: g 102 ARG cc_start: 0.5801 (ttm170) cc_final: 0.5182 (ptp-170) REVERT: h 3 MET cc_start: 0.7399 (ppp) cc_final: 0.7007 (pmm) REVERT: h 132 TRP cc_start: 0.7955 (p90) cc_final: 0.7437 (p90) REVERT: i 101 LYS cc_start: 0.6986 (mtpt) cc_final: 0.5937 (mmpt) REVERT: j 77 VAL cc_start: 0.3629 (OUTLIER) cc_final: 0.3323 (p) REVERT: l 10 LYS cc_start: 0.7811 (tmtt) cc_final: 0.7602 (mttp) REVERT: m 78 LYS cc_start: 0.8497 (pttt) cc_final: 0.8192 (pttm) REVERT: m 81 MET cc_start: 0.4257 (ptt) cc_final: 0.3571 (mtp) REVERT: o 41 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7526 (pp20) REVERT: p 18 TYR cc_start: 0.7189 (m-80) cc_final: 0.6816 (m-10) REVERT: p 19 ARG cc_start: 0.8289 (mtp180) cc_final: 0.7787 (mtp180) REVERT: q 46 TYR cc_start: 0.7763 (m-80) cc_final: 0.7546 (m-80) REVERT: r 39 SER cc_start: 0.8374 (p) cc_final: 0.7861 (t) REVERT: s 15 LEU cc_start: 0.4514 (mt) cc_final: 0.3863 (tp) REVERT: s 71 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7685 (tt) REVERT: u 47 LYS cc_start: 0.5936 (tptt) cc_final: 0.5106 (mptt) REVERT: v 47 TYR cc_start: 0.3109 (OUTLIER) cc_final: 0.2356 (t80) REVERT: v 93 LYS cc_start: 0.5968 (ttpt) cc_final: 0.5654 (tttm) REVERT: D 4 LYS cc_start: 0.7934 (mttp) cc_final: 0.7604 (mttp) REVERT: D 144 GLU cc_start: 0.7097 (mt-10) cc_final: 0.6873 (mt-10) REVERT: D 228 ASP cc_start: 0.8491 (m-30) cc_final: 0.8289 (m-30) REVERT: H 65 HIS cc_start: 0.6371 (OUTLIER) cc_final: 0.4731 (t-90) REVERT: O 33 ARG cc_start: 0.7725 (ttm-80) cc_final: 0.7311 (ttm-80) REVERT: P 68 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8501 (pt) REVERT: P 72 THR cc_start: 0.9080 (m) cc_final: 0.8737 (p) REVERT: Q 24 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8645 (tt) REVERT: Q 48 ILE cc_start: 0.6701 (pt) cc_final: 0.6357 (mm) REVERT: Q 118 ILE cc_start: 0.9376 (mt) cc_final: 0.9014 (tt) REVERT: R 48 ASN cc_start: 0.7186 (p0) cc_final: 0.6924 (p0) REVERT: V 4 LYS cc_start: 0.8281 (pttp) cc_final: 0.8067 (pttp) REVERT: X 24 ILE cc_start: 0.8516 (mm) cc_final: 0.8143 (mt) REVERT: Y 87 THR cc_start: 0.8352 (m) cc_final: 0.8045 (p) REVERT: 2 18 THR cc_start: 0.9112 (p) cc_final: 0.8826 (t) REVERT: 3 11 GLN cc_start: 0.2944 (tm-30) cc_final: 0.2368 (tm-30) REVERT: 3 34 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5337 (mpp) REVERT: 6 10 LYS cc_start: 0.8620 (mtmm) cc_final: 0.8334 (mtmm) REVERT: 8 26 ILE cc_start: 0.6435 (OUTLIER) cc_final: 0.6071 (mt) outliers start: 312 outliers final: 255 residues processed: 1239 average time/residue: 1.2089 time to fit residues: 2621.6384 Evaluate side-chains 1275 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1009 time to evaluate : 6.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 145 ILE Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 171 ASN Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 17 ASP Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 176 THR Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 45 SER Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 151 ILE Chi-restraints excluded: chain d residue 173 THR Chi-restraints excluded: chain d residue 179 LEU Chi-restraints excluded: chain d residue 195 VAL Chi-restraints excluded: chain e residue 7 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 26 LYS Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 138 ARG Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 36 GLU Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 81 LYS Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 20 VAL Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 34 ASN Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain j residue 77 VAL Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain k residue 125 LYS Chi-restraints excluded: chain l residue 7 LEU Chi-restraints excluded: chain l residue 20 ASP Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 53 MET Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 68 ASN Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 36 GLN Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain p residue 83 LYS Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 8 ILE Chi-restraints excluded: chain t residue 34 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 42 SER Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 56 VAL Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 72 ASP Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 81 ILE Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 129 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 65 SER Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 173 MET Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 46 GLN Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 60 ILE Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 20 ASP Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain N residue 12 ASP Chi-restraints excluded: chain N residue 18 GLU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 84 CYS Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain N residue 114 ILE Chi-restraints excluded: chain O residue 19 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 80 ASP Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 112 GLU Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain Q residue 22 THR Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 50 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 42 ILE Chi-restraints excluded: chain S residue 67 SER Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain S residue 102 LEU Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 5 ILE Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 33 ILE Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 75 TYR Chi-restraints excluded: chain V residue 97 ASN Chi-restraints excluded: chain W residue 26 THR Chi-restraints excluded: chain W residue 32 ARG Chi-restraints excluded: chain W residue 48 VAL Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 1 residue 9 LEU Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 2 residue 12 VAL Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 5 THR Chi-restraints excluded: chain 6 residue 26 LYS Chi-restraints excluded: chain 6 residue 37 ARG Chi-restraints excluded: chain 7 residue 4 MET Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 7 residue 50 VAL Chi-restraints excluded: chain 8 residue 26 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 859 optimal weight: 0.7980 chunk 904 optimal weight: 7.9990 chunk 825 optimal weight: 30.0000 chunk 880 optimal weight: 1.9990 chunk 529 optimal weight: 10.0000 chunk 383 optimal weight: 20.0000 chunk 691 optimal weight: 4.9990 chunk 270 optimal weight: 8.9990 chunk 795 optimal weight: 6.9990 chunk 832 optimal weight: 8.9990 chunk 877 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 226 GLN c 133 GLN h 16 ASN ** l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN l 85 HIS ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 88 GLN D 113 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN E 50 GLN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 ASN ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 153353 Z= 0.169 Angle : 0.617 14.946 229545 Z= 0.312 Chirality : 0.034 0.363 29387 Planarity : 0.005 0.124 12106 Dihedral : 23.112 178.882 76839 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.85 % Favored : 89.09 % Rotamer: Outliers : 4.66 % Allowed : 28.22 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.11), residues: 5353 helix: -0.47 (0.13), residues: 1493 sheet: -2.17 (0.17), residues: 833 loop : -2.79 (0.10), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP g 103 HIS 0.008 0.001 HIS k 118 PHE 0.051 0.002 PHE E 87 TYR 0.023 0.002 TYR P 74 ARG 0.012 0.001 ARG O 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1080 time to evaluate : 6.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.6877 (ptp) cc_final: 0.6575 (ptp) REVERT: b 219 ASP cc_start: 0.7450 (p0) cc_final: 0.6533 (t0) REVERT: c 106 LYS cc_start: 0.5034 (mptt) cc_final: 0.3947 (tttm) REVERT: c 141 MET cc_start: 0.5283 (mmm) cc_final: 0.5023 (mmp) REVERT: c 165 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5035 (tt0) REVERT: d 196 GLU cc_start: 0.7848 (pm20) cc_final: 0.7625 (pm20) REVERT: e 138 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8739 (mtt-85) REVERT: f 1 MET cc_start: 0.3965 (ttp) cc_final: 0.3743 (ptt) REVERT: f 81 LYS cc_start: 0.6822 (OUTLIER) cc_final: 0.6262 (mmtp) REVERT: g 102 ARG cc_start: 0.5623 (ttm170) cc_final: 0.5119 (ptp-170) REVERT: h 132 TRP cc_start: 0.7886 (p90) cc_final: 0.7449 (p90) REVERT: i 101 LYS cc_start: 0.7031 (mtpt) cc_final: 0.6024 (mmpt) REVERT: k 73 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7273 (t) REVERT: l 10 LYS cc_start: 0.7784 (tmtt) cc_final: 0.7539 (mttp) REVERT: l 44 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.6020 (ttt-90) REVERT: m 78 LYS cc_start: 0.8442 (pttt) cc_final: 0.8189 (pttm) REVERT: m 81 MET cc_start: 0.4146 (ptt) cc_final: 0.3815 (mtp) REVERT: o 41 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7441 (pp20) REVERT: o 58 LYS cc_start: 0.8707 (mttm) cc_final: 0.7974 (mtmm) REVERT: p 18 TYR cc_start: 0.7111 (m-80) cc_final: 0.6741 (m-80) REVERT: q 46 TYR cc_start: 0.7682 (m-80) cc_final: 0.7467 (m-80) REVERT: r 39 SER cc_start: 0.8270 (p) cc_final: 0.7805 (t) REVERT: s 15 LEU cc_start: 0.4006 (mt) cc_final: 0.3574 (tp) REVERT: s 71 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7507 (tt) REVERT: t 10 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8048 (mmm-85) REVERT: v 47 TYR cc_start: 0.2827 (OUTLIER) cc_final: 0.2089 (t80) REVERT: v 93 LYS cc_start: 0.5723 (ttpt) cc_final: 0.5375 (tttm) REVERT: D 4 LYS cc_start: 0.8057 (mttp) cc_final: 0.7847 (mmtp) REVERT: H 65 HIS cc_start: 0.6389 (OUTLIER) cc_final: 0.4821 (t-90) REVERT: M 1 MET cc_start: 0.4270 (mmm) cc_final: 0.4021 (mmm) REVERT: N 24 VAL cc_start: 0.8324 (OUTLIER) cc_final: 0.8084 (m) REVERT: P 72 THR cc_start: 0.9000 (m) cc_final: 0.8736 (p) REVERT: Q 48 ILE cc_start: 0.6652 (pt) cc_final: 0.6303 (mm) REVERT: Q 118 ILE cc_start: 0.9188 (mt) cc_final: 0.8792 (tt) REVERT: V 25 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7914 (ttm170) REVERT: V 37 LYS cc_start: 0.8089 (mmmm) cc_final: 0.7884 (mmtm) REVERT: X 24 ILE cc_start: 0.8483 (mm) cc_final: 0.8124 (mt) REVERT: Y 87 THR cc_start: 0.8230 (m) cc_final: 0.7896 (p) REVERT: 2 18 THR cc_start: 0.9054 (p) cc_final: 0.8748 (t) REVERT: 3 11 GLN cc_start: 0.2998 (tm-30) cc_final: 0.2385 (tm-30) REVERT: 3 34 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5544 (mpp) REVERT: 5 42 GLN cc_start: 0.6572 (mm110) cc_final: 0.6328 (mm-40) REVERT: 6 10 LYS cc_start: 0.8581 (mtmm) cc_final: 0.8325 (mtmm) REVERT: 8 1 MET cc_start: 0.7539 (ttp) cc_final: 0.6918 (tmm) outliers start: 216 outliers final: 165 residues processed: 1212 average time/residue: 1.2098 time to fit residues: 2547.5844 Evaluate side-chains 1188 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1012 time to evaluate : 8.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 171 ASN Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 179 LEU Chi-restraints excluded: chain e residue 7 GLU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 138 ARG Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 81 LYS Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 16 ASN Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 44 ARG Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 36 GLN Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain p residue 83 LYS Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 34 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 80 THR Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 81 ILE Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 79 SER Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 97 ASN Chi-restraints excluded: chain W residue 40 MET Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 26 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 578 optimal weight: 40.0000 chunk 930 optimal weight: 5.9990 chunk 568 optimal weight: 10.0000 chunk 441 optimal weight: 20.0000 chunk 647 optimal weight: 10.0000 chunk 976 optimal weight: 4.9990 chunk 898 optimal weight: 3.9990 chunk 777 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 600 optimal weight: 20.0000 chunk 476 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 226 GLN d 82 HIS g 28 ASN h 16 ASN i 128 GLN j 64 GLN k 119 ASN ** l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN l 85 HIS ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 142 ASN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 46 GLN 3 6 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 153353 Z= 0.231 Angle : 0.656 14.552 229545 Z= 0.331 Chirality : 0.035 0.346 29387 Planarity : 0.005 0.122 12106 Dihedral : 23.122 178.801 76839 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 12.39 % Favored : 87.58 % Rotamer: Outliers : 4.44 % Allowed : 28.91 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.11), residues: 5353 helix: -0.55 (0.13), residues: 1503 sheet: -2.17 (0.17), residues: 860 loop : -2.75 (0.10), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP g 103 HIS 0.018 0.001 HIS D 141 PHE 0.026 0.002 PHE E 53 TYR 0.028 0.002 TYR c 167 ARG 0.012 0.001 ARG O 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10706 Ramachandran restraints generated. 5353 Oldfield, 0 Emsley, 5353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1039 time to evaluate : 6.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 27 MET cc_start: 0.6922 (ptp) cc_final: 0.6506 (ptp) REVERT: b 219 ASP cc_start: 0.7430 (p0) cc_final: 0.6511 (t0) REVERT: c 106 LYS cc_start: 0.5058 (mptt) cc_final: 0.3987 (tttm) REVERT: c 165 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.5604 (tm-30) REVERT: e 138 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8750 (mtt-85) REVERT: f 1 MET cc_start: 0.3999 (ttp) cc_final: 0.3771 (ptt) REVERT: f 46 ARG cc_start: 0.6433 (ptp-110) cc_final: 0.6220 (ptp-110) REVERT: f 81 LYS cc_start: 0.6812 (OUTLIER) cc_final: 0.6331 (mmtp) REVERT: g 102 ARG cc_start: 0.5663 (ttm170) cc_final: 0.5171 (ptp-170) REVERT: h 3 MET cc_start: 0.7419 (tmm) cc_final: 0.6972 (pmm) REVERT: h 132 TRP cc_start: 0.7947 (p90) cc_final: 0.7468 (p90) REVERT: i 101 LYS cc_start: 0.6901 (mtpt) cc_final: 0.5970 (mmpt) REVERT: k 73 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7330 (t) REVERT: k 100 LEU cc_start: 0.7714 (tp) cc_final: 0.7274 (pp) REVERT: l 44 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.6084 (ttt-90) REVERT: m 78 LYS cc_start: 0.8451 (pttt) cc_final: 0.8192 (pttm) REVERT: m 81 MET cc_start: 0.4212 (ptt) cc_final: 0.3759 (mtp) REVERT: n 49 TYR cc_start: 0.6414 (m-80) cc_final: 0.5875 (m-80) REVERT: o 41 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7410 (pp20) REVERT: p 18 TYR cc_start: 0.7105 (m-80) cc_final: 0.6709 (m-10) REVERT: q 46 TYR cc_start: 0.7795 (m-80) cc_final: 0.7549 (m-80) REVERT: r 39 SER cc_start: 0.8251 (p) cc_final: 0.7746 (t) REVERT: s 15 LEU cc_start: 0.4207 (mt) cc_final: 0.3691 (tp) REVERT: s 71 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7930 (tt) REVERT: v 47 TYR cc_start: 0.2858 (OUTLIER) cc_final: 0.2158 (t80) REVERT: v 93 LYS cc_start: 0.5930 (ttpt) cc_final: 0.5572 (tttm) REVERT: D 4 LYS cc_start: 0.8095 (mttp) cc_final: 0.7729 (mttp) REVERT: D 144 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6924 (mt-10) REVERT: D 152 GLN cc_start: 0.8648 (mm-40) cc_final: 0.8402 (mm-40) REVERT: H 65 HIS cc_start: 0.6355 (OUTLIER) cc_final: 0.4706 (t-90) REVERT: M 1 MET cc_start: 0.4473 (mmm) cc_final: 0.3598 (mmm) REVERT: O 33 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7476 (ttm-80) REVERT: P 72 THR cc_start: 0.9053 (m) cc_final: 0.8755 (p) REVERT: Q 48 ILE cc_start: 0.6836 (pt) cc_final: 0.6474 (mm) REVERT: Q 118 ILE cc_start: 0.9353 (mt) cc_final: 0.9024 (tt) REVERT: V 90 GLN cc_start: 0.8576 (mp-120) cc_final: 0.7937 (mp10) REVERT: X 24 ILE cc_start: 0.8478 (mm) cc_final: 0.8109 (mt) REVERT: Y 87 THR cc_start: 0.8281 (m) cc_final: 0.7952 (p) REVERT: 2 18 THR cc_start: 0.9109 (p) cc_final: 0.8846 (t) REVERT: 3 11 GLN cc_start: 0.3148 (tm-30) cc_final: 0.2467 (tm-30) REVERT: 3 24 LEU cc_start: 0.2944 (OUTLIER) cc_final: 0.2585 (tp) REVERT: 3 34 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5341 (mpp) REVERT: 6 10 LYS cc_start: 0.8632 (mtmm) cc_final: 0.8412 (mtmm) REVERT: 8 1 MET cc_start: 0.7576 (ttp) cc_final: 0.7000 (tmm) outliers start: 206 outliers final: 173 residues processed: 1169 average time/residue: 1.2088 time to fit residues: 2462.6039 Evaluate side-chains 1188 residues out of total 4635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1004 time to evaluate : 6.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 10 LEU Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 131 LYS Chi-restraints excluded: chain b residue 171 ASN Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain c residue 43 ASP Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 165 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 147 LYS Chi-restraints excluded: chain d residue 179 LEU Chi-restraints excluded: chain e residue 24 VAL Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 106 ILE Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 138 ARG Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 74 ASP Chi-restraints excluded: chain f residue 81 LYS Chi-restraints excluded: chain g residue 51 GLU Chi-restraints excluded: chain g residue 99 LEU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 6 VAL Chi-restraints excluded: chain i residue 32 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain j residue 4 GLN Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 32 VAL Chi-restraints excluded: chain k residue 71 SER Chi-restraints excluded: chain k residue 73 SER Chi-restraints excluded: chain k residue 82 VAL Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain k residue 116 VAL Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 44 ARG Chi-restraints excluded: chain l residue 54 THR Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain m residue 16 VAL Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 49 THR Chi-restraints excluded: chain n residue 25 GLU Chi-restraints excluded: chain o residue 4 SER Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 41 GLU Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 56 LEU Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 81 LEU Chi-restraints excluded: chain p residue 3 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 36 GLN Chi-restraints excluded: chain p residue 37 ILE Chi-restraints excluded: chain p residue 80 ILE Chi-restraints excluded: chain p residue 83 LYS Chi-restraints excluded: chain q residue 19 MET Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 34 ASN Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain v residue 47 TYR Chi-restraints excluded: chain v residue 56 VAL Chi-restraints excluded: chain v residue 63 VAL Chi-restraints excluded: chain v residue 78 ILE Chi-restraints excluded: chain v residue 81 ILE Chi-restraints excluded: chain v residue 96 ILE Chi-restraints excluded: chain v residue 101 ARG Chi-restraints excluded: chain D residue 24 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 62 ASP Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 47 SER Chi-restraints excluded: chain G residue 85 ILE Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 38 ASN Chi-restraints excluded: chain H residue 65 HIS Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 115 ILE Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 110 LEU Chi-restraints excluded: chain M residue 123 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 25 LEU Chi-restraints excluded: chain N residue 61 VAL Chi-restraints excluded: chain N residue 62 ILE Chi-restraints excluded: chain N residue 67 SER Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 98 ILE Chi-restraints excluded: chain N residue 99 PHE Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 104 ASN Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 37 THR Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 52 ILE Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain P residue 105 GLU Chi-restraints excluded: chain P residue 122 SER Chi-restraints excluded: chain P residue 133 LYS Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 71 ILE Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 101 TYR Chi-restraints excluded: chain S residue 26 ASP Chi-restraints excluded: chain S residue 80 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain U residue 25 LEU Chi-restraints excluded: chain U residue 46 VAL Chi-restraints excluded: chain U residue 47 LYS Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 48 GLU Chi-restraints excluded: chain V residue 97 ASN Chi-restraints excluded: chain W residue 40 MET Chi-restraints excluded: chain Y residue 21 LEU Chi-restraints excluded: chain Y residue 84 ASN Chi-restraints excluded: chain Z residue 57 GLU Chi-restraints excluded: chain Z residue 74 VAL Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain 1 residue 8 ASP Chi-restraints excluded: chain 1 residue 40 THR Chi-restraints excluded: chain 1 residue 65 SER Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 24 LEU Chi-restraints excluded: chain 3 residue 34 MET Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 37 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 617 optimal weight: 10.0000 chunk 828 optimal weight: 4.9990 chunk 238 optimal weight: 9.9990 chunk 716 optimal weight: 20.0000 chunk 114 optimal weight: 50.0000 chunk 216 optimal weight: 6.9990 chunk 778 optimal weight: 5.9990 chunk 325 optimal weight: 30.0000 chunk 799 optimal weight: 10.0000 chunk 98 optimal weight: 50.0000 chunk 143 optimal weight: 20.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: i 128 GLN ** l 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 73 ASN l 85 HIS ** m 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 HIS ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN ** F 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 ASN P 13 HIS ** P 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 54 ASN ** X 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.101026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079485 restraints weight = 495533.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.080735 restraints weight = 266032.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.080625 restraints weight = 164605.708| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 153353 Z= 0.285 Angle : 0.708 14.910 229545 Z= 0.355 Chirality : 0.037 0.364 29387 Planarity : 0.006 0.120 12106 Dihedral : 23.185 178.876 76839 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.19 % Favored : 86.76 % Rotamer: Outliers : 5.01 % Allowed : 28.61 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 0.54 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.11), residues: 5353 helix: -0.73 (0.13), residues: 1516 sheet: -2.13 (0.17), residues: 836 loop : -2.81 (0.10), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP g 103 HIS 0.009 0.002 HIS q 33 PHE 0.039 0.002 PHE d 86 TYR 0.030 0.002 TYR c 167 ARG 0.014 0.001 ARG O 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36604.44 seconds wall clock time: 639 minutes 27.74 seconds (38367.74 seconds total)