Starting phenix.real_space_refine on Sun Apr 14 14:24:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd8_3624/04_2024/5nd8_3624.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd8_3624/04_2024/5nd8_3624.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/5nd8_3624/04_2024/5nd8_3624.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd8_3624/04_2024/5nd8_3624.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd8_3624/04_2024/5nd8_3624.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nd8_3624/04_2024/5nd8_3624.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= 0.016 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 4568 5.49 5 S 115 5.16 5 C 70708 2.51 5 N 26045 2.21 5 O 39607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 5": "OE1" <-> "OE2" Residue "v ARG 30": "NH1" <-> "NH2" Residue "v ARG 70": "NH1" <-> "NH2" Residue "v ARG 98": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" 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 TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 134": "NH1" <-> "NH2" Residue "P GLU 135": "OE1" <-> "OE2" Residue "Q ARG 96": "NH1" <-> "NH2" Residue "S PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 28": "NH1" <-> "NH2" 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-5288/modules/chem_data/mon_lib" Total number of atoms: 141043 Number of models: 1 Model: "" Number of chains: 52 Chain: "a" Number of atoms: 33026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1542, 33026 Classifications: {'RNA': 1542} Modifications used: {'rna2p_pur': 123, 'rna2p_pyr': 88, 'rna3p_pur': 744, 'rna3p_pyr': 587} Link IDs: {'rna2p': 211, 'rna3p': 1330} Chain: "b" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1789 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain: "c" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1609 Classifications: {'peptide': 204} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 198} 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: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1185 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 151} 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: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 880 Classifications: {'peptide': 118} Link IDs: {'CIS': 3, 'PTRANS': 7, 'TRANS': 107} 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: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 478 Classifications: {'peptide': 58} Link IDs: {'CIS': 2, 'PTRANS': 2, 'TRANS': 53} Chain: "s" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 661 Classifications: {'peptide': 82} Link IDs: {'CIS': 3, 'PTRANS': 4, 'TRANS': 74} 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: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 396 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "v" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 808 Classifications: {'peptide': 98} Link IDs: {'CIS': 7, 'PTRANS': 2, 'TRANS': 88} Chain: "A" Number of atoms: 62440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2912, 62440 Classifications: {'RNA': 2912} Modifications used: {'rna2p_pur': 302, 'rna2p_pyr': 168, 'rna3p_pur': 1366, 'rna3p_pyr': 1076} Link IDs: {'rna2p': 470, 'rna3p': 2441} 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: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1056 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} 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': 4, 'PTRANS': 1, 'TRANS': 113} 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: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 585 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} 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: 677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 677 Classifications: {'peptide': 83} Link IDs: {'CIS': 2, 'PTRANS': 3, 'TRANS': 77} Chain: "4" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} 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: 54.42, per 1000 atoms: 0.39 Number of scatterers: 141043 At special positions: 0 Unit cell: (249.7, 271.7, 228.8, 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 115 16.00 P 4568 15.00 O 39607 8.00 N 26045 7.00 C 70708 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: 62.05 Conformation dependent library (CDL) restraints added in 6.0 seconds 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10050 Finding SS restraints... Secondary structure from input PDB file: 154 helices and 68 sheets defined 31.0% alpha, 11.0% beta 1472 base pairs and 2240 stacking pairs defined. Time for finding SS restraints: 45.93 Creating SS restraints... Processing helix chain 'b' and resid 8 through 14 Processing helix chain 'b' and resid 24 through 28 Processing helix chain 'b' and resid 42 through 63 removed outlier: 4.466A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS b 48 " --> pdb=" O GLN b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.540A pdb=" N ALA b 87 " --> pdb=" O GLU b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 104 through 119 removed outlier: 3.602A pdb=" N SER b 108 " --> pdb=" O TYR b 104 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS b 119 " --> pdb=" O SER b 115 " (cutoff:3.500A) Processing helix chain 'b' and resid 119 through 124 Processing helix chain 'b' and resid 130 through 149 removed outlier: 3.911A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLU b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 180 removed outlier: 6.509A pdb=" N ASN b 171 " --> pdb=" O ARG b 167 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA b 172 " --> pdb=" O LYS b 168 " (cutoff:3.500A) Processing helix chain 'b' and resid 192 through 196 removed outlier: 3.535A 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 6 through 12 removed outlier: 4.122A pdb=" N LEU c 10 " --> pdb=" O ASN c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 50 removed outlier: 3.647A pdb=" N HIS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS c 37 " --> pdb=" O HIS c 33 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE c 38 " --> pdb=" O GLU c 34 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE c 41 " --> pdb=" O LYS c 37 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ASP c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASN c 44 " --> pdb=" O LYS c 40 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU c 45 " --> pdb=" O PHE c 41 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU c 48 " --> pdb=" O ASN c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 Processing helix chain 'c' and resid 82 through 95 removed outlier: 3.638A pdb=" N LEU c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 125 removed outlier: 3.529A pdb=" N VAL c 115 " --> pdb=" O ASP c 111 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.194A pdb=" N VAL c 132 " --> pdb=" O SER c 128 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN c 133 " --> pdb=" O PHE c 129 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.550A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 77 removed outlier: 3.622A pdb=" N ASN d 70 " --> pdb=" O ARG d 66 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE d 74 " --> pdb=" O ASN d 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA d 75 " --> pdb=" O THR d 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY d 76 " --> pdb=" O PHE d 72 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 90 removed outlier: 4.485A pdb=" N ASN d 85 " --> pdb=" O VAL d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 102 Processing helix chain 'd' and resid 107 through 117 removed outlier: 3.530A pdb=" N ARG d 111 " --> pdb=" O ARG d 107 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN d 112 " --> pdb=" O ARG d 108 " (cutoff:3.500A) removed outlier: 4.035A 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 156 removed outlier: 4.169A pdb=" N GLU d 156 " --> pdb=" O VAL d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 193 through 198 removed outlier: 3.830A pdb=" N TYR d 197 " --> pdb=" O LEU d 193 " (cutoff:3.500A) removed outlier: 3.584A 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: 3.695A pdb=" N LYS e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 117 Processing helix chain 'e' and resid 132 through 145 Processing helix chain 'e' and resid 149 through 155 removed outlier: 3.518A pdb=" N LYS e 155 " --> pdb=" O GLU e 151 " (cutoff:3.500A) Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.515A pdb=" N LYS f 19 " --> pdb=" O GLU f 15 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR f 32 " --> pdb=" O GLY f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 72 through 83 removed outlier: 5.000A pdb=" N ARG f 78 " --> pdb=" O ASP f 74 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS f 81 " --> pdb=" O GLN f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 31 removed outlier: 3.573A pdb=" N LYS g 25 " --> pdb=" O LYS g 21 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS g 29 " --> pdb=" O LYS g 25 " (cutoff:3.500A) Processing helix chain 'g' and resid 36 through 50 Processing helix chain 'g' and resid 57 through 66 removed outlier: 4.235A 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 Processing helix chain 'g' and resid 131 through 145 removed outlier: 4.051A pdb=" N VAL g 135 " --> pdb=" O THR g 131 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.720A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.942A pdb=" N GLU h 35 " --> pdb=" O ASN h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 115 through 120 removed outlier: 3.661A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) Processing helix chain 'i' and resid 36 through 41 removed outlier: 3.560A pdb=" N TYR i 40 " --> pdb=" O ASP i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 47 through 57 Proline residue: i 53 - end of helix Processing helix chain 'i' and resid 73 through 80 Processing helix chain 'i' and resid 81 through 93 Processing helix chain 'i' and resid 96 through 102 removed outlier: 3.670A pdb=" N ARG i 102 " --> pdb=" O GLY i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.509A pdb=" N ILE j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 88 removed outlier: 3.773A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 58 Processing helix chain 'k' and resid 59 through 78 removed outlier: 4.400A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY k 78 " --> pdb=" O ALA k 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 90 through 93 removed outlier: 3.795A pdb=" N ARG k 93 " --> pdb=" O GLY k 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 90 through 93' Processing helix chain 'k' and resid 94 through 103 removed outlier: 3.629A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER k 102 " --> pdb=" O ARG k 98 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 9 removed outlier: 3.578A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 19 removed outlier: 3.609A pdb=" N LEU m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 38 removed outlier: 3.540A pdb=" N ALA m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 59 removed outlier: 3.601A pdb=" N LEU m 53 " --> pdb=" O THR m 49 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY m 54 " --> pdb=" O ASP m 50 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ARG m 55 " --> pdb=" O ASP m 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 60 through 63 removed outlier: 3.964A pdb=" N TYR m 63 " --> pdb=" O VAL m 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 60 through 63' Processing helix chain 'm' and resid 66 through 83 removed outlier: 3.810A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE m 83 " --> pdb=" O ARG m 79 " (cutoff:3.500A) Processing helix chain 'n' and resid 3 through 10 removed outlier: 4.231A pdb=" N ALA n 8 " --> pdb=" O THR n 4 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 50 removed outlier: 3.552A pdb=" N PHE n 44 " --> pdb=" O CYS n 40 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 4.016A pdb=" N ILE o 12 " --> pdb=" O LYS o 8 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS o 13 " --> pdb=" O ASN o 9 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLU o 14 " --> pdb=" O GLU o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 25 through 46 Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.221A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 83 Processing helix chain 'p' and resid 56 through 64 removed outlier: 3.542A pdb=" N TRP p 60 " --> pdb=" O LEU p 56 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN p 62 " --> pdb=" O LEU p 58 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP p 63 " --> pdb=" O LYS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 79 removed outlier: 3.503A pdb=" N HIS p 72 " --> pdb=" O THR p 68 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN p 73 " --> pdb=" O ASP p 69 " (cutoff:3.500A) Processing helix chain 'p' and resid 80 through 82 No H-bonds generated for 'chain 'p' and resid 80 through 82' Processing helix chain 'p' and resid 83 through 89 Processing helix chain 'r' and resid 30 through 35 Processing helix chain 'r' and resid 36 through 38 No H-bonds generated for 'chain 'r' and resid 36 through 38' Processing helix chain 'r' and resid 46 through 51 removed outlier: 3.712A pdb=" N THR r 50 " --> pdb=" O PRO r 46 " (cutoff:3.500A) Processing helix chain 'r' and resid 53 through 70 removed outlier: 3.598A pdb=" N THR r 62 " --> pdb=" O ARG r 58 " (cutoff:3.500A) Processing helix chain 's' and resid 14 through 24 removed outlier: 3.835A pdb=" N ALA s 21 " --> pdb=" O LYS s 17 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 38 Processing helix chain 't' and resid 46 through 62 removed outlier: 3.702A pdb=" N GLN t 62 " --> pdb=" O ASP t 58 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 80 Processing helix chain 'u' and resid 11 through 26 removed outlier: 3.518A pdb=" N SER u 26 " --> pdb=" O SER u 22 " (cutoff:3.500A) Processing helix chain 'u' and resid 29 through 36 Processing helix chain 'u' and resid 42 through 51 Processing helix chain 'v' and resid 14 through 27 removed outlier: 3.852A pdb=" N LYS v 27 " --> pdb=" O GLU v 23 " (cutoff:3.500A) Processing helix chain 'v' and resid 28 through 31 Processing helix chain 'v' and resid 73 through 82 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 197 through 201 removed outlier: 4.209A pdb=" N GLU D 200 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 213 removed outlier: 4.420A pdb=" N SER D 210 " --> pdb=" O LYS D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 removed outlier: 4.577A pdb=" N LYS D 267 " --> pdb=" O SER D 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.855A pdb=" N GLU E 74 " --> pdb=" O ASN E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 81 No H-bonds generated for 'chain 'E' and resid 79 through 81' Processing helix chain 'E' and resid 106 through 110 Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 30 through 43 Processing helix chain 'F' and resid 103 through 121 Processing helix chain 'F' and resid 133 through 142 removed outlier: 4.377A pdb=" N THR F 136 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS F 137 " --> pdb=" O PRO F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 165 removed outlier: 4.017A pdb=" N GLU F 164 " --> pdb=" O VAL F 161 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU F 165 " --> pdb=" O ASN F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 removed outlier: 3.552A pdb=" N LEU F 181 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 177 through 182' Processing helix chain 'F' and resid 192 through 201 removed outlier: 3.602A pdb=" N GLU F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 removed outlier: 3.690A 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 46 through 58 Processing helix chain 'G' and resid 90 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: 3.928A pdb=" N THR G 158 " --> pdb=" O ILE G 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 81 removed outlier: 4.273A pdb=" N ARG H 62 " --> pdb=" O SER H 58 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 150 removed outlier: 3.644A pdb=" N VAL H 141 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 59 through 63 Processing helix chain 'M' and resid 66 through 72 removed outlier: 3.950A pdb=" N LYS M 69 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 92 through 96 Processing helix chain 'M' and resid 97 through 106 removed outlier: 4.251A pdb=" N LEU M 101 " --> pdb=" O ASN M 97 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 110 Processing helix chain 'M' and resid 119 through 121 No H-bonds generated for 'chain 'M' and resid 119 through 121' Processing helix chain 'M' and resid 132 through 137 removed outlier: 4.631A 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 removed outlier: 3.942A pdb=" N VAL N 115 " --> pdb=" O PHE N 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 125 removed outlier: 3.652A pdb=" N LYS O 124 " --> pdb=" O LYS O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 56 Processing helix chain 'P' and resid 57 through 59 No H-bonds generated for 'chain 'P' and resid 57 through 59' Processing helix chain 'P' and resid 111 through 123 Processing helix chain 'Q' and resid 9 through 23 Processing helix chain 'Q' and resid 33 through 52 removed outlier: 3.665A pdb=" N ALA Q 37 " --> pdb=" O THR Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 63 Processing helix chain 'Q' and resid 84 through 93 removed outlier: 6.584A pdb=" N ALA Q 90 " --> pdb=" O PHE Q 86 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU Q 91 " --> pdb=" O GLY Q 87 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG Q 92 " --> pdb=" O GLU Q 88 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR Q 93 " --> pdb=" O ILE Q 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 22 removed outlier: 3.725A pdb=" N VAL R 10 " --> pdb=" O ASP R 6 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG R 19 " --> pdb=" O HIS R 15 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN R 21 " --> pdb=" O ARG R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 58 through 62 Processing helix chain 'R' and resid 69 through 84 removed outlier: 3.672A pdb=" N ALA R 73 " --> pdb=" O LYS R 69 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR R 74 " --> pdb=" O VAL R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 114 Processing helix chain 'S' and resid 66 through 70 removed outlier: 3.573A pdb=" N GLY S 69 " --> pdb=" O ILE S 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 19 Processing helix chain 'T' and resid 25 through 30 removed outlier: 3.881A pdb=" N LYS T 28 " --> pdb=" O PHE T 25 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 70 removed outlier: 4.449A pdb=" N ARG T 51 " --> pdb=" O PHE T 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG T 70 " --> pdb=" O ASN T 66 " (cutoff:3.500A) Processing helix chain 'T' and resid 75 through 87 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: 3.853A pdb=" N VAL V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL V 20 " --> pdb=" O LYS V 16 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE V 24 " --> pdb=" O VAL V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 39 removed outlier: 3.687A pdb=" N LEU V 38 " --> pdb=" O ALA V 34 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR V 39 " --> pdb=" O ILE V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 61 removed outlier: 4.835A pdb=" N VAL V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE V 47 " --> pdb=" O SER V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 89 through 91 No H-bonds generated for 'chain 'V' and resid 89 through 91' Processing helix chain 'W' and resid 2 through 6 Processing helix chain 'W' and resid 13 through 18 Processing helix chain 'W' and resid 34 through 47 removed outlier: 4.060A pdb=" N VAL W 38 " --> pdb=" O ASN W 34 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS W 39 " --> pdb=" O LYS W 35 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET W 40 " --> pdb=" O THR W 36 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA W 41 " --> pdb=" O GLN W 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 24 Processing helix chain 'Y' and resid 45 through 56 removed outlier: 3.562A pdb=" N ARG Y 53 " --> pdb=" O ILE Y 49 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 33 removed outlier: 4.227A pdb=" N GLN 1 17 " --> pdb=" O GLU 1 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE 1 18 " --> pdb=" O ILE 1 14 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA 1 33 " --> pdb=" O ARG 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 40 through 66 removed outlier: 4.136A pdb=" N ARG 1 44 " --> pdb=" O THR 1 40 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS 1 66 " --> pdb=" O ILE 1 62 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 25 Processing helix chain '2' and resid 40 through 49 removed outlier: 3.742A pdb=" N ARG 2 44 " --> pdb=" O ASN 2 40 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLY 2 45 " --> pdb=" O PRO 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 52 No H-bonds generated for 'chain '2' and resid 50 through 52' Processing helix chain '3' and resid 68 through 81 removed outlier: 3.860A pdb=" N GLU 3 72 " --> pdb=" O ASP 3 68 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG 3 73 " --> pdb=" O GLY 3 69 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE 3 74 " --> pdb=" O ARG 3 70 " (cutoff:3.500A) Processing helix chain '4' and resid 10 through 16 Processing helix chain '6' and resid 9 through 15 Processing helix chain '6' and resid 21 through 24 Processing helix chain '6' and resid 25 through 39 removed outlier: 3.750A pdb=" N LYS 6 38 " --> pdb=" O ARG 6 34 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY 6 39 " --> pdb=" O ARG 6 35 " (cutoff:3.500A) Processing helix chain '8' and resid 29 through 33 removed outlier: 3.666A pdb=" N LYS 8 33 " --> pdb=" O PRO 8 30 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 184 through 186 removed outlier: 6.950A 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 64 through 65 removed outlier: 3.867A pdb=" N ILE c 65 " --> pdb=" O HIS c 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'c' and resid 163 through 166 removed outlier: 3.677A pdb=" N LYS c 149 " --> pdb=" O TRP c 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 124 through 125 Processing sheet with id=AA5, first strand: chain 'd' and resid 165 through 167 removed outlier: 3.646A pdb=" N ASN d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR d 175 " --> pdb=" O ASN d 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'e' and resid 20 through 21 Processing sheet with id=AA7, first strand: chain 'e' and resid 94 through 98 removed outlier: 3.545A pdb=" N PHE e 95 " --> pdb=" O LYS e 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 36 through 47 removed outlier: 6.611A pdb=" N ARG f 64 " --> pdb=" O LEU f 38 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA f 40 " --> pdb=" O ILE f 62 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE f 62 " --> pdb=" O ALA f 40 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP f 42 " --> pdb=" O TYR f 60 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N TYR f 60 " --> pdb=" O ASP f 42 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLY f 44 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY f 58 " --> pdb=" O GLY f 44 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N GLU f 5 " --> pdb=" O VAL f 91 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VAL f 91 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N MET f 7 " --> pdb=" O TYR f 89 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR f 89 " --> pdb=" O MET f 7 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ILE f 9 " --> pdb=" O ILE f 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'g' and resid 73 through 76 Processing sheet with id=AB1, first strand: chain 'h' and resid 48 through 49 removed outlier: 3.552A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'h' and resid 76 through 79 removed outlier: 6.731A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'i' and resid 8 through 9 Processing sheet with id=AB4, first strand: chain 'i' and resid 8 through 9 removed outlier: 3.887A pdb=" N ASN i 68 " --> pdb=" O ARG i 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'j' and resid 5 through 9 removed outlier: 4.235A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'j' and resid 49 through 52 Processing sheet with id=AB7, first strand: chain 'k' and resid 41 through 46 removed outlier: 3.849A pdb=" N SER k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY k 19 " --> pdb=" O THR k 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER k 25 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ARG k 111 " --> pdb=" O VAL k 82 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL k 84 " --> pdb=" O ARG k 111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'l' and resid 92 through 93 removed outlier: 5.814A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE l 76 " --> pdb=" O VAL l 68 " (cutoff:3.500A) removed outlier: 13.090A pdb=" N GLU l 75 " --> pdb=" O VAL l 106 " (cutoff:3.500A) removed outlier: 10.402A pdb=" N TYR l 108 " --> pdb=" O GLU l 75 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ASN l 77 " --> pdb=" O TYR l 108 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE l 110 " --> pdb=" O ASN l 77 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N TYR l 79 " --> pdb=" O ILE l 110 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS l 109 " --> pdb=" O ARG l 96 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'p' and resid 6 through 7 removed outlier: 4.082A pdb=" N ILE p 20 " --> pdb=" O ILE p 37 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE p 37 " --> pdb=" O ILE p 20 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR p 39 " --> pdb=" O LYS p 51 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS p 51 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU p 49 " --> pdb=" O ASN p 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'q' and resid 12 through 19 removed outlier: 6.383A pdb=" N THR q 24 " --> pdb=" O VAL q 15 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASP q 17 " --> pdb=" O THR q 22 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR q 22 " --> pdb=" O ASP q 17 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR q 48 " --> pdb=" O ILE q 23 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE q 75 " --> pdb=" O LYS q 47 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN q 64 " --> pdb=" O ARG q 76 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL q 78 " --> pdb=" O LYS q 62 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ILE q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE q 60 " --> pdb=" O ILE q 80 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 's' and resid 48 through 49 Processing sheet with id=AC3, first strand: chain 'v' and resid 7 through 9 removed outlier: 3.703A pdb=" N HIS v 7 " --> pdb=" O ALA v 40 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL v 42 " --> pdb=" O HIS v 7 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR v 57 " --> pdb=" O VAL v 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 33 through 34 Processing sheet with id=AC5, first strand: chain 'D' and resid 75 through 76 Processing sheet with id=AC6, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AC7, first strand: chain 'D' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'D' and resid 180 through 181 Processing sheet with id=AC9, first strand: chain 'E' and resid 6 through 8 Processing sheet with id=AD1, first strand: chain 'E' and resid 12 through 16 removed outlier: 3.734A pdb=" N GLN E 187 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS E 198 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL E 185 " --> pdb=" O LYS E 198 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 34 through 37 removed outlier: 7.123A pdb=" N GLN E 50 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE E 49 " --> pdb=" O PHE E 91 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 119 through 121 Processing sheet with id=AD4, first strand: chain 'E' and resid 127 through 128 removed outlier: 3.934A pdb=" N GLN E 128 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY E 171 " --> pdb=" O GLN E 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 6 through 8 removed outlier: 4.800A pdb=" N LEU F 7 " --> pdb=" O SER F 14 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 85 through 86 removed outlier: 3.806A pdb=" N LYS G 33 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL G 35 " --> pdb=" O SER G 147 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 9 through 10 removed outlier: 3.905A pdb=" N ILE H 9 " --> pdb=" O ILE H 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 16 through 20 Processing sheet with id=AD9, first strand: chain 'H' and resid 87 through 88 Processing sheet with id=AE1, first strand: chain 'H' and resid 95 through 97 removed outlier: 3.519A pdb=" N GLN H 97 " --> pdb=" O ILE H 104 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 125 through 127 Processing sheet with id=AE3, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.383A pdb=" N TYR M 17 " --> pdb=" O ILE M 56 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE M 58 " --> pdb=" O TYR M 17 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE M 19 " --> pdb=" O ILE M 58 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL M 55 " --> pdb=" O PHE M 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'M' and resid 74 through 78 removed outlier: 8.152A pdb=" N TYR M 75 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ILE M 88 " --> pdb=" O TYR M 75 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 16 through 18 removed outlier: 6.742A pdb=" N ASN N 45 " --> pdb=" O ARG N 17 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 21 through 23 removed outlier: 6.983A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL N 63 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 76 through 79 removed outlier: 4.072A pdb=" N THR S 75 " --> pdb=" O TYR N 76 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR S 60 " --> pdb=" O ARG S 52 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG S 52 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N THR S 62 " --> pdb=" O ILE S 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU S 87 " --> pdb=" O ARG S 29 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS S 31 " --> pdb=" O LYS S 85 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS S 85 " --> pdb=" O HIS S 31 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ARG S 33 " --> pdb=" O ILE S 83 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE S 83 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'P' and resid 34 through 36 Processing sheet with id=AE9, first strand: chain 'P' and resid 40 through 43 removed outlier: 3.612A pdb=" N GLY P 92 " --> pdb=" O TYR P 74 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 63 through 66 Processing sheet with id=AF2, first strand: chain 'Q' and resid 30 through 32 removed outlier: 3.758A pdb=" N ILE Q 119 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE Q 118 " --> pdb=" O LYS Q 105 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LYS Q 105 " --> pdb=" O ILE Q 118 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 30 through 35 removed outlier: 3.727A pdb=" N ARG R 30 " --> pdb=" O ILE R 45 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE R 45 " --> pdb=" O ARG R 30 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN R 43 " --> pdb=" O ASN R 32 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N ILE R 40 " --> pdb=" O SER R 57 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N SER R 57 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ALA R 42 " --> pdb=" O GLN R 55 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLN R 55 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE R 44 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP R 46 " --> pdb=" O VAL R 51 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL R 51 " --> pdb=" O ASP R 46 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 10 through 15 removed outlier: 3.721A pdb=" N ILE U 12 " --> pdb=" O ILE U 5 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE U 2 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL U 41 " --> pdb=" O PHE U 2 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE U 4 " --> pdb=" O LEU U 39 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'U' and resid 19 through 22 Processing sheet with id=AF6, first strand: chain 'U' and resid 71 through 72 Processing sheet with id=AF7, first strand: chain 'U' and resid 75 through 76 removed outlier: 3.730A pdb=" N THR U 75 " --> pdb=" O ARG U 84 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG U 84 " --> pdb=" O THR U 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'V' and resid 3 through 6 removed outlier: 4.109A pdb=" N GLU V 73 " --> pdb=" O VAL V 106 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N SER V 108 " --> pdb=" O VAL V 71 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL V 71 " --> pdb=" O SER V 108 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 82 through 83 Processing sheet with id=AG1, first strand: chain 'V' and resid 86 through 87 removed outlier: 3.535A pdb=" N ARG V 86 " --> pdb=" O SER V 94 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'W' and resid 9 through 10 removed outlier: 3.739A pdb=" N ARG W 75 " --> pdb=" O TYR W 58 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'W' and resid 62 through 63 removed outlier: 4.038A pdb=" N GLY W 70 " --> pdb=" O LYS W 63 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'X' and resid 23 through 24 removed outlier: 3.700A pdb=" N VAL X 34 " --> pdb=" O ILE X 24 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Y' and resid 39 through 44 removed outlier: 11.404A pdb=" N LYS Y 26 " --> pdb=" O THR Y 87 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N ILE Y 89 " --> pdb=" O LYS Y 26 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE Y 86 " --> pdb=" O ASP Y 80 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ASP Y 80 " --> pdb=" O ILE Y 86 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS Y 88 " --> pdb=" O GLN Y 78 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN Y 78 " --> pdb=" O HIS Y 88 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP Y 76 " --> pdb=" O ASP Y 90 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Z' and resid 74 through 77 Processing sheet with id=AG7, first strand: chain '0' and resid 17 through 18 Processing sheet with id=AG8, first strand: chain '0' and resid 36 through 39 removed outlier: 3.939A pdb=" N ILE 0 38 " --> pdb=" O VAL 0 47 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL 0 47 " --> pdb=" O ILE 0 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '2' and resid 36 through 38 removed outlier: 3.800A pdb=" N THR 2 7 " --> pdb=" O THR 2 55 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR 2 55 " --> pdb=" O THR 2 7 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '3' and resid 27 through 29 Processing sheet with id=AH2, first strand: chain '4' and resid 27 through 29 Processing sheet with id=AH3, first strand: chain '5' and resid 34 through 35 Processing sheet with id=AH4, first strand: chain '7' and resid 14 through 15 Processing sheet with id=AH5, first strand: chain '8' and resid 15 through 17 removed outlier: 3.821A pdb=" N VAL 8 25 " --> pdb=" O GLN 8 34 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLN 8 34 " --> pdb=" O VAL 8 25 " (cutoff:3.500A) 1260 hydrogen bonds defined for protein. 3468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3652 hydrogen bonds 5850 hydrogen bond angles 0 basepair planarities 1472 basepair parallelities 2240 stacking parallelities Total time for adding SS restraints: 199.41 Time building geometry restraints manager: 67.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 16464 1.32 - 1.45: 66469 1.45 - 1.57: 61066 1.57 - 1.70: 9133 1.70 - 1.82: 211 Bond restraints: 153343 Sorted by residual: bond pdb=" C TYR W 58 " pdb=" N LYS W 59 " ideal model delta sigma weight residual 1.331 1.199 0.132 1.48e-02 4.57e+03 7.93e+01 bond pdb=" C ILE Z 53 " pdb=" N TYR Z 54 " ideal model delta sigma weight residual 1.331 1.213 0.118 2.83e-02 1.25e+03 1.73e+01 bond pdb=" N SER D 247 " pdb=" CA SER D 247 " ideal model delta sigma weight residual 1.453 1.425 0.029 8.30e-03 1.45e+04 1.19e+01 bond pdb=" C MET D 246 " pdb=" N SER D 247 " ideal model delta sigma weight residual 1.325 1.284 0.041 1.25e-02 6.40e+03 1.08e+01 bond pdb=" CB ARG D 155 " pdb=" CG ARG D 155 " ideal model delta sigma weight residual 1.520 1.431 0.089 3.00e-02 1.11e+03 8.74e+00 ... (remaining 153338 not shown) Histogram of bond angle deviations from ideal: 94.63 - 102.76: 8571 102.76 - 110.89: 78094 110.89 - 119.02: 67841 119.02 - 127.15: 63764 127.15 - 135.28: 11256 Bond angle restraints: 229526 Sorted by residual: angle pdb=" C ARG v 95 " pdb=" N ILE v 96 " pdb=" CA ILE v 96 " ideal model delta sigma weight residual 121.97 135.28 -13.31 1.80e+00 3.09e-01 5.47e+01 angle pdb=" N ILE v 96 " pdb=" CA ILE v 96 " pdb=" C ILE v 96 " ideal model delta sigma weight residual 109.34 94.63 14.71 2.08e+00 2.31e-01 5.00e+01 angle pdb=" N SER v 50 " pdb=" CA SER v 50 " pdb=" C SER v 50 " ideal model delta sigma weight residual 110.80 125.38 -14.58 2.13e+00 2.20e-01 4.69e+01 angle pdb=" C VAL n 56 " pdb=" N ARG n 57 " pdb=" CA ARG n 57 " ideal model delta sigma weight residual 121.70 133.40 -11.70 1.80e+00 3.09e-01 4.22e+01 angle pdb=" N LYS D 213 " pdb=" CA LYS D 213 " pdb=" C LYS D 213 " ideal model delta sigma weight residual 111.03 118.23 -7.20 1.11e+00 8.12e-01 4.21e+01 ... (remaining 229521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 86755 35.94 - 71.87: 10196 71.87 - 107.81: 1024 107.81 - 143.75: 24 143.75 - 179.68: 10 Dihedral angle restraints: 98009 sinusoidal: 82407 harmonic: 15602 Sorted by residual: dihedral pdb=" CA ILE r 26 " pdb=" C ILE r 26 " pdb=" N ASP r 27 " pdb=" CA ASP r 27 " ideal model delta harmonic sigma weight residual -180.00 -51.80 -128.20 0 5.00e+00 4.00e-02 6.57e+02 dihedral pdb=" CA ARG v 95 " pdb=" C ARG v 95 " pdb=" N ILE v 96 " pdb=" CA ILE v 96 " ideal model delta harmonic sigma weight residual 180.00 -76.08 -103.92 0 5.00e+00 4.00e-02 4.32e+02 dihedral pdb=" CA ALA v 51 " pdb=" C ALA v 51 " pdb=" N THR v 52 " pdb=" CA THR v 52 " ideal model delta harmonic sigma weight residual 180.00 115.63 64.37 0 5.00e+00 4.00e-02 1.66e+02 ... (remaining 98006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.318: 29380 0.318 - 0.637: 2 0.637 - 0.955: 0 0.955 - 1.273: 0 1.273 - 1.592: 2 Chirality restraints: 29384 Sorted by residual: chirality pdb=" CB VAL v 35 " pdb=" CA VAL v 35 " pdb=" CG1 VAL v 35 " pdb=" CG2 VAL v 35 " both_signs ideal model delta sigma weight residual False -2.63 -1.04 -1.59 2.00e-01 2.50e+01 6.33e+01 chirality pdb=" CB VAL c 108 " pdb=" CA VAL c 108 " pdb=" CG1 VAL c 108 " pdb=" CG2 VAL c 108 " both_signs ideal model delta sigma weight residual False -2.63 -1.15 -1.48 2.00e-01 2.50e+01 5.50e+01 chirality pdb=" CA ARG v 95 " pdb=" N ARG v 95 " pdb=" C ARG v 95 " pdb=" CB ARG v 95 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 ... (remaining 29381 not shown) Planarity restraints: 12106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG v 66 " -0.880 9.50e-02 1.11e+02 3.94e-01 9.44e+01 pdb=" NE ARG v 66 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG v 66 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG v 66 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG v 66 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 624 " -0.041 2.00e-02 2.50e+03 4.25e-02 4.06e+01 pdb=" N1 C A 624 " 0.028 2.00e-02 2.50e+03 pdb=" C2 C A 624 " 0.099 2.00e-02 2.50e+03 pdb=" O2 C A 624 " -0.050 2.00e-02 2.50e+03 pdb=" N3 C A 624 " -0.011 2.00e-02 2.50e+03 pdb=" C4 C A 624 " 0.016 2.00e-02 2.50e+03 pdb=" N4 C A 624 " -0.030 2.00e-02 2.50e+03 pdb=" C5 C A 624 " -0.011 2.00e-02 2.50e+03 pdb=" C6 C A 624 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU g 13 " 0.094 5.00e-02 4.00e+02 1.45e-01 3.35e+01 pdb=" N PRO g 14 " -0.250 5.00e-02 4.00e+02 pdb=" CA PRO g 14 " 0.081 5.00e-02 4.00e+02 pdb=" CD PRO g 14 " 0.075 5.00e-02 4.00e+02 ... (remaining 12103 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 10 1.80 - 2.57: 2666 2.57 - 3.35: 177494 3.35 - 4.12: 448809 4.12 - 4.90: 647593 Nonbonded interactions: 1276572 Sorted by model distance: nonbonded pdb=" CB PHE v 4 " pdb=" O ALA v 38 " model vdw 1.019 3.440 nonbonded pdb=" CG PHE v 4 " pdb=" O ALA v 38 " model vdw 1.485 3.260 nonbonded pdb=" O ILE v 58 " pdb=" OG1 THR v 64 " model vdw 1.554 2.440 nonbonded pdb=" N1 A a 975 " pdb=" OE1 GLU v 5 " model vdw 1.585 3.120 nonbonded pdb=" CD1 PHE P 32 " pdb=" CZ PHE P 131 " model vdw 1.594 3.640 ... (remaining 1276567 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: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 13.860 Check model and map are aligned: 1.530 Set scattering table: 0.970 Process input model: 456.180 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 480.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 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 : 0.009 0.132 153343 Z= 0.563 Angle : 1.028 14.833 229526 Z= 0.516 Chirality : 0.052 1.592 29384 Planarity : 0.008 0.394 12106 Dihedral : 22.748 179.684 87959 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.56 % Allowed : 17.31 % Favored : 82.13 % Rotamer: Outliers : 0.73 % Allowed : 3.73 % Favored : 95.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.96 % Twisted Proline : 1.09 % Twisted General : 0.84 % 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: -5.61 (0.09), residues: 5354 helix: -3.54 (0.09), residues: 1407 sheet: -4.02 (0.13), residues: 838 loop : -3.87 (0.09), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP s 34 HIS 0.028 0.004 HIS S 31 PHE 0.034 0.004 PHE 3 78 TYR 0.038 0.004 TYR D 5 ARG 0.022 0.003 ARG P 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1675 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1641 time to evaluate : 5.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 219 ASP cc_start: 0.8536 (t0) cc_final: 0.6986 (t70) REVERT: c 109 ASP cc_start: 0.7206 (m-30) cc_final: 0.6936 (m-30) REVERT: d 38 PRO cc_start: 0.7186 (Cg_endo) cc_final: 0.6930 (Cg_exo) REVERT: d 131 TYR cc_start: 0.7182 (t80) cc_final: 0.6634 (t80) REVERT: d 137 GLN cc_start: 0.7139 (mt0) cc_final: 0.6753 (tp-100) REVERT: e 71 LEU cc_start: 0.7775 (mt) cc_final: 0.7271 (mt) REVERT: e 88 ARG cc_start: 0.6765 (ttp-110) cc_final: 0.6540 (mtm110) REVERT: f 81 LYS cc_start: 0.7547 (mptm) cc_final: 0.7252 (mmmt) REVERT: g 106 ASN cc_start: 0.7371 (m110) cc_final: 0.6847 (t0) REVERT: g 135 VAL cc_start: 0.6148 (t) cc_final: 0.5857 (t) REVERT: h 21 ARG cc_start: 0.7010 (mtt180) cc_final: 0.6789 (mtp85) REVERT: h 39 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7143 (mp) REVERT: h 72 ARG cc_start: 0.7168 (ptp-110) cc_final: 0.4833 (mmm160) REVERT: h 77 LEU cc_start: 0.7307 (tp) cc_final: 0.7054 (tt) REVERT: i 16 ASN cc_start: 0.7400 (m-40) cc_final: 0.6555 (t0) REVERT: i 62 ASN cc_start: 0.6736 (m-40) cc_final: 0.6500 (m-40) REVERT: i 64 ASP cc_start: 0.6857 (m-30) cc_final: 0.6457 (t70) REVERT: m 45 VAL cc_start: 0.5727 (p) cc_final: 0.5323 (m) REVERT: m 76 ASN cc_start: 0.7684 (m-40) cc_final: 0.7175 (m-40) REVERT: n 30 PRO cc_start: 0.7861 (Cg_endo) cc_final: 0.6513 (Cg_exo) REVERT: n 43 CYS cc_start: 0.7800 (m) cc_final: 0.7488 (m) REVERT: n 50 LYS cc_start: 0.7776 (tppp) cc_final: 0.6691 (ttmm) REVERT: o 3 ILE cc_start: 0.5994 (pt) cc_final: 0.5769 (pt) REVERT: r 43 LYS cc_start: 0.7727 (mttm) cc_final: 0.7468 (mttm) REVERT: r 65 LYS cc_start: 0.8501 (mttt) cc_final: 0.8291 (mttp) REVERT: r 70 MET cc_start: 0.7069 (ptp) cc_final: 0.6422 (ptp) REVERT: v 22 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.4901 (mt-10) REVERT: E 91 PHE cc_start: 0.8178 (m-80) cc_final: 0.7692 (m-80) REVERT: E 208 LEU cc_start: 0.8447 (tp) cc_final: 0.8067 (tp) REVERT: E 210 GLU cc_start: 0.7140 (pp20) cc_final: 0.6871 (tm-30) REVERT: F 34 PHE cc_start: 0.7739 (t80) cc_final: 0.7468 (t80) REVERT: M 101 LEU cc_start: 0.7524 (tt) cc_final: 0.7179 (tt) REVERT: M 103 GLU cc_start: 0.7622 (pt0) cc_final: 0.7345 (pt0) REVERT: N 17 ARG cc_start: 0.8874 (ttm170) cc_final: 0.8594 (mtt-85) REVERT: Q 16 MET cc_start: 0.7305 (ttm) cc_final: 0.7083 (ttm) REVERT: R 1 MET cc_start: 0.1418 (ttp) cc_final: 0.0456 (ttp) REVERT: R 4 LYS cc_start: 0.5297 (mttt) cc_final: 0.4994 (mttt) REVERT: R 14 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7257 (mtm-85) REVERT: R 43 GLN cc_start: 0.6930 (mt0) cc_final: 0.6702 (mt0) REVERT: R 94 PHE cc_start: 0.7163 (t80) cc_final: 0.6852 (t80) REVERT: S 28 LEU cc_start: 0.7721 (tp) cc_final: 0.7321 (tp) REVERT: S 89 LYS cc_start: 0.7292 (mtpm) cc_final: 0.7020 (ttmm) REVERT: T 22 LYS cc_start: 0.7583 (mmmt) cc_final: 0.7289 (mttt) REVERT: T 91 ASN cc_start: 0.8189 (m110) cc_final: 0.7911 (m-40) REVERT: X 39 ASN cc_start: 0.8037 (m-40) cc_final: 0.7677 (p0) REVERT: X 71 LEU cc_start: 0.6444 (tt) cc_final: 0.6188 (tt) REVERT: Y 78 GLN cc_start: 0.6213 (mt0) cc_final: 0.5993 (mt0) REVERT: 1 20 SER cc_start: 0.7698 (p) cc_final: 0.7273 (t) REVERT: 1 43 ILE cc_start: 0.8190 (mm) cc_final: 0.7985 (tt) REVERT: 1 60 ARG cc_start: 0.7619 (mtm180) cc_final: 0.7247 (ttm170) REVERT: 2 21 LYS cc_start: 0.8546 (mtmp) cc_final: 0.8283 (mtmm) REVERT: 4 41 HIS cc_start: 0.6309 (m90) cc_final: 0.5825 (m90) outliers start: 34 outliers final: 10 residues processed: 1666 average time/residue: 1.4368 time to fit residues: 4019.0731 Evaluate side-chains 1139 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1127 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain l residue 101 LYS Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 22 GLU Chi-restraints excluded: chain v residue 68 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 134 ARG Chi-restraints excluded: chain Z residue 28 ARG Chi-restraints excluded: chain Z residue 33 ARG Chi-restraints excluded: chain 5 residue 35 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 825 optimal weight: 30.0000 chunk 741 optimal weight: 7.9990 chunk 411 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 500 optimal weight: 50.0000 chunk 396 optimal weight: 20.0000 chunk 766 optimal weight: 0.7980 chunk 296 optimal weight: 8.9990 chunk 466 optimal weight: 10.0000 chunk 570 optimal weight: 6.9990 chunk 888 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 GLN ** b 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 53 HIS c 61 ASN c 99 HIS d 35 GLN ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN f 53 ASN g 19 ASN h 22 HIS h 48 ASN j 64 GLN j 78 ASN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN l 6 GLN o 68 ASN p 72 HIS ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 21 ASN t 62 GLN ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 33 ASN v 41 HIS v 49 ASN v 83 ASN v 88 GLN D 14 ASN D 196 ASN E 128 GLN E 136 GLN F 38 ASN F 82 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 119 GLN M 137 GLN O 70 ASN P 46 GLN Q 73 ASN Q 106 GLN R 8 ASN S 79 HIS T 71 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 GLN 0 34 GLN 3 6 HIS 3 20 ASN 3 75 ASN 3 83 ASN 5 42 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 153343 Z= 0.224 Angle : 0.695 12.274 229526 Z= 0.355 Chirality : 0.037 0.306 29384 Planarity : 0.006 0.150 12106 Dihedral : 23.355 178.384 76847 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 10.31 % Favored : 89.39 % Rotamer: Outliers : 3.34 % Allowed : 13.42 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.98 % Twisted Proline : 1.09 % Twisted General : 0.40 % 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: -4.30 (0.10), residues: 5354 helix: -1.97 (0.12), residues: 1474 sheet: -3.30 (0.14), residues: 880 loop : -3.29 (0.10), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP 0 29 HIS 0.011 0.002 HIS i 83 PHE 0.051 0.003 PHE 3 23 TYR 0.031 0.003 TYR R 101 ARG 0.015 0.001 ARG S 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1538 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1383 time to evaluate : 5.861 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 154 MET cc_start: 0.4261 (tpp) cc_final: 0.4038 (tpp) REVERT: b 186 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.7074 (mm) REVERT: c 117 GLU cc_start: 0.7911 (tp30) cc_final: 0.7622 (tp30) REVERT: d 38 PRO cc_start: 0.6945 (Cg_endo) cc_final: 0.6683 (Cg_exo) REVERT: d 51 LEU cc_start: 0.8283 (tp) cc_final: 0.8074 (tp) REVERT: d 87 MET cc_start: 0.7858 (tpp) cc_final: 0.7596 (tpt) REVERT: e 71 LEU cc_start: 0.7865 (mt) cc_final: 0.7298 (mt) REVERT: f 81 LYS cc_start: 0.7586 (mptm) cc_final: 0.7182 (mmmt) REVERT: g 33 ASP cc_start: 0.7499 (t0) cc_final: 0.7268 (t0) REVERT: h 130 TYR cc_start: 0.7700 (m-80) cc_final: 0.7389 (m-80) REVERT: i 16 ASN cc_start: 0.7112 (m-40) cc_final: 0.6279 (t0) REVERT: i 87 ARG cc_start: 0.6184 (OUTLIER) cc_final: 0.5626 (mtt-85) REVERT: i 112 MET cc_start: 0.5476 (ptt) cc_final: 0.5224 (ptm) REVERT: j 10 LEU cc_start: 0.5499 (mp) cc_final: 0.5176 (mt) REVERT: k 76 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7826 (tm-30) REVERT: l 117 THR cc_start: 0.6611 (t) cc_final: 0.6410 (t) REVERT: m 19 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7581 (mt) REVERT: n 50 LYS cc_start: 0.7914 (tppp) cc_final: 0.7655 (mtpp) REVERT: o 14 GLU cc_start: 0.7720 (mp0) cc_final: 0.7351 (pt0) REVERT: p 35 GLU cc_start: 0.6858 (pt0) cc_final: 0.6067 (pt0) REVERT: p 41 ASN cc_start: 0.7604 (t0) cc_final: 0.7101 (t0) REVERT: q 57 LEU cc_start: 0.7780 (mt) cc_final: 0.7325 (mp) REVERT: r 43 LYS cc_start: 0.7595 (mttm) cc_final: 0.7393 (mttm) REVERT: t 58 ASP cc_start: 0.7555 (m-30) cc_final: 0.7286 (m-30) REVERT: v 22 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.4080 (mt-10) REVERT: D 53 HIS cc_start: 0.8438 (OUTLIER) cc_final: 0.7981 (t-90) REVERT: E 208 LEU cc_start: 0.8619 (tp) cc_final: 0.8150 (tt) REVERT: F 34 PHE cc_start: 0.8154 (t80) cc_final: 0.7945 (t80) REVERT: M 58 ILE cc_start: 0.8230 (tt) cc_final: 0.7998 (pt) REVERT: M 74 VAL cc_start: 0.9262 (t) cc_final: 0.8998 (m) REVERT: O 1 MET cc_start: 0.7068 (mtt) cc_final: 0.6854 (mtt) REVERT: P 28 THR cc_start: 0.6175 (OUTLIER) cc_final: 0.5907 (p) REVERT: P 32 PHE cc_start: 0.7584 (m-80) cc_final: 0.7329 (m-10) REVERT: Q 24 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7826 (tp) REVERT: Q 45 GLU cc_start: 0.6643 (mt-10) cc_final: 0.5401 (mm-30) REVERT: R 4 LYS cc_start: 0.6193 (mttt) cc_final: 0.5924 (mttt) REVERT: R 94 PHE cc_start: 0.7162 (t80) cc_final: 0.6720 (t80) REVERT: S 51 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8405 (mtpp) REVERT: T 22 LYS cc_start: 0.7848 (mmmt) cc_final: 0.7508 (mttt) REVERT: V 21 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8667 (mp) REVERT: V 48 GLU cc_start: 0.7550 (tp30) cc_final: 0.7229 (tp30) REVERT: W 12 ILE cc_start: 0.8511 (mp) cc_final: 0.8236 (mt) REVERT: 1 14 ILE cc_start: 0.8114 (tp) cc_final: 0.7838 (tp) REVERT: 2 21 LYS cc_start: 0.8412 (mtmp) cc_final: 0.8115 (mttt) REVERT: 2 34 SER cc_start: 0.7733 (m) cc_final: 0.7288 (p) REVERT: 7 35 ASN cc_start: 0.8309 (p0) cc_final: 0.8079 (p0) REVERT: 8 2 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8220 (ttmm) outliers start: 155 outliers final: 81 residues processed: 1450 average time/residue: 1.3953 time to fit residues: 3460.6088 Evaluate side-chains 1224 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1134 time to evaluate : 5.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 36 HIS Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 130 SER Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 87 ARG Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 118 SER Chi-restraints excluded: chain m residue 19 LEU Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain o residue 75 ILE Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain u residue 44 LYS Chi-restraints excluded: chain v residue 4 PHE Chi-restraints excluded: chain v residue 22 GLU Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain G residue 46 ASN Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain O residue 85 PHE Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 28 THR Chi-restraints excluded: chain P residue 41 TRP Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 23 SER Chi-restraints excluded: chain Q residue 24 LEU Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 8 ASN Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain U residue 28 ASN Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 21 LEU Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 26 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 33 ARG Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 7 residue 25 SER Chi-restraints excluded: chain 7 residue 55 MET Chi-restraints excluded: chain 8 residue 2 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 493 optimal weight: 20.0000 chunk 275 optimal weight: 8.9990 chunk 739 optimal weight: 5.9990 chunk 604 optimal weight: 50.0000 chunk 244 optimal weight: 10.0000 chunk 889 optimal weight: 5.9990 chunk 961 optimal weight: 10.0000 chunk 792 optimal weight: 20.0000 chunk 882 optimal weight: 20.0000 chunk 303 optimal weight: 8.9990 chunk 713 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 ASN ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 106 ASN h 48 ASN i 33 ASN j 56 HIS ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 14 GLN q 64 GLN s 47 HIS ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 62 ASN ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 131 HIS O 27 ASN R 8 ASN ** R 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 GLN T 81 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.147 153343 Z= 0.301 Angle : 0.715 11.622 229526 Z= 0.364 Chirality : 0.038 0.312 29384 Planarity : 0.006 0.080 12106 Dihedral : 23.189 179.323 76824 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.05 % Favored : 87.82 % Rotamer: Outliers : 5.03 % Allowed : 17.43 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.00 % Twisted Proline : 0.00 % 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: -3.75 (0.10), residues: 5354 helix: -1.48 (0.12), residues: 1489 sheet: -2.72 (0.15), residues: 909 loop : -3.05 (0.10), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP g 103 HIS 0.013 0.002 HIS 3 55 PHE 0.026 0.003 PHE d 176 TYR 0.022 0.002 TYR p 18 ARG 0.044 0.001 ARG d 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1218 time to evaluate : 5.980 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: b 131 LYS cc_start: 0.4906 (ptmt) cc_final: 0.4568 (ptmm) REVERT: b 136 GLU cc_start: 0.7571 (tp30) cc_final: 0.7110 (tp30) REVERT: d 38 PRO cc_start: 0.7081 (Cg_endo) cc_final: 0.6852 (Cg_exo) REVERT: e 96 MET cc_start: 0.6374 (tmm) cc_final: 0.6017 (tmm) REVERT: h 80 ILE cc_start: 0.8703 (mp) cc_final: 0.8467 (mm) REVERT: h 130 TYR cc_start: 0.7947 (m-80) cc_final: 0.7667 (m-80) REVERT: i 64 ASP cc_start: 0.6450 (m-30) cc_final: 0.5896 (t70) REVERT: i 87 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5673 (mtt-85) REVERT: j 10 LEU cc_start: 0.5781 (mp) cc_final: 0.5199 (mt) REVERT: j 88 MET cc_start: 0.6521 (tmm) cc_final: 0.5878 (ptp) REVERT: k 114 THR cc_start: 0.7627 (OUTLIER) cc_final: 0.7270 (p) REVERT: l 88 GLN cc_start: 0.7933 (pp30) cc_final: 0.7459 (pp30) REVERT: l 108 TYR cc_start: 0.7077 (m-80) cc_final: 0.6369 (m-10) REVERT: l 115 LEU cc_start: 0.7164 (mt) cc_final: 0.6853 (mt) REVERT: m 19 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7558 (mt) REVERT: m 69 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7042 (tt) REVERT: o 26 GLU cc_start: 0.7204 (pm20) cc_final: 0.6905 (mt-10) REVERT: o 59 MET cc_start: 0.7560 (mtt) cc_final: 0.6807 (mtt) REVERT: r 55 LYS cc_start: 0.8405 (ptpt) cc_final: 0.8183 (ptmt) REVERT: v 5 GLU cc_start: 0.3706 (OUTLIER) cc_final: 0.3270 (pp20) REVERT: v 65 LEU cc_start: 0.6758 (tt) cc_final: 0.6489 (pp) REVERT: D 22 GLU cc_start: 0.7647 (mp0) cc_final: 0.7338 (mt-10) REVERT: D 53 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8123 (t-90) REVERT: D 167 GLU cc_start: 0.5571 (mm-30) cc_final: 0.5327 (mm-30) REVERT: F 24 PHE cc_start: 0.6528 (m-80) cc_final: 0.6306 (m-80) REVERT: F 114 LEU cc_start: 0.9016 (tp) cc_final: 0.8459 (pp) REVERT: M 58 ILE cc_start: 0.8309 (tt) cc_final: 0.8106 (pt) REVERT: M 74 VAL cc_start: 0.9228 (t) cc_final: 0.8977 (m) REVERT: Q 24 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7903 (tp) REVERT: Q 45 GLU cc_start: 0.6671 (mt-10) cc_final: 0.5753 (mm-30) REVERT: R 4 LYS cc_start: 0.6735 (mttt) cc_final: 0.6270 (tptp) REVERT: R 14 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7481 (mtm-85) REVERT: R 94 PHE cc_start: 0.7234 (t80) cc_final: 0.6656 (t80) REVERT: S 89 LYS cc_start: 0.7505 (mmmm) cc_final: 0.7233 (ttmm) REVERT: T 22 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7790 (mttt) REVERT: U 74 PHE cc_start: 0.8762 (t80) cc_final: 0.8488 (t80) REVERT: V 9 THR cc_start: 0.9028 (m) cc_final: 0.8764 (p) REVERT: Y 19 LYS cc_start: 0.6534 (ttpt) cc_final: 0.5926 (ttpt) REVERT: 2 21 LYS cc_start: 0.8489 (mtmp) cc_final: 0.8281 (mttt) REVERT: 2 34 SER cc_start: 0.7993 (m) cc_final: 0.7603 (p) REVERT: 3 34 MET cc_start: 0.6387 (tmm) cc_final: 0.6181 (tmm) REVERT: 4 41 HIS cc_start: 0.6844 (m170) cc_final: 0.6416 (m170) REVERT: 6 34 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.8005 (mtm180) REVERT: 6 41 LYS cc_start: 0.7885 (mmtp) cc_final: 0.7681 (mmtp) REVERT: 7 35 ASN cc_start: 0.8602 (p0) cc_final: 0.8299 (p0) REVERT: 8 2 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8146 (ttmm) outliers start: 233 outliers final: 152 residues processed: 1333 average time/residue: 1.2557 time to fit residues: 2875.2470 Evaluate side-chains 1257 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1096 time to evaluate : 5.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 54 TYR Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 36 HIS Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 58 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 87 ARG Chi-restraints excluded: chain i residue 111 ARG Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 64 LYS 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 19 LEU Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 3 LYS Chi-restraints excluded: chain n residue 6 MET Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 74 ILE Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 144 GLU Chi-restraints excluded: chain D residue 182 MET 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 64 LYS Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 85 PHE Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 41 TRP Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 16 MET 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 47 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 43 GLN Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 63 THR Chi-restraints excluded: chain T residue 79 LEU Chi-restraints excluded: chain U residue 32 THR Chi-restraints excluded: chain U residue 34 THR Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain W residue 22 GLU Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 26 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 3 residue 55 HIS Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 6 residue 34 ARG Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 7 residue 25 SER Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 2 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 879 optimal weight: 3.9990 chunk 668 optimal weight: 30.0000 chunk 461 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 424 optimal weight: 20.0000 chunk 597 optimal weight: 10.0000 chunk 892 optimal weight: 10.0000 chunk 945 optimal weight: 5.9990 chunk 466 optimal weight: 10.0000 chunk 846 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 40 GLN g 68 ASN ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 48 ASN j 64 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 64 GLN ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN H 74 ASN H 81 GLN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 ASN R 43 GLN T 81 ASN V 40 ASN ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 153343 Z= 0.287 Angle : 0.690 11.774 229526 Z= 0.353 Chirality : 0.038 0.336 29384 Planarity : 0.005 0.074 12106 Dihedral : 23.127 178.754 76815 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.64 % Favored : 88.25 % Rotamer: Outliers : 5.74 % Allowed : 19.50 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.10), residues: 5354 helix: -1.15 (0.12), residues: 1501 sheet: -2.38 (0.16), residues: 887 loop : -2.86 (0.10), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP g 103 HIS 0.011 0.002 HIS 3 55 PHE 0.033 0.003 PHE P 32 TYR 0.023 0.002 TYR 4 37 ARG 0.010 0.001 ARG q 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1194 time to evaluate : 6.336 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: b 131 LYS cc_start: 0.4920 (ptmt) cc_final: 0.4611 (ptmm) REVERT: b 136 GLU cc_start: 0.7602 (tp30) cc_final: 0.7182 (tp30) REVERT: d 119 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7593 (pp) REVERT: d 122 ASP cc_start: 0.6153 (t70) cc_final: 0.5493 (t70) REVERT: d 160 PHE cc_start: 0.6078 (t80) cc_final: 0.5765 (t80) REVERT: e 96 MET cc_start: 0.6312 (tmm) cc_final: 0.5854 (tmm) REVERT: h 130 TYR cc_start: 0.7988 (m-80) cc_final: 0.7674 (m-80) REVERT: j 10 LEU cc_start: 0.5914 (mp) cc_final: 0.5293 (mt) REVERT: k 114 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7223 (p) REVERT: l 88 GLN cc_start: 0.7654 (pp30) cc_final: 0.7253 (pp30) REVERT: l 108 TYR cc_start: 0.7049 (m-80) cc_final: 0.6464 (m-80) REVERT: m 69 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7106 (tt) REVERT: o 26 GLU cc_start: 0.7199 (pm20) cc_final: 0.6821 (mt-10) REVERT: p 35 GLU cc_start: 0.7229 (pt0) cc_final: 0.6943 (pt0) REVERT: p 84 PHE cc_start: 0.8078 (t80) cc_final: 0.7198 (t80) REVERT: q 57 LEU cc_start: 0.7736 (mt) cc_final: 0.7252 (mp) REVERT: r 70 MET cc_start: 0.6918 (ptp) cc_final: 0.6658 (ptp) REVERT: v 5 GLU cc_start: 0.3997 (OUTLIER) cc_final: 0.3622 (pp20) REVERT: D 22 GLU cc_start: 0.7664 (mp0) cc_final: 0.7367 (mt-10) REVERT: D 53 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.8186 (t-90) REVERT: F 114 LEU cc_start: 0.9002 (tp) cc_final: 0.8460 (pp) REVERT: M 74 VAL cc_start: 0.9188 (t) cc_final: 0.8912 (m) REVERT: N 71 ARG cc_start: 0.5803 (mtp85) cc_final: 0.5579 (mtp180) REVERT: O 5 GLU cc_start: 0.6627 (pp20) cc_final: 0.6264 (pp20) REVERT: Q 24 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8061 (tp) REVERT: Q 25 ILE cc_start: 0.8072 (mt) cc_final: 0.7813 (mm) REVERT: Q 45 GLU cc_start: 0.6739 (mt-10) cc_final: 0.5977 (mm-30) REVERT: Q 84 LYS cc_start: 0.8225 (ptmt) cc_final: 0.7910 (pttt) REVERT: R 14 ARG cc_start: 0.8169 (mtm-85) cc_final: 0.7572 (mtm-85) REVERT: R 94 PHE cc_start: 0.7262 (t80) cc_final: 0.6622 (t80) REVERT: R 110 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: S 51 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8422 (mtpp) REVERT: T 22 LYS cc_start: 0.8122 (mmmt) cc_final: 0.7785 (mttt) REVERT: V 9 THR cc_start: 0.9010 (m) cc_final: 0.8719 (p) REVERT: W 14 GLU cc_start: 0.6958 (pp20) cc_final: 0.6721 (pp20) REVERT: Z 52 LYS cc_start: 0.8194 (mmmm) cc_final: 0.7633 (mtpt) REVERT: 1 38 GLU cc_start: 0.7216 (mm-30) cc_final: 0.7009 (mm-30) REVERT: 1 63 GLU cc_start: 0.5258 (pp20) cc_final: 0.4950 (pp20) REVERT: 2 34 SER cc_start: 0.8007 (m) cc_final: 0.7644 (p) REVERT: 2 53 LEU cc_start: 0.8366 (pp) cc_final: 0.8011 (pp) REVERT: 3 34 MET cc_start: 0.6570 (tmm) cc_final: 0.6322 (tmm) REVERT: 4 38 LYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6697 (pttp) REVERT: 6 34 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7884 (mtm180) REVERT: 7 35 ASN cc_start: 0.8635 (p0) cc_final: 0.8279 (p0) REVERT: 8 2 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8149 (ttmm) REVERT: 8 35 ARG cc_start: 0.8273 (ttp80) cc_final: 0.8072 (ttt90) outliers start: 266 outliers final: 179 residues processed: 1344 average time/residue: 1.2430 time to fit residues: 2877.4364 Evaluate side-chains 1277 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1088 time to evaluate : 5.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 36 HIS Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 58 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 21 LYS Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 113 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 69 THR Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 73 ASN 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 47 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 74 ILE Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 64 THR Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 182 MET 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 64 LYS Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 74 ASN Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 24 VAL Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 41 TRP Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 16 MET 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 47 LEU Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 26 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 1 residue 10 THR Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 3 residue 10 HIS Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 4 residue 38 LYS Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 34 ARG Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 7 residue 25 SER Chi-restraints excluded: chain 8 residue 2 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 787 optimal weight: 20.0000 chunk 536 optimal weight: 20.0000 chunk 13 optimal weight: 30.0000 chunk 703 optimal weight: 5.9990 chunk 390 optimal weight: 20.0000 chunk 806 optimal weight: 10.0000 chunk 653 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 482 optimal weight: 20.0000 chunk 848 optimal weight: 10.0000 chunk 238 optimal weight: 0.3980 overall best weight: 9.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 ASN e 43 ASN ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 29 ASN j 64 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN l 13 GLN l 42 GLN ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 72 HIS q 53 ASN q 64 GLN s 47 HIS ** s 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 3 ASN t 24 GLN v 88 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 8 ASN T 81 ASN U 81 ASN ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 10 HIS ** 4 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 40 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 153343 Z= 0.328 Angle : 0.722 11.494 229526 Z= 0.367 Chirality : 0.039 0.354 29384 Planarity : 0.006 0.076 12106 Dihedral : 23.145 178.014 76815 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.53 % Favored : 87.36 % Rotamer: Outliers : 6.79 % Allowed : 21.03 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.10), residues: 5354 helix: -1.11 (0.12), residues: 1491 sheet: -2.23 (0.16), residues: 903 loop : -2.80 (0.10), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP 0 29 HIS 0.012 0.002 HIS r 69 PHE 0.026 0.003 PHE T 25 TYR 0.023 0.002 TYR m 86 ARG 0.007 0.001 ARG 7 48 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1471 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 1156 time to evaluate : 5.879 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: b 131 LYS cc_start: 0.4903 (ptmt) cc_final: 0.4548 (ptmm) REVERT: b 136 GLU cc_start: 0.7589 (tp30) cc_final: 0.7191 (tp30) REVERT: b 140 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8009 (mt-10) REVERT: c 121 ARG cc_start: 0.8184 (ptp-170) cc_final: 0.7835 (ptt-90) REVERT: d 87 MET cc_start: 0.8028 (tpt) cc_final: 0.7700 (tpt) REVERT: d 160 PHE cc_start: 0.6200 (t80) cc_final: 0.5841 (t80) REVERT: d 182 ARG cc_start: 0.5817 (ptp-170) cc_final: 0.5374 (mmm160) REVERT: d 196 GLU cc_start: 0.7073 (pm20) cc_final: 0.6081 (mp0) REVERT: e 70 ASP cc_start: 0.8058 (m-30) cc_final: 0.7265 (p0) REVERT: e 96 MET cc_start: 0.6360 (tmm) cc_final: 0.5987 (tmm) REVERT: i 29 ASN cc_start: 0.7050 (OUTLIER) cc_final: 0.6647 (m110) REVERT: j 10 LEU cc_start: 0.5989 (mp) cc_final: 0.5398 (mt) REVERT: j 88 MET cc_start: 0.6471 (tmm) cc_final: 0.6089 (ttm) REVERT: k 114 THR cc_start: 0.7542 (OUTLIER) cc_final: 0.7226 (p) REVERT: l 15 LYS cc_start: 0.7119 (pttm) cc_final: 0.6873 (tppt) REVERT: l 103 LEU cc_start: 0.7684 (mp) cc_final: 0.7390 (tt) REVERT: l 108 TYR cc_start: 0.7095 (m-80) cc_final: 0.6409 (m-80) REVERT: o 26 GLU cc_start: 0.7245 (pm20) cc_final: 0.6839 (mt-10) REVERT: p 81 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6203 (ppp) REVERT: p 84 PHE cc_start: 0.7740 (t80) cc_final: 0.7378 (t80) REVERT: q 57 LEU cc_start: 0.7603 (mt) cc_final: 0.7096 (mp) REVERT: s 17 LYS cc_start: 0.6591 (mmtp) cc_final: 0.5685 (ttmt) REVERT: s 47 HIS cc_start: 0.5916 (OUTLIER) cc_final: 0.5695 (m90) REVERT: D 22 GLU cc_start: 0.7762 (mp0) cc_final: 0.7343 (mt-10) REVERT: D 53 HIS cc_start: 0.8610 (OUTLIER) cc_final: 0.8096 (t-90) REVERT: M 74 VAL cc_start: 0.9195 (t) cc_final: 0.8904 (m) REVERT: N 71 ARG cc_start: 0.5814 (mtp85) cc_final: 0.5613 (mtp85) REVERT: P 32 PHE cc_start: 0.7311 (m-10) cc_final: 0.6763 (m-10) REVERT: Q 24 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8024 (tp) REVERT: Q 45 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6019 (mm-30) REVERT: R 14 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: R 110 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: T 22 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7775 (mttt) REVERT: V 9 THR cc_start: 0.9029 (m) cc_final: 0.8733 (p) REVERT: W 14 GLU cc_start: 0.6974 (pp20) cc_final: 0.6712 (pp20) REVERT: X 76 ASN cc_start: 0.7390 (OUTLIER) cc_final: 0.6992 (m-40) REVERT: 1 63 GLU cc_start: 0.5644 (pp20) cc_final: 0.5373 (pp20) REVERT: 2 34 SER cc_start: 0.8045 (m) cc_final: 0.7753 (p) REVERT: 2 53 LEU cc_start: 0.8419 (pp) cc_final: 0.8035 (pp) REVERT: 7 35 ASN cc_start: 0.8665 (p0) cc_final: 0.8327 (p0) REVERT: 8 2 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8150 (ttmm) outliers start: 315 outliers final: 240 residues processed: 1341 average time/residue: 1.2556 time to fit residues: 2902.3348 Evaluate side-chains 1336 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1087 time to evaluate : 5.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 54 TYR Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 36 HIS Chi-restraints excluded: chain d residue 85 ASN Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 58 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 ASP Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 21 LYS Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 61 ARG Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 29 ASN Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 73 ASN 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 l residue 132 THR Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 57 ARG Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 47 HIS Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 41 HIS Chi-restraints excluded: chain v residue 85 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 197 VAL 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 125 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 85 PHE Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 91 VAL Chi-restraints excluded: chain O residue 98 GLU Chi-restraints excluded: chain O residue 99 SER Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 41 TRP Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 96 VAL Chi-restraints excluded: chain P residue 103 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 16 MET 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 47 LEU Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 112 ASP 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 66 THR Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 52 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 37 LYS Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain W residue 22 GLU Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 26 THR Chi-restraints excluded: chain X residue 39 ASN Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 44 HIS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 76 ASN Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Y residue 89 ILE Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 1 residue 10 THR Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 10 HIS Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 3 residue 77 LYS Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 24 VAL Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 7 residue 22 LEU Chi-restraints excluded: chain 7 residue 25 SER Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 2 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 318 optimal weight: 9.9990 chunk 851 optimal weight: 8.9990 chunk 186 optimal weight: 9.9990 chunk 555 optimal weight: 10.0000 chunk 233 optimal weight: 6.9990 chunk 946 optimal weight: 20.0000 chunk 785 optimal weight: 6.9990 chunk 438 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 313 optimal weight: 30.0000 chunk 496 optimal weight: 50.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 61 ASN ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 33 HIS q 64 GLN t 3 ASN t 24 GLN t 45 ASN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 GLN T 81 ASN ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 10 GLN 3 10 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 153343 Z= 0.304 Angle : 0.707 12.017 229526 Z= 0.360 Chirality : 0.038 0.380 29384 Planarity : 0.005 0.088 12106 Dihedral : 23.143 177.439 76815 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.48 % Favored : 87.43 % Rotamer: Outliers : 7.12 % Allowed : 22.24 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.11), residues: 5354 helix: -0.99 (0.13), residues: 1483 sheet: -2.01 (0.17), residues: 889 loop : -2.75 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP g 103 HIS 0.033 0.002 HIS 3 10 PHE 0.029 0.002 PHE T 25 TYR 0.022 0.002 TYR 4 37 ARG 0.011 0.001 ARG q 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1479 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 1149 time to evaluate : 5.947 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: b 136 GLU cc_start: 0.7634 (tp30) cc_final: 0.7279 (tp30) REVERT: c 52 SER cc_start: 0.6764 (p) cc_final: 0.6354 (m) REVERT: c 94 THR cc_start: 0.5529 (OUTLIER) cc_final: 0.5283 (p) REVERT: c 121 ARG cc_start: 0.8195 (ptp-170) cc_final: 0.7890 (ptt-90) REVERT: d 59 TYR cc_start: 0.6514 (OUTLIER) cc_final: 0.6285 (m-80) REVERT: d 87 MET cc_start: 0.7989 (tpt) cc_final: 0.7769 (tpt) REVERT: d 160 PHE cc_start: 0.6087 (t80) cc_final: 0.5770 (t80) REVERT: d 182 ARG cc_start: 0.5935 (ptp-170) cc_final: 0.5334 (mmm160) REVERT: d 196 GLU cc_start: 0.7072 (pm20) cc_final: 0.6756 (pm20) REVERT: e 70 ASP cc_start: 0.7998 (m-30) cc_final: 0.7247 (p0) REVERT: e 96 MET cc_start: 0.6294 (tmm) cc_final: 0.5988 (tmm) REVERT: h 57 GLN cc_start: 0.6999 (mm110) cc_final: 0.6589 (mm-40) REVERT: j 10 LEU cc_start: 0.6253 (mp) cc_final: 0.5810 (mt) REVERT: k 114 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7207 (p) REVERT: l 15 LYS cc_start: 0.7115 (pttm) cc_final: 0.6894 (tppt) REVERT: l 103 LEU cc_start: 0.7613 (mp) cc_final: 0.7399 (tt) REVERT: l 108 TYR cc_start: 0.7261 (OUTLIER) cc_final: 0.6602 (m-80) REVERT: o 26 GLU cc_start: 0.7256 (pm20) cc_final: 0.6863 (mt-10) REVERT: p 35 GLU cc_start: 0.7218 (pt0) cc_final: 0.6931 (pt0) REVERT: p 81 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6290 (ppp) REVERT: q 76 ARG cc_start: 0.7409 (ttp80) cc_final: 0.7076 (ttp80) REVERT: D 22 GLU cc_start: 0.7794 (mp0) cc_final: 0.7435 (mt-10) REVERT: D 53 HIS cc_start: 0.8619 (OUTLIER) cc_final: 0.8121 (t-90) REVERT: M 74 VAL cc_start: 0.9183 (t) cc_final: 0.8904 (m) REVERT: Q 24 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8013 (tp) REVERT: Q 45 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6213 (mm-30) REVERT: T 22 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7734 (mtmt) REVERT: U 6 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: V 9 THR cc_start: 0.9027 (m) cc_final: 0.8743 (p) REVERT: V 37 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8420 (ptpp) REVERT: W 14 GLU cc_start: 0.6920 (pp20) cc_final: 0.6711 (pp20) REVERT: 1 38 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7086 (mm-30) REVERT: 1 63 GLU cc_start: 0.5720 (pp20) cc_final: 0.5510 (pp20) REVERT: 2 34 SER cc_start: 0.8111 (m) cc_final: 0.7811 (p) REVERT: 2 53 LEU cc_start: 0.8418 (pp) cc_final: 0.8023 (pp) REVERT: 4 38 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7053 (pttp) REVERT: 7 35 ASN cc_start: 0.8632 (p0) cc_final: 0.8304 (p0) REVERT: 8 2 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8193 (ttmm) REVERT: 8 35 ARG cc_start: 0.8458 (ttt90) cc_final: 0.8142 (ttt90) outliers start: 330 outliers final: 251 residues processed: 1333 average time/residue: 1.2439 time to fit residues: 2858.9282 Evaluate side-chains 1349 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1087 time to evaluate : 5.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 65 ILE Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 36 HIS Chi-restraints excluded: chain d residue 59 TYR Chi-restraints excluded: chain d residue 85 ASN Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 58 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 ASP Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 21 LYS Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 54 SER Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain j residue 35 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain k residue 114 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 46 VAL Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 108 TYR Chi-restraints excluded: chain l residue 118 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 57 ARG Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 33 HIS Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 78 VAL Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 182 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 208 LEU 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 125 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 148 ILE Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 85 PHE Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain P residue 10 ARG Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 41 TRP Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 16 MET 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 47 LEU Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 6 LEU Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 36 ASP Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 37 LYS Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain W residue 22 GLU Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 16 ASP Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 26 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 77 LYS Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 38 LYS Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 6 residue 42 VAL Chi-restraints excluded: chain 7 residue 22 LEU Chi-restraints excluded: chain 7 residue 25 SER Chi-restraints excluded: chain 7 residue 29 THR Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 22 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 912 optimal weight: 9.9990 chunk 106 optimal weight: 30.0000 chunk 539 optimal weight: 30.0000 chunk 691 optimal weight: 0.0670 chunk 535 optimal weight: 20.0000 chunk 796 optimal weight: 10.0000 chunk 528 optimal weight: 10.0000 chunk 942 optimal weight: 0.9990 chunk 589 optimal weight: 10.0000 chunk 574 optimal weight: 20.0000 chunk 435 optimal weight: 20.0000 overall best weight: 6.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 16 ASN ** j 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 33 HIS q 64 GLN t 3 ASN t 24 GLN t 77 GLN v 97 ASN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 97 ASN T 81 ASN U 11 GLN Y 38 ASN ** 3 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 153343 Z= 0.237 Angle : 0.657 12.433 229526 Z= 0.336 Chirality : 0.036 0.428 29384 Planarity : 0.005 0.085 12106 Dihedral : 23.083 177.226 76815 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.88 % Favored : 88.03 % Rotamer: Outliers : 6.38 % Allowed : 24.27 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.11), residues: 5354 helix: -0.80 (0.13), residues: 1489 sheet: -1.96 (0.17), residues: 900 loop : -2.70 (0.10), residues: 2965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP g 103 HIS 0.007 0.001 HIS k 118 PHE 0.031 0.002 PHE T 25 TYR 0.021 0.002 TYR G 143 ARG 0.011 0.001 ARG X 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1162 time to evaluate : 5.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 136 GLU cc_start: 0.7576 (tp30) cc_final: 0.7222 (tp30) REVERT: b 217 MET cc_start: 0.7840 (mmp) cc_final: 0.7468 (mmm) REVERT: c 52 SER cc_start: 0.6788 (p) cc_final: 0.6382 (m) REVERT: c 94 THR cc_start: 0.5584 (OUTLIER) cc_final: 0.5359 (p) REVERT: d 87 MET cc_start: 0.7991 (tpt) cc_final: 0.7769 (tpt) REVERT: d 160 PHE cc_start: 0.6115 (t80) cc_final: 0.5817 (t80) REVERT: d 182 ARG cc_start: 0.6257 (ptp-170) cc_final: 0.5508 (tpt170) REVERT: d 196 GLU cc_start: 0.7114 (pm20) cc_final: 0.6588 (pm20) REVERT: e 70 ASP cc_start: 0.7970 (m-30) cc_final: 0.7319 (p0) REVERT: e 96 MET cc_start: 0.6299 (tmm) cc_final: 0.6052 (tmm) REVERT: h 130 TYR cc_start: 0.8064 (m-10) cc_final: 0.7714 (m-80) REVERT: j 10 LEU cc_start: 0.6416 (mp) cc_final: 0.6082 (mt) REVERT: j 88 MET cc_start: 0.6294 (tmm) cc_final: 0.5869 (ttm) REVERT: k 114 THR cc_start: 0.7297 (m) cc_final: 0.7074 (p) REVERT: l 38 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7335 (mt) REVERT: l 108 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: m 109 ARG cc_start: 0.5216 (OUTLIER) cc_final: 0.4762 (mpp-170) REVERT: o 26 GLU cc_start: 0.7206 (pm20) cc_final: 0.6801 (mt-10) REVERT: D 22 GLU cc_start: 0.7788 (mp0) cc_final: 0.7433 (mt-10) REVERT: D 53 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.8109 (t-90) REVERT: D 212 TRP cc_start: 0.7651 (m100) cc_final: 0.7407 (m100) REVERT: H 19 PHE cc_start: 0.5811 (OUTLIER) cc_final: 0.3928 (p90) REVERT: H 41 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.5744 (mtm) REVERT: M 74 VAL cc_start: 0.9162 (t) cc_final: 0.8892 (m) REVERT: N 13 ASN cc_start: 0.7369 (m110) cc_final: 0.6526 (p0) REVERT: N 73 ASP cc_start: 0.7627 (p0) cc_final: 0.6964 (p0) REVERT: P 32 PHE cc_start: 0.7030 (m-10) cc_final: 0.6327 (m-10) REVERT: P 41 TRP cc_start: 0.7871 (OUTLIER) cc_final: 0.7611 (p90) REVERT: Q 24 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7991 (tp) REVERT: Q 45 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6237 (mm-30) REVERT: R 14 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7374 (mtm-85) REVERT: R 110 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: S 82 LYS cc_start: 0.7920 (mmmm) cc_final: 0.7563 (mttt) REVERT: V 9 THR cc_start: 0.8996 (m) cc_final: 0.8735 (p) REVERT: 2 3 LYS cc_start: 0.7968 (ptmt) cc_final: 0.7532 (mtmt) REVERT: 2 34 SER cc_start: 0.8177 (m) cc_final: 0.7922 (p) REVERT: 2 53 LEU cc_start: 0.8432 (pp) cc_final: 0.8074 (pp) REVERT: 4 7 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7197 (ttm170) REVERT: 4 38 LYS cc_start: 0.7103 (OUTLIER) cc_final: 0.6879 (pttp) REVERT: 7 35 ASN cc_start: 0.8620 (p0) cc_final: 0.8351 (p0) REVERT: 8 2 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8223 (ttmm) outliers start: 296 outliers final: 229 residues processed: 1322 average time/residue: 1.2330 time to fit residues: 2816.3824 Evaluate side-chains 1338 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1096 time to evaluate : 5.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 94 THR Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 58 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 21 LYS Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 38 LEU Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 108 TYR Chi-restraints excluded: chain l residue 118 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 61 LEU Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 69 ILE Chi-restraints excluded: chain O residue 85 PHE Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 107 SER Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 41 TRP Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 16 MET 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 47 LEU Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 91 ASN Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 37 LYS Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain W residue 22 GLU Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 26 THR Chi-restraints excluded: chain X residue 39 ASN Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 44 HIS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 80 ARG Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 1 residue 22 LYS Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 10 HIS Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 77 LYS Chi-restraints excluded: chain 4 residue 7 ARG Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 38 LYS Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 7 residue 25 SER Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 22 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 583 optimal weight: 20.0000 chunk 376 optimal weight: 7.9990 chunk 562 optimal weight: 30.0000 chunk 283 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 599 optimal weight: 50.0000 chunk 642 optimal weight: 20.0000 chunk 466 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 740 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 GLN j 56 HIS j 64 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 13 GLN l 25 ASN ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 64 GLN t 3 ASN t 24 GLN ** E 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 ASN ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 153343 Z= 0.289 Angle : 0.695 11.997 229526 Z= 0.354 Chirality : 0.038 0.435 29384 Planarity : 0.005 0.113 12106 Dihedral : 23.100 177.104 76815 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.68 % Favored : 87.22 % Rotamer: Outliers : 6.69 % Allowed : 24.65 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.11), residues: 5354 helix: -0.80 (0.13), residues: 1477 sheet: -1.93 (0.17), residues: 895 loop : -2.70 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP g 103 HIS 0.014 0.002 HIS 3 55 PHE 0.032 0.002 PHE T 25 TYR 0.024 0.002 TYR H 83 ARG 0.011 0.001 ARG t 10 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1426 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 310 poor density : 1116 time to evaluate : 5.886 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 120 MET cc_start: 0.8114 (ppp) cc_final: 0.7845 (tmm) REVERT: b 136 GLU cc_start: 0.7597 (tp30) cc_final: 0.7243 (tp30) REVERT: c 52 SER cc_start: 0.6800 (p) cc_final: 0.6353 (m) REVERT: e 70 ASP cc_start: 0.7947 (m-30) cc_final: 0.7246 (p0) REVERT: e 122 ASP cc_start: 0.7112 (p0) cc_final: 0.6817 (p0) REVERT: g 31 MET cc_start: 0.5438 (mmt) cc_final: 0.5008 (mmm) REVERT: j 10 LEU cc_start: 0.6409 (mp) cc_final: 0.5994 (mt) REVERT: j 74 ILE cc_start: 0.6973 (mp) cc_final: 0.6735 (mm) REVERT: j 88 MET cc_start: 0.6183 (tmm) cc_final: 0.5775 (ttm) REVERT: k 33 THR cc_start: 0.6102 (p) cc_final: 0.5848 (p) REVERT: k 114 THR cc_start: 0.7371 (m) cc_final: 0.7158 (p) REVERT: l 38 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7361 (mt) REVERT: l 108 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6726 (m-80) REVERT: m 109 ARG cc_start: 0.5520 (OUTLIER) cc_final: 0.4925 (mpp-170) REVERT: n 39 LEU cc_start: 0.7616 (pp) cc_final: 0.6673 (tp) REVERT: o 26 GLU cc_start: 0.7237 (pm20) cc_final: 0.6855 (mt-10) REVERT: o 76 GLN cc_start: 0.7008 (tp40) cc_final: 0.6757 (tp40) REVERT: p 81 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5881 (ppp) REVERT: r 70 MET cc_start: 0.7230 (ptp) cc_final: 0.6884 (ptp) REVERT: D 22 GLU cc_start: 0.7782 (mp0) cc_final: 0.7433 (mt-10) REVERT: D 53 HIS cc_start: 0.8597 (OUTLIER) cc_final: 0.8098 (t-90) REVERT: D 212 TRP cc_start: 0.7796 (m100) cc_final: 0.7510 (m100) REVERT: H 19 PHE cc_start: 0.5580 (OUTLIER) cc_final: 0.3682 (p90) REVERT: H 41 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5965 (mtm) REVERT: M 46 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7566 (p) REVERT: M 74 VAL cc_start: 0.9160 (t) cc_final: 0.8885 (m) REVERT: N 13 ASN cc_start: 0.7227 (m110) cc_final: 0.6529 (p0) REVERT: Q 24 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7992 (tp) REVERT: Q 45 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6249 (mm-30) REVERT: Q 67 ARG cc_start: 0.7468 (mmm160) cc_final: 0.7162 (mmp-170) REVERT: R 14 ARG cc_start: 0.8282 (mtm-85) cc_final: 0.7413 (mtm-85) REVERT: R 110 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: S 8 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6700 (mt-10) REVERT: S 51 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8493 (mtpp) REVERT: T 81 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7119 (t0) REVERT: U 6 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: U 97 ILE cc_start: 0.8712 (mm) cc_final: 0.8473 (mm) REVERT: V 9 THR cc_start: 0.9014 (m) cc_final: 0.8730 (p) REVERT: Z 52 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7874 (mtpt) REVERT: 2 3 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7583 (mtmt) REVERT: 2 34 SER cc_start: 0.8232 (m) cc_final: 0.7976 (p) REVERT: 2 53 LEU cc_start: 0.8481 (pp) cc_final: 0.8115 (pp) REVERT: 4 7 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7286 (ttm170) REVERT: 4 38 LYS cc_start: 0.7216 (OUTLIER) cc_final: 0.6977 (pttp) REVERT: 7 35 ASN cc_start: 0.8637 (p0) cc_final: 0.8371 (p0) REVERT: 8 2 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8191 (ttmm) outliers start: 310 outliers final: 258 residues processed: 1289 average time/residue: 1.2365 time to fit residues: 2768.8371 Evaluate side-chains 1360 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1085 time to evaluate : 5.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 63 MET Chi-restraints excluded: chain d residue 89 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 58 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 135 ASN Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 ASP Chi-restraints excluded: chain f residue 63 VAL Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 21 LYS Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 61 ARG Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 18 VAL Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain i residue 77 GLN Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 38 LEU Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 79 TYR Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 108 TYR Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 118 SER Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain m residue 109 ARG Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 48 THR Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 76 SER Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain D residue 8 ILE Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 185 ASP Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 101 ASP Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 85 PHE Chi-restraints excluded: chain O residue 86 GLU Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 16 MET 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 47 LEU Chi-restraints excluded: chain Q residue 49 THR Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 30 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 91 ASN Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 10 ILE Chi-restraints excluded: chain V residue 37 LYS Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain W residue 22 GLU Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 26 THR Chi-restraints excluded: chain X residue 39 ASN Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 44 HIS Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain X residue 80 ARG Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain Z residue 52 LYS Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 1 residue 10 THR Chi-restraints excluded: chain 1 residue 22 LYS Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 30 LYS Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 10 HIS Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 77 LYS Chi-restraints excluded: chain 4 residue 7 ARG Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 38 LYS Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 7 residue 22 LEU Chi-restraints excluded: chain 7 residue 25 SER Chi-restraints excluded: chain 7 residue 56 LYS Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 22 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 857 optimal weight: 30.0000 chunk 903 optimal weight: 6.9990 chunk 823 optimal weight: 5.9990 chunk 878 optimal weight: 4.9990 chunk 902 optimal weight: 8.9990 chunk 528 optimal weight: 10.0000 chunk 382 optimal weight: 10.0000 chunk 689 optimal weight: 0.0370 chunk 269 optimal weight: 8.9990 chunk 793 optimal weight: 7.9990 chunk 830 optimal weight: 20.0000 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 44 ASN c 122 GLN ** f 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 64 GLN t 3 ASN t 24 GLN ** F 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 HIS T 81 ASN ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 153343 Z= 0.208 Angle : 0.635 13.743 229526 Z= 0.325 Chirality : 0.035 0.432 29384 Planarity : 0.005 0.084 12106 Dihedral : 23.041 177.447 76815 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.43 % Favored : 88.51 % Rotamer: Outliers : 6.13 % Allowed : 25.45 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.11), residues: 5354 helix: -0.67 (0.13), residues: 1491 sheet: -1.78 (0.17), residues: 886 loop : -2.64 (0.11), residues: 2977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP g 103 HIS 0.016 0.001 HIS 3 55 PHE 0.042 0.002 PHE G 114 TYR 0.026 0.002 TYR d 198 ARG 0.010 0.001 ARG u 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1137 time to evaluate : 5.925 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: b 120 MET cc_start: 0.8141 (ppp) cc_final: 0.7910 (tmm) REVERT: b 136 GLU cc_start: 0.7517 (tp30) cc_final: 0.7188 (tp30) REVERT: c 52 SER cc_start: 0.6765 (p) cc_final: 0.6442 (m) REVERT: e 70 ASP cc_start: 0.7938 (m-30) cc_final: 0.7337 (p0) REVERT: g 31 MET cc_start: 0.5352 (mmt) cc_final: 0.5086 (mmm) REVERT: h 130 TYR cc_start: 0.8037 (m-10) cc_final: 0.7679 (m-80) REVERT: j 10 LEU cc_start: 0.6511 (mp) cc_final: 0.6144 (mt) REVERT: j 74 ILE cc_start: 0.6990 (mp) cc_final: 0.6741 (mm) REVERT: j 88 MET cc_start: 0.6209 (tmm) cc_final: 0.5788 (ttm) REVERT: k 16 ILE cc_start: 0.6522 (pt) cc_final: 0.6171 (pt) REVERT: k 33 THR cc_start: 0.5909 (p) cc_final: 0.5685 (p) REVERT: l 38 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7151 (mt) REVERT: l 108 TYR cc_start: 0.7358 (OUTLIER) cc_final: 0.6632 (m-80) REVERT: m 110 LYS cc_start: 0.5906 (ptmm) cc_final: 0.5518 (ptmm) REVERT: n 38 LYS cc_start: 0.7361 (tptp) cc_final: 0.6933 (pttp) REVERT: n 39 LEU cc_start: 0.7009 (pp) cc_final: 0.6073 (tp) REVERT: o 26 GLU cc_start: 0.7162 (pm20) cc_final: 0.6818 (mt-10) REVERT: p 81 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6162 (ppp) REVERT: r 70 MET cc_start: 0.7239 (ptp) cc_final: 0.7035 (ptp) REVERT: D 22 GLU cc_start: 0.7794 (mp0) cc_final: 0.7326 (mt-10) REVERT: D 53 HIS cc_start: 0.8555 (OUTLIER) cc_final: 0.8107 (t-90) REVERT: H 19 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.3870 (p90) REVERT: H 41 MET cc_start: 0.6382 (OUTLIER) cc_final: 0.5602 (mtm) REVERT: H 89 LEU cc_start: 0.8475 (mt) cc_final: 0.8265 (mm) REVERT: M 74 VAL cc_start: 0.9150 (t) cc_final: 0.8875 (m) REVERT: N 13 ASN cc_start: 0.6962 (m110) cc_final: 0.6685 (p0) REVERT: P 41 TRP cc_start: 0.7772 (p90) cc_final: 0.7436 (p90) REVERT: P 112 GLU cc_start: 0.7573 (pp20) cc_final: 0.7271 (pm20) REVERT: Q 24 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7964 (tp) REVERT: Q 45 GLU cc_start: 0.6845 (mt-10) cc_final: 0.6003 (mm-30) REVERT: R 14 ARG cc_start: 0.8243 (mtm-85) cc_final: 0.7405 (mtm-85) REVERT: R 110 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7019 (mp0) REVERT: S 8 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6578 (mt-10) REVERT: S 51 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8470 (mtpp) REVERT: S 82 LYS cc_start: 0.7907 (mmmm) cc_final: 0.7459 (mttt) REVERT: U 97 ILE cc_start: 0.8671 (mm) cc_final: 0.8426 (mm) REVERT: V 9 THR cc_start: 0.8959 (m) cc_final: 0.8705 (p) REVERT: 2 3 LYS cc_start: 0.7803 (ptmt) cc_final: 0.7405 (mtmt) REVERT: 2 34 SER cc_start: 0.8195 (m) cc_final: 0.7954 (p) REVERT: 2 53 LEU cc_start: 0.8429 (pp) cc_final: 0.8063 (pp) REVERT: 3 77 LYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5631 (mmmt) REVERT: 4 7 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7169 (ttm170) REVERT: 7 35 ASN cc_start: 0.8589 (p0) cc_final: 0.8314 (p0) outliers start: 284 outliers final: 224 residues processed: 1293 average time/residue: 1.2324 time to fit residues: 2761.5096 Evaluate side-chains 1319 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1084 time to evaluate : 5.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 ASP Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 26 LEU Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain i residue 77 GLN Chi-restraints excluded: chain j residue 35 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 38 LEU Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 108 TYR Chi-restraints excluded: chain l residue 115 LEU Chi-restraints excluded: chain l residue 118 SER Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 95 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 61 LEU Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 148 GLN Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain H residue 150 SER Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 85 PHE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 16 MET 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 47 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 69 VAL Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 117 LEU Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 81 ASN Chi-restraints excluded: chain T residue 91 ASN Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 37 LYS Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain W residue 22 GLU Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 26 THR Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 10 HIS Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 77 LYS Chi-restraints excluded: chain 4 residue 7 ARG Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 4 residue 39 LEU Chi-restraints excluded: chain 5 residue 10 THR Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 7 residue 56 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 875 optimal weight: 0.9980 chunk 576 optimal weight: 30.0000 chunk 928 optimal weight: 7.9990 chunk 566 optimal weight: 10.0000 chunk 440 optimal weight: 20.0000 chunk 645 optimal weight: 10.0000 chunk 974 optimal weight: 0.9980 chunk 896 optimal weight: 9.9990 chunk 775 optimal weight: 8.9990 chunk 80 optimal weight: 20.0000 chunk 599 optimal weight: 50.0000 overall best weight: 5.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 149 ASN ** f 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN q 64 GLN t 24 GLN F 82 GLN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 ASN T 81 ASN ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 38 ASN 5 42 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 153343 Z= 0.226 Angle : 0.648 14.027 229526 Z= 0.330 Chirality : 0.035 0.419 29384 Planarity : 0.005 0.086 12106 Dihedral : 23.020 177.168 76815 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.38 % Favored : 87.56 % Rotamer: Outliers : 5.52 % Allowed : 25.82 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.11), residues: 5354 helix: -0.61 (0.13), residues: 1473 sheet: -1.82 (0.17), residues: 903 loop : -2.58 (0.11), residues: 2978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP g 103 HIS 0.013 0.001 HIS 3 55 PHE 0.037 0.002 PHE d 86 TYR 0.023 0.002 TYR F 97 ARG 0.013 0.001 ARG n 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10708 Ramachandran restraints generated. 5354 Oldfield, 0 Emsley, 5354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1105 time to evaluate : 5.972 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 120 MET cc_start: 0.8206 (ppp) cc_final: 0.7960 (tmm) REVERT: b 136 GLU cc_start: 0.7555 (tp30) cc_final: 0.7254 (tp30) REVERT: c 52 SER cc_start: 0.6849 (p) cc_final: 0.6444 (m) REVERT: e 70 ASP cc_start: 0.7837 (m-30) cc_final: 0.7306 (p0) REVERT: e 122 ASP cc_start: 0.6893 (p0) cc_final: 0.6637 (p0) REVERT: g 31 MET cc_start: 0.5421 (mmt) cc_final: 0.5102 (mmm) REVERT: h 130 TYR cc_start: 0.8039 (m-10) cc_final: 0.7679 (m-80) REVERT: j 10 LEU cc_start: 0.6434 (mp) cc_final: 0.6083 (mt) REVERT: j 74 ILE cc_start: 0.6995 (mp) cc_final: 0.6731 (mm) REVERT: k 16 ILE cc_start: 0.6412 (pt) cc_final: 0.6049 (pt) REVERT: k 33 THR cc_start: 0.5968 (p) cc_final: 0.5765 (p) REVERT: l 38 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7265 (mt) REVERT: l 47 CYS cc_start: 0.6882 (t) cc_final: 0.6559 (t) REVERT: l 108 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6643 (m-80) REVERT: o 26 GLU cc_start: 0.7091 (pm20) cc_final: 0.6688 (mt-10) REVERT: p 81 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6022 (ppp) REVERT: p 83 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7750 (mttp) REVERT: r 70 MET cc_start: 0.7175 (ptp) cc_final: 0.6956 (ptp) REVERT: D 22 GLU cc_start: 0.7819 (mp0) cc_final: 0.7327 (mt-10) REVERT: D 53 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.8070 (t-90) REVERT: E 127 PHE cc_start: 0.7848 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: H 19 PHE cc_start: 0.5948 (OUTLIER) cc_final: 0.3850 (p90) REVERT: H 41 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5831 (mtm) REVERT: H 89 LEU cc_start: 0.8494 (mt) cc_final: 0.8279 (mm) REVERT: M 74 VAL cc_start: 0.9149 (t) cc_final: 0.8879 (m) REVERT: P 41 TRP cc_start: 0.7774 (p90) cc_final: 0.7449 (p90) REVERT: P 112 GLU cc_start: 0.7720 (pp20) cc_final: 0.6904 (pm20) REVERT: Q 24 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7981 (tp) REVERT: Q 45 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6227 (mm-30) REVERT: R 14 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.7417 (mtm-85) REVERT: R 110 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: S 8 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6561 (mt-10) REVERT: S 51 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8447 (mtpp) REVERT: S 82 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7448 (mttt) REVERT: U 6 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7026 (tp30) REVERT: U 97 ILE cc_start: 0.8661 (mm) cc_final: 0.8432 (mm) REVERT: V 9 THR cc_start: 0.8988 (m) cc_final: 0.8720 (p) REVERT: 0 10 ARG cc_start: 0.5182 (mtt90) cc_final: 0.4846 (mtt90) REVERT: 1 10 THR cc_start: 0.7466 (p) cc_final: 0.7117 (m) REVERT: 2 3 LYS cc_start: 0.7911 (ptmt) cc_final: 0.7492 (mtmt) REVERT: 2 34 SER cc_start: 0.8186 (m) cc_final: 0.7959 (p) REVERT: 2 53 LEU cc_start: 0.8496 (pp) cc_final: 0.8111 (pp) REVERT: 3 77 LYS cc_start: 0.6111 (OUTLIER) cc_final: 0.5657 (mmmt) REVERT: 4 7 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7217 (ttm170) REVERT: 7 35 ASN cc_start: 0.8603 (p0) cc_final: 0.8326 (p0) outliers start: 256 outliers final: 219 residues processed: 1250 average time/residue: 1.2070 time to fit residues: 2609.8979 Evaluate side-chains 1306 residues out of total 4636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1074 time to evaluate : 5.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 14 VAL Chi-restraints excluded: chain b residue 16 PHE Chi-restraints excluded: chain b residue 80 VAL Chi-restraints excluded: chain b residue 90 PHE Chi-restraints excluded: chain b residue 134 VAL Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 212 LEU Chi-restraints excluded: chain c residue 8 ILE Chi-restraints excluded: chain c residue 56 ILE Chi-restraints excluded: chain c residue 64 ASN Chi-restraints excluded: chain c residue 97 LYS Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 182 ASP Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 38 VAL Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 86 THR Chi-restraints excluded: chain e residue 103 THR Chi-restraints excluded: chain e residue 124 LEU Chi-restraints excluded: chain e residue 144 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 3 THR Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 17 ASP Chi-restraints excluded: chain g residue 11 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 61 VAL Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 94 MET Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain i residue 24 VAL Chi-restraints excluded: chain i residue 49 ASP Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain i residue 77 GLN Chi-restraints excluded: chain j residue 35 ASP Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 31 ILE Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 69 THR Chi-restraints excluded: chain k residue 81 THR Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 28 PHE Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 38 LEU Chi-restraints excluded: chain l residue 64 LYS Chi-restraints excluded: chain l residue 73 ASN Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 108 TYR Chi-restraints excluded: chain l residue 118 SER Chi-restraints excluded: chain m residue 9 ILE Chi-restraints excluded: chain m residue 13 LYS Chi-restraints excluded: chain m residue 47 ASP Chi-restraints excluded: chain m residue 53 LEU Chi-restraints excluded: chain m residue 102 THR Chi-restraints excluded: chain n residue 33 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 61 LEU Chi-restraints excluded: chain p residue 81 MET Chi-restraints excluded: chain q residue 11 VAL Chi-restraints excluded: chain q residue 29 THR Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 64 GLN Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain s residue 22 GLN Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 54 VAL Chi-restraints excluded: chain t residue 58 ASP Chi-restraints excluded: chain t residue 79 MET Chi-restraints excluded: chain u residue 28 THR Chi-restraints excluded: chain u residue 29 ILE Chi-restraints excluded: chain v residue 5 GLU Chi-restraints excluded: chain v residue 28 LEU Chi-restraints excluded: chain v residue 42 VAL Chi-restraints excluded: chain D residue 9 THR Chi-restraints excluded: chain D residue 15 MET Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 69 ASN Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain E residue 93 ASN Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 194 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 170 ILE Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 138 PHE Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 41 MET Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 102 ASP Chi-restraints excluded: chain H residue 124 SER Chi-restraints excluded: chain M residue 20 ASP Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 65 PHE Chi-restraints excluded: chain M residue 89 THR Chi-restraints excluded: chain M residue 105 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 28 SER Chi-restraints excluded: chain N residue 42 THR Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 30 THR Chi-restraints excluded: chain O residue 85 PHE Chi-restraints excluded: chain O residue 89 THR Chi-restraints excluded: chain O residue 112 LEU Chi-restraints excluded: chain O residue 126 HIS Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 54 MET Chi-restraints excluded: chain P residue 74 TYR Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 94 ILE Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 11 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 16 MET 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 47 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 112 ASP Chi-restraints excluded: chain Q residue 118 ILE Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 20 THR Chi-restraints excluded: chain R residue 31 LEU Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain S residue 8 GLU Chi-restraints excluded: chain S residue 12 LYS Chi-restraints excluded: chain S residue 27 THR Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 73 GLU Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 17 THR Chi-restraints excluded: chain T residue 18 ILE Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 39 VAL Chi-restraints excluded: chain T residue 91 ASN Chi-restraints excluded: chain U residue 6 GLU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain V residue 12 ILE Chi-restraints excluded: chain V residue 38 LEU Chi-restraints excluded: chain V residue 39 THR Chi-restraints excluded: chain V residue 40 ASN Chi-restraints excluded: chain V residue 53 SER Chi-restraints excluded: chain V residue 63 ASP Chi-restraints excluded: chain V residue 71 VAL Chi-restraints excluded: chain V residue 107 VAL Chi-restraints excluded: chain W residue 22 GLU Chi-restraints excluded: chain W residue 72 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain X residue 7 ASP Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 24 ILE Chi-restraints excluded: chain X residue 40 ILE Chi-restraints excluded: chain X residue 57 LEU Chi-restraints excluded: chain X residue 59 THR Chi-restraints excluded: chain X residue 75 THR Chi-restraints excluded: chain Y residue 38 ASN Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 71 LYS Chi-restraints excluded: chain Y residue 76 ASP Chi-restraints excluded: chain Z residue 23 ASP Chi-restraints excluded: chain Z residue 29 LEU Chi-restraints excluded: chain Z residue 48 GLN Chi-restraints excluded: chain Z residue 59 VAL Chi-restraints excluded: chain 0 residue 33 LEU Chi-restraints excluded: chain 0 residue 39 LEU Chi-restraints excluded: chain 1 residue 23 GLU Chi-restraints excluded: chain 1 residue 50 ILE Chi-restraints excluded: chain 1 residue 53 LEU Chi-restraints excluded: chain 1 residue 62 ILE Chi-restraints excluded: chain 2 residue 6 ILE Chi-restraints excluded: chain 2 residue 7 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 28 LEU Chi-restraints excluded: chain 2 residue 54 VAL Chi-restraints excluded: chain 3 residue 10 HIS Chi-restraints excluded: chain 3 residue 43 TYR Chi-restraints excluded: chain 3 residue 74 PHE Chi-restraints excluded: chain 3 residue 77 LYS Chi-restraints excluded: chain 4 residue 7 ARG Chi-restraints excluded: chain 4 residue 11 THR Chi-restraints excluded: chain 4 residue 22 ILE Chi-restraints excluded: chain 6 residue 14 SER Chi-restraints excluded: chain 6 residue 27 ASN Chi-restraints excluded: chain 7 residue 56 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 978 random chunks: chunk 475 optimal weight: 20.0000 chunk 616 optimal weight: 10.0000 chunk 826 optimal weight: 5.9990 chunk 237 optimal weight: 0.3980 chunk 715 optimal weight: 7.9990 chunk 114 optimal weight: 30.0000 chunk 215 optimal weight: 0.8980 chunk 777 optimal weight: 7.9990 chunk 325 optimal weight: 4.9990 chunk 797 optimal weight: 20.0000 chunk 98 optimal weight: 40.0000 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 137 GLN ** e 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 149 ASN ** f 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 64 GLN ** k 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 64 GLN t 24 GLN v 33 ASN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 70 ASN T 81 ASN ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 45 HIS ** 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 = 0.3770 r_free = 0.3770 target = 0.089862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.071575 restraints weight = 578646.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.072990 restraints weight = 241477.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.073179 restraints weight = 144120.725| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 153343 Z= 0.181 Angle : 0.619 18.088 229526 Z= 0.316 Chirality : 0.034 0.405 29384 Planarity : 0.005 0.084 12106 Dihedral : 22.986 177.494 76815 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.37 % Favored : 88.57 % Rotamer: Outliers : 5.00 % Allowed : 26.55 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 1.01 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.11), residues: 5354 helix: -0.48 (0.13), residues: 1469 sheet: -1.65 (0.17), residues: 871 loop : -2.53 (0.11), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP g 103 HIS 0.012 0.001 HIS 3 55 PHE 0.037 0.002 PHE T 25 TYR 0.028 0.002 TYR f 8 ARG 0.020 0.001 ARG O 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 38898.65 seconds wall clock time: 677 minutes 1.14 seconds (40621.14 seconds total)