Starting phenix.real_space_refine on Tue Mar 19 13:37:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/03_2024/7ope_13017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/03_2024/7ope_13017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/03_2024/7ope_13017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/03_2024/7ope_13017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/03_2024/7ope_13017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ope_13017/03_2024/7ope_13017.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 2994 5.49 5 S 102 5.16 5 C 47195 2.51 5 N 17431 2.21 5 O 26140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 3": "NH1" <-> "NH2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ARG 78": "NH1" <-> "NH2" Residue "H ARG 80": "NH1" <-> "NH2" Residue "H GLU 81": "OE1" <-> "OE2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H GLU 94": "OE1" <-> "OE2" Residue "H ARG 110": "NH1" <-> "NH2" Residue "H ARG 112": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H GLU 164": "OE1" <-> "OE2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "1 GLU 62": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 93862 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 60436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2814, 60436 Classifications: {'RNA': 2814} Modifications used: {'5*END': 1, 'rna2p_pur': 282, 'rna2p_pyr': 144, 'rna3p_pur': 1354, 'rna3p_pyr': 1034} Link IDs: {'rna2p': 426, 'rna3p': 2387} Chain breaks: 6 Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 97} Chain: "E" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "F" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "G" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "H" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1387 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "I" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "K" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 974 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 10, 'TRANS': 121} Chain: "L" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 886 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 2 Chain: "N" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1124 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "O" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 921 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "P" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1082 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "Q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "R" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "S" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "T" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 945 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "U" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "V" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 781 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "W" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "X" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Y" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "2" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1496 Classifications: {'RNA': 70} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 29} Link IDs: {'rna2p': 11, 'rna3p': 58} Chain breaks: 2 Chain: "a" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 624 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "c" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "d" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 456 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "f" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 418 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "g" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "h" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "i" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "j" 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} Chain: "1" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 659 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "0" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 3962 Classifications: {'peptide': 532} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 26, 'TRANS': 505} Chain breaks: 6 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 278 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 9, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 187 Time building chain proxies: 38.11, per 1000 atoms: 0.41 Number of scatterers: 93862 At special positions: 0 Unit cell: (223.04, 227.96, 201.72, 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 102 16.00 P 2994 15.00 O 26140 8.00 N 17431 7.00 C 47195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS f 30 " - pdb=" SG CYS f 43 " distance=2.03 Simple disulfide: pdb=" SG CYS f 33 " - pdb=" SG CYS f 46 " distance=2.02 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: 44.14 Conformation dependent library (CDL) restraints added in 4.9 seconds 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7006 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 53 sheets defined 32.2% alpha, 19.5% beta 1022 base pairs and 1624 stacking pairs defined. Time for finding SS restraints: 36.96 Creating SS restraints... Processing helix chain 'E' and resid 207 through 214 removed outlier: 4.126A pdb=" N SER E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 71 Processing helix chain 'F' and resid 98 through 102 removed outlier: 3.676A pdb=" N ILE F 101 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 102 through 121 Processing helix chain 'G' and resid 135 through 146 removed outlier: 3.988A pdb=" N MET G 139 " --> pdb=" O LYS G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 166 Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 183 through 189 Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'H' and resid 4 through 11 Processing helix chain 'H' and resid 11 through 21 Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 41 through 44 removed outlier: 3.605A pdb=" N VAL H 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 46 through 62 removed outlier: 3.795A pdb=" N ILE H 50 " --> pdb=" O ASN H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 92 through 106 removed outlier: 3.516A pdb=" N MET H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.774A pdb=" N ILE H 137 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 173 removed outlier: 3.709A pdb=" N VAL H 173 " --> pdb=" O LEU H 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 82 removed outlier: 3.747A pdb=" N ALA I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG I 70 " --> pdb=" O HIS I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 151 Processing helix chain 'K' and resid 20 through 30 removed outlier: 4.214A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Proline residue: K 26 - end of helix removed outlier: 3.878A pdb=" N GLN K 30 " --> pdb=" O PRO K 26 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 46 Processing helix chain 'K' and resid 74 through 84 Processing helix chain 'K' and resid 102 through 113 Processing helix chain 'K' and resid 120 through 136 Processing helix chain 'L' and resid 6 through 22 Processing helix chain 'L' and resid 34 through 49 Processing helix chain 'L' and resid 56 through 65 Processing helix chain 'L' and resid 73 through 77 removed outlier: 3.780A pdb=" N THR L 77 " --> pdb=" O ASP L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 93 through 104 Processing helix chain 'L' and resid 119 through 128 Processing helix chain 'N' and resid 25 through 39 removed outlier: 4.124A pdb=" N GLU N 32 " --> pdb=" O ARG N 28 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 63 Processing helix chain 'N' and resid 68 through 73 Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'N' and resid 97 through 110 removed outlier: 4.114A pdb=" N MET N 101 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 121 Processing helix chain 'O' and resid 103 through 107 removed outlier: 3.900A pdb=" N LEU O 106 " --> pdb=" O ALA O 103 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'P' and resid 56 through 61 Processing helix chain 'P' and resid 80 through 85 removed outlier: 3.654A pdb=" N GLY P 84 " --> pdb=" O LYS P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 100 Processing helix chain 'P' and resid 129 through 140 Processing helix chain 'Q' and resid 44 through 59 Processing helix chain 'Q' and resid 110 through 125 Processing helix chain 'R' and resid 9 through 28 Processing helix chain 'R' and resid 34 through 54 removed outlier: 4.240A pdb=" N SER R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL R 43 " --> pdb=" O GLU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 66 Processing helix chain 'R' and resid 79 through 91 Processing helix chain 'S' and resid 6 through 20 Processing helix chain 'S' and resid 70 through 88 Processing helix chain 'S' and resid 104 through 117 Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 53 through 56 Processing helix chain 'U' and resid 7 through 21 removed outlier: 4.067A pdb=" N ARG U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) Processing helix chain 'U' and resid 26 through 31 Processing helix chain 'U' and resid 31 through 73 removed outlier: 3.570A pdb=" N GLN U 38 " --> pdb=" O VAL U 34 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS U 41 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG U 55 " --> pdb=" O ARG U 51 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS U 59 " --> pdb=" O ARG U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 87 Processing helix chain 'U' and resid 91 through 101 Processing helix chain 'U' and resid 102 through 117 removed outlier: 3.542A pdb=" N PHE U 106 " --> pdb=" O ASP U 102 " (cutoff:3.500A) Processing helix chain 'W' and resid 13 through 25 removed outlier: 3.767A pdb=" N ALA W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE W 24 " --> pdb=" O VAL W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 43 through 62 Processing helix chain 'W' and resid 65 through 67 No H-bonds generated for 'chain 'W' and resid 65 through 67' Processing helix chain 'X' and resid 3 through 7 Processing helix chain 'X' and resid 14 through 23 removed outlier: 3.565A pdb=" N GLU X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 48 Processing helix chain 'b' and resid 20 through 22 No H-bonds generated for 'chain 'b' and resid 20 through 22' Processing helix chain 'b' and resid 51 through 55 Processing helix chain 'c' and resid 2 through 8 Processing helix chain 'c' and resid 12 through 35 Processing helix chain 'c' and resid 40 through 65 removed outlier: 4.159A pdb=" N ARG c 44 " --> pdb=" O THR c 40 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE c 57 " --> pdb=" O MET c 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 27 Processing helix chain 'd' and resid 40 through 51 Processing helix chain 'f' and resid 9 through 17 Processing helix chain 'h' and resid 8 through 16 Processing helix chain 'h' and resid 17 through 24 removed outlier: 3.626A pdb=" N SER h 24 " --> pdb=" O SER h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 24 through 37 Processing helix chain 'i' and resid 7 through 14 Processing helix chain 'i' and resid 37 through 45 Processing helix chain 'i' and resid 51 through 59 Processing helix chain 'i' and resid 60 through 63 removed outlier: 3.868A pdb=" N ALA i 63 " --> pdb=" O GLN i 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 60 through 63' Processing helix chain 'j' and resid 29 through 32 Processing helix chain '1' and resid 2 through 10 Processing helix chain '1' and resid 15 through 26 Processing helix chain '1' and resid 70 through 74 removed outlier: 3.532A pdb=" N ALA 1 73 " --> pdb=" O GLU 1 70 " (cutoff:3.500A) Processing helix chain '0' and resid 4 through 17 Processing helix chain '0' and resid 73 through 84 removed outlier: 3.556A pdb=" N GLU 0 84 " --> pdb=" O ARG 0 80 " (cutoff:3.500A) Processing helix chain '0' and resid 147 through 151 removed outlier: 3.597A pdb=" N MET 0 150 " --> pdb=" O SER 0 147 " (cutoff:3.500A) Processing helix chain '0' and resid 180 through 185 Processing helix chain '0' and resid 186 through 190 removed outlier: 3.700A pdb=" N GLY 0 190 " --> pdb=" O PHE 0 187 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 196 removed outlier: 4.000A pdb=" N GLN 0 195 " --> pdb=" O ARG 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 204 through 213 Processing helix chain '0' and resid 223 through 236 removed outlier: 3.977A pdb=" N LEU 0 227 " --> pdb=" O LEU 0 223 " (cutoff:3.500A) Processing helix chain '0' and resid 269 through 277 Processing helix chain '0' and resid 283 through 317 removed outlier: 3.605A pdb=" N PHE 0 297 " --> pdb=" O ASP 0 293 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 0 317 " --> pdb=" O GLU 0 313 " (cutoff:3.500A) Processing helix chain '0' and resid 321 through 335 removed outlier: 3.691A pdb=" N PHE 0 325 " --> pdb=" O ASN 0 321 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 413 Processing helix chain '0' and resid 415 through 429 removed outlier: 3.984A pdb=" N GLU 0 421 " --> pdb=" O ARG 0 417 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU 0 424 " --> pdb=" O SER 0 420 " (cutoff:3.500A) Processing helix chain '0' and resid 456 through 458 No H-bonds generated for 'chain '0' and resid 456 through 458' Processing helix chain '0' and resid 466 through 477 Processing helix chain '0' and resid 503 through 517 removed outlier: 3.593A pdb=" N ALA 0 511 " --> pdb=" O ILE 0 507 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR 0 512 " --> pdb=" O MET 0 508 " (cutoff:3.500A) Processing helix chain '0' and resid 534 through 536 No H-bonds generated for 'chain '0' and resid 534 through 536' Processing helix chain '0' and resid 561 through 565 Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AA3, first strand: chain 'E' and resid 101 through 105 removed outlier: 6.612A pdb=" N ILE E 91 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL E 81 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU E 93 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 129 through 131 removed outlier: 6.702A pdb=" N LEU E 173 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LYS E 167 " --> pdb=" O TYR E 171 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N TYR E 171 " --> pdb=" O LYS E 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 14 removed outlier: 5.391A pdb=" N LYS F 9 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU F 29 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY F 11 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU F 185 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL F 179 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU F 187 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLU F 175 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N VAL F 108 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL F 113 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU F 199 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 79 through 84 removed outlier: 3.678A pdb=" N PHE F 79 " --> pdb=" O PHE F 53 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 48 " --> pdb=" O LYS F 39 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLN F 37 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLY F 52 " --> pdb=" O VAL F 35 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N VAL F 35 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 116 through 120 Processing sheet with id=AA8, first strand: chain 'G' and resid 13 through 18 removed outlier: 5.661A pdb=" N GLY G 15 " --> pdb=" O LEU G 6 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU G 6 " --> pdb=" O GLY G 15 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N ILE G 123 " --> pdb=" O LYS G 3 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA G 5 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL G 125 " --> pdb=" O ALA G 5 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU G 153 " --> pdb=" O LEU G 193 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA G 152 " --> pdb=" O THR G 174 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N VAL G 176 " --> pdb=" O ALA G 152 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ILE G 154 " --> pdb=" O VAL G 176 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 66 through 69 Processing sheet with id=AB1, first strand: chain 'I' and resid 9 through 10 Processing sheet with id=AB2, first strand: chain 'I' and resid 16 through 19 Processing sheet with id=AB3, first strand: chain 'I' and resid 123 through 125 Processing sheet with id=AB4, first strand: chain 'I' and resid 96 through 98 Processing sheet with id=AB5, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.613A pdb=" N SER K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 98 through 101 Processing sheet with id=AB7, first strand: chain 'L' and resid 51 through 54 Processing sheet with id=AB8, first strand: chain 'N' and resid 123 through 125 removed outlier: 6.414A pdb=" N TRP N 16 " --> pdb=" O GLU N 139 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 74 through 78 Processing sheet with id=AC1, first strand: chain 'O' and resid 7 through 10 removed outlier: 6.286A pdb=" N ARG O 17 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA O 16 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA O 46 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLU O 18 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL O 40 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N VAL O 24 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL O 38 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ALA O 83 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N CYS O 84 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LYS O 9 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE O 86 " --> pdb=" O LYS O 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.720A pdb=" N THR T 58 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG T 50 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR T 60 " --> pdb=" O ILE T 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ILE T 64 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLU T 44 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP T 24 " --> pdb=" O VAL T 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR T 25 " --> pdb=" O VAL T 87 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS T 83 " --> pdb=" O HIS T 29 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS T 31 " --> pdb=" O ILE T 81 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE T 81 " --> pdb=" O LYS T 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'P' and resid 75 through 77 removed outlier: 6.053A pdb=" N ALA P 75 " --> pdb=" O LYS P 110 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL P 109 " --> pdb=" O LYS P 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'P' and resid 90 through 91 removed outlier: 6.303A pdb=" N VAL P 123 " --> pdb=" O GLU P 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Q' and resid 102 through 104 removed outlier: 6.665A pdb=" N VAL Q 102 " --> pdb=" O ALA Q 36 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA Q 36 " --> pdb=" O VAL Q 102 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N PHE Q 104 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 40 through 43 removed outlier: 5.391A pdb=" N ALA Q 76 " --> pdb=" O PRO Q 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY Q 92 " --> pdb=" O TYR Q 74 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR Q 74 " --> pdb=" O GLY Q 92 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 29 through 33 removed outlier: 4.273A pdb=" N MET R 114 " --> pdb=" O LEU R 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 70 through 72 removed outlier: 3.702A pdb=" N ASN R 72 " --> pdb=" O GLN R 77 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 51 through 57 removed outlier: 6.747A pdb=" N ILE S 44 " --> pdb=" O LEU S 53 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER S 55 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA S 42 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL S 33 " --> pdb=" O ASP S 96 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'V' and resid 11 through 14 Processing sheet with id=AD2, first strand: chain 'V' and resid 19 through 22 removed outlier: 3.573A pdb=" N LYS V 64 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N THR V 96 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N VAL V 62 " --> pdb=" O THR V 96 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU V 98 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA V 60 " --> pdb=" O GLU V 98 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE V 100 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL V 58 " --> pdb=" O ILE V 100 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'V' and resid 71 through 75 Processing sheet with id=AD4, first strand: chain 'W' and resid 3 through 10 removed outlier: 6.337A pdb=" N SER W 101 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER W 108 " --> pdb=" O ILE W 71 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ILE W 71 " --> pdb=" O SER W 108 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'W' and resid 82 through 87 Processing sheet with id=AD6, first strand: chain 'X' and resid 8 through 10 removed outlier: 4.013A pdb=" N ARG X 77 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Y' and resid 20 through 21 Processing sheet with id=AD8, first strand: chain 'Y' and resid 23 through 27 removed outlier: 4.220A pdb=" N ALA Y 25 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Y' and resid 40 through 44 Processing sheet with id=AE1, first strand: chain 'Y' and resid 81 through 85 removed outlier: 3.949A pdb=" N GLN Y 99 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'a' and resid 30 through 31 removed outlier: 6.851A pdb=" N LEU a 67 " --> pdb=" O LEU a 45 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'a' and resid 38 through 39 Processing sheet with id=AE4, first strand: chain 'b' and resid 13 through 18 Processing sheet with id=AE5, first strand: chain 'b' and resid 33 through 36 Processing sheet with id=AE6, first strand: chain 'd' and resid 35 through 38 Processing sheet with id=AE7, first strand: chain 'f' and resid 27 through 29 Processing sheet with id=AE8, first strand: chain 'f' and resid 48 through 49 Processing sheet with id=AE9, first strand: chain 'g' and resid 18 through 22 Processing sheet with id=AF1, first strand: chain 'i' and resid 15 through 16 Processing sheet with id=AF2, first strand: chain 'j' and resid 2 through 3 removed outlier: 6.122A pdb=" N LYS j 2 " --> pdb=" O LYS j 35 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN j 34 " --> pdb=" O VAL j 25 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '1' and resid 33 through 34 removed outlier: 6.843A pdb=" N LEU 1 55 " --> pdb=" O GLU 1 81 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU 1 81 " --> pdb=" O LEU 1 55 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR 1 57 " --> pdb=" O LEU 1 79 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '0' and resid 23 through 31 removed outlier: 6.586A pdb=" N HIS 0 38 " --> pdb=" O THR 0 25 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE 0 27 " --> pdb=" O ILE 0 36 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE 0 36 " --> pdb=" O ILE 0 27 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLN 0 29 " --> pdb=" O ASP 0 34 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP 0 34 " --> pdb=" O GLN 0 29 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '0' and resid 87 through 92 removed outlier: 5.394A pdb=" N ILE 0 88 " --> pdb=" O LYS 0 105 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS 0 105 " --> pdb=" O ILE 0 88 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE 0 129 " --> pdb=" O GLY 0 142 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY 0 142 " --> pdb=" O ILE 0 129 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU 0 131 " --> pdb=" O ILE 0 140 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '0' and resid 250 through 253 removed outlier: 3.651A pdb=" N TYR 0 253 " --> pdb=" O ASN 0 242 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN 0 242 " --> pdb=" O TYR 0 253 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '0' and resid 345 through 349 Processing sheet with id=AF8, first strand: chain '0' and resid 451 through 454 removed outlier: 3.530A pdb=" N TYR 0 453 " --> pdb=" O ILE 0 461 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE 0 461 " --> pdb=" O TYR 0 453 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY 0 464 " --> pdb=" O HIS 0 494 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N HIS 0 494 " --> pdb=" O GLY 0 464 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ILE 0 497 " --> pdb=" O ILE 0 483 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE 0 483 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) 1219 hydrogen bonds defined for protein. 3399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2605 hydrogen bonds 4244 hydrogen bond angles 0 basepair planarities 1022 basepair parallelities 1624 stacking parallelities Total time for adding SS restraints: 153.88 Time building geometry restraints manager: 47.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7798 1.29 - 1.43: 45927 1.43 - 1.56: 42046 1.56 - 1.70: 6004 1.70 - 1.83: 189 Bond restraints: 101964 Sorted by residual: bond pdb=" C VAL 1 58 " pdb=" N GLN 1 59 " ideal model delta sigma weight residual 1.331 1.458 -0.128 1.34e-02 5.57e+03 9.06e+01 bond pdb=" C1' U A1940 " pdb=" N1 U A1940 " ideal model delta sigma weight residual 1.480 1.587 -0.107 1.50e-02 4.44e+03 5.08e+01 bond pdb=" C LEU H 170 " pdb=" O LEU H 170 " ideal model delta sigma weight residual 1.237 1.158 0.079 1.19e-02 7.06e+03 4.40e+01 bond pdb=" P G A1220 " pdb=" OP2 G A1220 " ideal model delta sigma weight residual 1.485 1.610 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" P G A1220 " pdb=" OP1 G A1220 " ideal model delta sigma weight residual 1.485 1.610 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 101959 not shown) Histogram of bond angle deviations from ideal: 56.69 - 74.74: 1 74.74 - 92.80: 5 92.80 - 110.85: 57817 110.85 - 128.91: 90616 128.91 - 146.97: 4048 Bond angle restraints: 152487 Sorted by residual: angle pdb=" C ILE 0 490 " pdb=" N PRO 0 491 " pdb=" CD PRO 0 491 " ideal model delta sigma weight residual 125.00 56.69 68.31 4.10e+00 5.95e-02 2.78e+02 angle pdb=" O3' G A1939 " pdb=" P U A1940 " pdb=" O5' U A1940 " ideal model delta sigma weight residual 104.00 84.73 19.27 1.50e+00 4.44e-01 1.65e+02 angle pdb=" C3' A A1947 " pdb=" C2' A A1947 " pdb=" O2' A A1947 " ideal model delta sigma weight residual 114.60 98.69 15.91 1.50e+00 4.44e-01 1.13e+02 angle pdb=" O3' A A1947 " pdb=" C3' A A1947 " pdb=" C2' A A1947 " ideal model delta sigma weight residual 109.50 124.95 -15.45 1.50e+00 4.44e-01 1.06e+02 angle pdb=" O3' C 2 48 " pdb=" P A 2 49 " pdb=" OP1 A 2 49 " ideal model delta sigma weight residual 108.00 77.72 30.28 3.00e+00 1.11e-01 1.02e+02 ... (remaining 152482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 57520 35.88 - 71.77: 6960 71.77 - 107.65: 776 107.65 - 143.54: 35 143.54 - 179.42: 45 Dihedral angle restraints: 65336 sinusoidal: 54465 harmonic: 10871 Sorted by residual: dihedral pdb=" CA ASN V 50 " pdb=" C ASN V 50 " pdb=" N PRO V 51 " pdb=" CA PRO V 51 " ideal model delta harmonic sigma weight residual 180.00 129.53 50.47 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" O4' U A2105 " pdb=" C1' U A2105 " pdb=" N1 U A2105 " pdb=" C2 U A2105 " ideal model delta sinusoidal sigma weight residual 200.00 26.52 173.48 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U A 794 " pdb=" C1' U A 794 " pdb=" N1 U A 794 " pdb=" C2 U A 794 " ideal model delta sinusoidal sigma weight residual 200.00 33.05 166.95 1 1.50e+01 4.44e-03 8.42e+01 ... (remaining 65333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.179: 19300 0.179 - 0.357: 189 0.357 - 0.536: 7 0.536 - 0.715: 1 0.715 - 0.893: 2 Chirality restraints: 19499 Sorted by residual: chirality pdb=" P A 2 49 " pdb=" OP1 A 2 49 " pdb=" OP2 A 2 49 " pdb=" O5' A 2 49 " both_signs ideal model delta sigma weight residual True 2.41 1.52 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" P G A1220 " pdb=" OP1 G A1220 " pdb=" OP2 G A1220 " pdb=" O5' G A1220 " both_signs ideal model delta sigma weight residual True 2.41 -3.21 -0.80 2.00e-01 2.50e+01 1.60e+01 chirality pdb=" P G 2 19 " pdb=" OP1 G 2 19 " pdb=" OP2 G 2 19 " pdb=" O5' G 2 19 " both_signs ideal model delta sigma weight residual True 2.41 -2.97 -0.56 2.00e-01 2.50e+01 7.95e+00 ... (remaining 19496 not shown) Planarity restraints: 8177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U A2334 " 0.450 2.00e-02 2.50e+03 2.07e-01 9.68e+02 pdb=" N1 U A2334 " -0.146 2.00e-02 2.50e+03 pdb=" C2 U A2334 " -0.096 2.00e-02 2.50e+03 pdb=" O2 U A2334 " -0.164 2.00e-02 2.50e+03 pdb=" N3 U A2334 " 0.062 2.00e-02 2.50e+03 pdb=" C4 U A2334 " 0.060 2.00e-02 2.50e+03 pdb=" O4 U A2334 " 0.205 2.00e-02 2.50e+03 pdb=" C5 U A2334 " -0.117 2.00e-02 2.50e+03 pdb=" C6 U A2334 " -0.254 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2338 " 0.335 2.00e-02 2.50e+03 1.37e-01 5.14e+02 pdb=" N9 A A2338 " -0.085 2.00e-02 2.50e+03 pdb=" C8 A A2338 " -0.102 2.00e-02 2.50e+03 pdb=" N7 A A2338 " -0.071 2.00e-02 2.50e+03 pdb=" C5 A A2338 " -0.047 2.00e-02 2.50e+03 pdb=" C6 A A2338 " 0.056 2.00e-02 2.50e+03 pdb=" N6 A A2338 " 0.168 2.00e-02 2.50e+03 pdb=" N1 A A2338 " 0.052 2.00e-02 2.50e+03 pdb=" C2 A A2338 " -0.057 2.00e-02 2.50e+03 pdb=" N3 A A2338 " -0.133 2.00e-02 2.50e+03 pdb=" C4 A A2338 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 2 23 " -0.292 2.00e-02 2.50e+03 1.24e-01 4.24e+02 pdb=" N9 A 2 23 " 0.043 2.00e-02 2.50e+03 pdb=" C8 A 2 23 " 0.075 2.00e-02 2.50e+03 pdb=" N7 A 2 23 " 0.067 2.00e-02 2.50e+03 pdb=" C5 A 2 23 " 0.073 2.00e-02 2.50e+03 pdb=" C6 A 2 23 " -0.029 2.00e-02 2.50e+03 pdb=" N6 A 2 23 " -0.176 2.00e-02 2.50e+03 pdb=" N1 A 2 23 " -0.049 2.00e-02 2.50e+03 pdb=" C2 A 2 23 " 0.035 2.00e-02 2.50e+03 pdb=" N3 A 2 23 " 0.127 2.00e-02 2.50e+03 pdb=" C4 A 2 23 " 0.125 2.00e-02 2.50e+03 ... (remaining 8174 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.80: 11 1.80 - 2.58: 1936 2.58 - 3.35: 114681 3.35 - 4.13: 314035 4.13 - 4.90: 446632 Nonbonded interactions: 877295 Sorted by model distance: nonbonded pdb=" C2 G 2 30 " pdb=" CZ ARG 0 125 " model vdw 1.028 3.490 nonbonded pdb=" N3 G 2 30 " pdb=" NE ARG 0 125 " model vdw 1.321 2.600 nonbonded pdb=" C2 G 2 30 " pdb=" NE ARG 0 125 " model vdw 1.373 3.340 nonbonded pdb=" N1 G 2 30 " pdb=" NH2 ARG 0 125 " model vdw 1.413 3.200 nonbonded pdb=" N1 G 2 30 " pdb=" CZ ARG 0 125 " model vdw 1.584 3.350 ... (remaining 877290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 18.450 Check model and map are aligned: 1.070 Set scattering table: 0.710 Process input model: 346.230 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.250 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 377.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.194 101964 Z= 0.697 Angle : 1.042 68.312 152487 Z= 0.552 Chirality : 0.058 0.893 19499 Planarity : 0.011 0.277 8177 Dihedral : 23.468 179.421 58324 Min Nonbonded Distance : 1.028 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.20 % Favored : 91.61 % Rotamer: Outliers : 0.23 % Allowed : 3.86 % Favored : 95.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.35 % Twisted General : 0.06 % 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: -3.62 (0.12), residues: 3742 helix: -1.63 (0.12), residues: 1143 sheet: -2.79 (0.16), residues: 700 loop : -2.74 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP U 61 HIS 0.031 0.003 HIS Q 13 PHE 0.089 0.004 PHE H 20 TYR 0.122 0.005 TYR H 97 ARG 0.025 0.002 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1453 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1446 time to evaluate : 4.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 16 MET cc_start: 0.6169 (ttm) cc_final: 0.5834 (ttt) REVERT: I 20 ASN cc_start: 0.8327 (m110) cc_final: 0.8104 (m-40) REVERT: I 145 ILE cc_start: 0.9359 (mm) cc_final: 0.9141 (mm) REVERT: N 17 LEU cc_start: 0.8327 (mt) cc_final: 0.7863 (mm) REVERT: N 37 LEU cc_start: 0.8757 (mt) cc_final: 0.8432 (mp) REVERT: N 59 ASN cc_start: 0.7737 (m-40) cc_final: 0.7444 (m110) REVERT: N 93 MET cc_start: 0.7190 (mmm) cc_final: 0.6990 (mmm) REVERT: N 124 ASN cc_start: 0.7992 (m-40) cc_final: 0.7667 (m-40) REVERT: P 106 ASN cc_start: 0.7740 (m-40) cc_final: 0.7448 (m-40) REVERT: Q 74 TYR cc_start: 0.8228 (p90) cc_final: 0.7898 (p90) REVERT: Q 116 GLU cc_start: 0.7787 (tp30) cc_final: 0.7519 (tp30) REVERT: Q 118 LEU cc_start: 0.9001 (mt) cc_final: 0.8541 (mt) REVERT: R 25 ILE cc_start: 0.8961 (mt) cc_final: 0.8658 (tt) REVERT: S 21 LYS cc_start: 0.9068 (mmmm) cc_final: 0.8395 (tttm) REVERT: U 49 ASP cc_start: 0.5863 (m-30) cc_final: 0.5558 (m-30) REVERT: V 74 PHE cc_start: 0.6960 (t80) cc_final: 0.6575 (t80) REVERT: W 19 LEU cc_start: 0.9101 (mp) cc_final: 0.8835 (tp) REVERT: a 66 THR cc_start: 0.5551 (p) cc_final: 0.5308 (p) REVERT: b 26 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7601 (mmtp) REVERT: c 57 ILE cc_start: 0.9242 (mt) cc_final: 0.8788 (mm) REVERT: d 49 LYS cc_start: 0.8591 (tttt) cc_final: 0.8180 (ttmt) REVERT: d 50 VAL cc_start: 0.8138 (t) cc_final: 0.7886 (m) REVERT: g 35 TYR cc_start: 0.6274 (t80) cc_final: 0.5794 (t80) REVERT: h 42 LEU cc_start: 0.8389 (pt) cc_final: 0.8097 (pp) REVERT: 1 8 LYS cc_start: 0.8738 (ttpt) cc_final: 0.8521 (mmmm) REVERT: 1 20 LYS cc_start: 0.8906 (tttp) cc_final: 0.8532 (tttt) outliers start: 7 outliers final: 2 residues processed: 1449 average time/residue: 0.9664 time to fit residues: 2307.6350 Evaluate side-chains 870 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 868 time to evaluate : 4.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 150 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 564 optimal weight: 20.0000 chunk 506 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 172 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 523 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 318 optimal weight: 6.9990 chunk 389 optimal weight: 5.9990 chunk 606 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 86 ASN E 163 GLN E 194 GLN E 200 HIS ** E 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN I 20 ASN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN O 45 GLN O 82 ASN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 110 ASN P 54 GLN P 70 ASN P 114 ASN R 12 GLN R 27 ASN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 2 GLN ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 2 GLN Y 99 GLN b 16 ASN b 20 HIS b 34 GLN d 32 ASN d 37 HIS ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 ASN ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 126 HIS 0 145 HIS 0 151 ASN 0 307 ASN 0 326 GLN 0 335 ASN 0 385 ASN 0 393 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 101964 Z= 0.242 Angle : 0.743 32.957 152487 Z= 0.373 Chirality : 0.039 0.700 19499 Planarity : 0.006 0.151 8177 Dihedral : 24.558 179.901 50824 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.33 % Favored : 93.53 % Rotamer: Outliers : 4.79 % Allowed : 19.72 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.03 % 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: -2.19 (0.13), residues: 3742 helix: -0.29 (0.14), residues: 1149 sheet: -1.73 (0.17), residues: 700 loop : -2.09 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 65 HIS 0.009 0.002 HIS T 77 PHE 0.026 0.003 PHE H 177 TYR 0.031 0.003 TYR H 128 ARG 0.019 0.001 ARG T 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1027 time to evaluate : 4.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 91 TYR cc_start: 0.7926 (m-10) cc_final: 0.7600 (m-10) REVERT: G 143 LEU cc_start: 0.8873 (mm) cc_final: 0.8659 (mm) REVERT: L 34 ASN cc_start: 0.9256 (p0) cc_final: 0.9046 (p0) REVERT: L 36 SER cc_start: 0.9164 (OUTLIER) cc_final: 0.8914 (p) REVERT: L 44 GLN cc_start: 0.8868 (pt0) cc_final: 0.8542 (pt0) REVERT: N 12 ILE cc_start: 0.8517 (mm) cc_final: 0.8299 (mp) REVERT: N 59 ASN cc_start: 0.7931 (m-40) cc_final: 0.6949 (m110) REVERT: N 61 GLU cc_start: 0.8071 (pm20) cc_final: 0.7759 (pm20) REVERT: N 119 MET cc_start: 0.7874 (ppp) cc_final: 0.7184 (ppp) REVERT: O 6 THR cc_start: 0.7221 (OUTLIER) cc_final: 0.6913 (p) REVERT: Q 44 ASN cc_start: 0.7910 (p0) cc_final: 0.7363 (p0) REVERT: R 103 LYS cc_start: 0.8188 (mttt) cc_final: 0.7858 (mttt) REVERT: U 52 GLN cc_start: 0.7122 (pp30) cc_final: 0.6886 (pp30) REVERT: U 61 TRP cc_start: 0.8239 (m-10) cc_final: 0.7448 (m-10) REVERT: V 74 PHE cc_start: 0.7017 (t80) cc_final: 0.5995 (t80) REVERT: W 38 LEU cc_start: 0.9048 (mp) cc_final: 0.8778 (mt) REVERT: X 10 ARG cc_start: 0.8499 (ptt-90) cc_final: 0.8166 (ptt180) REVERT: X 30 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8109 (p) REVERT: a 84 ARG cc_start: 0.7746 (mmm-85) cc_final: 0.7464 (tpp80) REVERT: b 26 LYS cc_start: 0.7880 (mmtt) cc_final: 0.7610 (mmtp) REVERT: c 58 ARG cc_start: 0.8597 (tpt90) cc_final: 0.8296 (tpt90) REVERT: h 2 LYS cc_start: 0.8173 (tttt) cc_final: 0.7824 (tttt) REVERT: h 14 LYS cc_start: 0.8764 (tppt) cc_final: 0.8517 (tppt) REVERT: 1 13 ILE cc_start: 0.8853 (mp) cc_final: 0.8363 (mp) REVERT: 0 100 MET cc_start: 0.2509 (tpp) cc_final: 0.2058 (tpp) outliers start: 149 outliers final: 76 residues processed: 1089 average time/residue: 0.9281 time to fit residues: 1702.8521 Evaluate side-chains 910 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 831 time to evaluate : 4.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 99 GLU Chi-restraints excluded: chain N residue 118 GLN Chi-restraints excluded: chain N residue 120 PHE Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 11 ARG Chi-restraints excluded: chain U residue 94 MET Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 97 ASN Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 65 ASP Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain g residue 47 GLU Chi-restraints excluded: chain 0 residue 251 TYR Chi-restraints excluded: chain 0 residue 266 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 337 optimal weight: 0.6980 chunk 188 optimal weight: 20.0000 chunk 504 optimal weight: 20.0000 chunk 413 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 607 optimal weight: 7.9990 chunk 656 optimal weight: 30.0000 chunk 541 optimal weight: 8.9990 chunk 602 optimal weight: 10.0000 chunk 207 optimal weight: 20.0000 chunk 487 optimal weight: 7.9990 overall best weight: 7.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 GLN E 194 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN N 124 ASN O 45 GLN ** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 GLN ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 18 GLN ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 ASN b 20 HIS d 19 GLN g 16 ASN ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 13 HIS 0 237 HIS ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 372 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 101964 Z= 0.263 Angle : 0.714 37.533 152487 Z= 0.363 Chirality : 0.039 0.623 19499 Planarity : 0.006 0.083 8177 Dihedral : 24.550 179.986 50819 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 23.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.97 % Favored : 92.94 % Rotamer: Outliers : 5.73 % Allowed : 21.81 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3742 helix: -0.04 (0.15), residues: 1152 sheet: -1.41 (0.18), residues: 720 loop : -1.80 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP U 61 HIS 0.011 0.002 HIS I 39 PHE 0.033 0.003 PHE O 79 TYR 0.025 0.002 TYR S 102 ARG 0.016 0.001 ARG 0 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 908 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 133 MET cc_start: 0.7789 (mmm) cc_final: 0.7573 (mmm) REVERT: G 39 MET cc_start: 0.7603 (ppp) cc_final: 0.6901 (ppp) REVERT: G 132 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7979 (p0) REVERT: K 125 MET cc_start: 0.9576 (ptp) cc_final: 0.9052 (ptp) REVERT: K 135 MET cc_start: 0.8266 (mtp) cc_final: 0.8000 (mpp) REVERT: L 36 SER cc_start: 0.9139 (m) cc_final: 0.8875 (p) REVERT: N 119 MET cc_start: 0.7843 (ppp) cc_final: 0.7184 (ppp) REVERT: O 6 THR cc_start: 0.7301 (OUTLIER) cc_final: 0.6976 (p) REVERT: O 12 ASP cc_start: 0.6591 (p0) cc_final: 0.6358 (p0) REVERT: O 18 GLU cc_start: 0.6346 (tm-30) cc_final: 0.5342 (tm-30) REVERT: O 67 SER cc_start: 0.7989 (m) cc_final: 0.7751 (p) REVERT: P 61 LEU cc_start: 0.8464 (mm) cc_final: 0.8198 (mm) REVERT: P 114 ASN cc_start: 0.7538 (t0) cc_final: 0.6655 (t0) REVERT: Q 44 ASN cc_start: 0.7839 (p0) cc_final: 0.7605 (p0) REVERT: R 69 GLU cc_start: 0.5877 (mm-30) cc_final: 0.5601 (mm-30) REVERT: R 78 ASP cc_start: 0.8386 (p0) cc_final: 0.7617 (p0) REVERT: R 103 LYS cc_start: 0.8109 (mttt) cc_final: 0.7723 (mttt) REVERT: T 43 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7376 (t80) REVERT: T 63 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7315 (mtmm) REVERT: T 99 TYR cc_start: 0.8432 (p90) cc_final: 0.7860 (p90) REVERT: U 25 PHE cc_start: 0.6240 (OUTLIER) cc_final: 0.5814 (t80) REVERT: U 97 ASP cc_start: 0.7209 (t0) cc_final: 0.6447 (t0) REVERT: V 74 PHE cc_start: 0.7095 (t80) cc_final: 0.6398 (t80) REVERT: W 68 ASN cc_start: 0.8089 (t0) cc_final: 0.7874 (t0) REVERT: X 5 ARG cc_start: 0.8094 (mmt90) cc_final: 0.7565 (mtp85) REVERT: X 10 ARG cc_start: 0.8477 (ptt-90) cc_final: 0.8207 (ptt180) REVERT: Y 89 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.7072 (pmmt) REVERT: b 22 MET cc_start: 0.7593 (mmm) cc_final: 0.7158 (mmt) REVERT: c 22 LYS cc_start: 0.9342 (mmmm) cc_final: 0.8919 (mmmm) REVERT: d 57 LYS cc_start: 0.8661 (tptp) cc_final: 0.8300 (tptp) REVERT: h 2 LYS cc_start: 0.8145 (tttt) cc_final: 0.7941 (tttt) REVERT: h 14 LYS cc_start: 0.8707 (tppt) cc_final: 0.8465 (tppt) REVERT: i 45 ARG cc_start: 0.8447 (ptp-170) cc_final: 0.7991 (ptp-170) REVERT: 1 7 LEU cc_start: 0.9390 (mt) cc_final: 0.9113 (tp) REVERT: 1 74 ASN cc_start: 0.8595 (p0) cc_final: 0.8277 (p0) REVERT: 1 75 MET cc_start: 0.8769 (ptt) cc_final: 0.8048 (pmm) REVERT: 0 11 MET cc_start: 0.7484 (ptt) cc_final: 0.7255 (ptt) REVERT: 0 20 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8123 (mmm) REVERT: 0 77 MET cc_start: 0.5920 (tmm) cc_final: 0.5640 (tmm) REVERT: 0 100 MET cc_start: 0.3255 (tpp) cc_final: 0.2696 (tpp) outliers start: 178 outliers final: 113 residues processed: 990 average time/residue: 0.9220 time to fit residues: 1543.6156 Evaluate side-chains 903 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 783 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 207 LYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 75 ASN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 70 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain S residue 2 ILE Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 43 PHE Chi-restraints excluded: chain T residue 63 LYS Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 25 PHE Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 65 ASP Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain b residue 20 HIS Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 7 ARG Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain h residue 24 SER Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain j residue 13 LYS Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 49 VAL Chi-restraints excluded: chain 0 residue 20 MET Chi-restraints excluded: chain 0 residue 125 ARG Chi-restraints excluded: chain 0 residue 149 SER Chi-restraints excluded: chain 0 residue 251 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 600 optimal weight: 20.0000 chunk 456 optimal weight: 6.9990 chunk 315 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 290 optimal weight: 20.0000 chunk 408 optimal weight: 50.0000 chunk 609 optimal weight: 2.9990 chunk 645 optimal weight: 20.0000 chunk 318 optimal weight: 10.0000 chunk 578 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 ASN ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 16 GLN c 27 ASN ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 9 ASN ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 237 HIS ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 372 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 101964 Z= 0.259 Angle : 0.685 11.015 152487 Z= 0.353 Chirality : 0.038 0.556 19499 Planarity : 0.005 0.069 8177 Dihedral : 24.595 179.912 50819 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 25.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.92 % Favored : 93.00 % Rotamer: Outliers : 6.24 % Allowed : 22.91 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.13), residues: 3742 helix: 0.07 (0.15), residues: 1149 sheet: -1.18 (0.18), residues: 723 loop : -1.78 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Q 93 HIS 0.037 0.002 HIS b 20 PHE 0.036 0.002 PHE L 99 TYR 0.019 0.002 TYR N 126 ARG 0.016 0.001 ARG 0 266 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 835 time to evaluate : 4.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 207 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7917 (ptpp) REVERT: G 39 MET cc_start: 0.7565 (ppp) cc_final: 0.6920 (ppp) REVERT: G 132 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8025 (p0) REVERT: K 125 MET cc_start: 0.9581 (ptp) cc_final: 0.9377 (ppp) REVERT: K 129 GLU cc_start: 0.9167 (pt0) cc_final: 0.8842 (tm-30) REVERT: L 36 SER cc_start: 0.9144 (m) cc_final: 0.8891 (p) REVERT: N 119 MET cc_start: 0.7967 (ppp) cc_final: 0.7433 (ppp) REVERT: O 6 THR cc_start: 0.7342 (OUTLIER) cc_final: 0.7031 (p) REVERT: O 66 LYS cc_start: 0.7992 (mtmm) cc_final: 0.7401 (mtmm) REVERT: P 58 PHE cc_start: 0.7181 (p90) cc_final: 0.6074 (p90) REVERT: Q 44 ASN cc_start: 0.7801 (p0) cc_final: 0.7518 (p0) REVERT: R 69 GLU cc_start: 0.6172 (mm-30) cc_final: 0.5775 (mm-30) REVERT: R 103 LYS cc_start: 0.7993 (mttt) cc_final: 0.7392 (mttt) REVERT: S 60 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7300 (t0) REVERT: T 43 PHE cc_start: 0.7758 (OUTLIER) cc_final: 0.7521 (t80) REVERT: T 63 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7197 (mtmm) REVERT: T 98 TYR cc_start: 0.8352 (m-80) cc_final: 0.8062 (m-80) REVERT: T 113 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7606 (mt) REVERT: W 73 GLN cc_start: 0.8264 (pm20) cc_final: 0.8011 (pm20) REVERT: a 80 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7471 (m-80) REVERT: b 22 MET cc_start: 0.7753 (mmm) cc_final: 0.7287 (mmm) REVERT: c 58 ARG cc_start: 0.8634 (tpt90) cc_final: 0.8221 (tpt90) REVERT: h 14 LYS cc_start: 0.8680 (tppt) cc_final: 0.8444 (tppt) REVERT: 1 16 ARG cc_start: 0.7741 (ttt180) cc_final: 0.6500 (ttt-90) REVERT: 1 74 ASN cc_start: 0.8703 (p0) cc_final: 0.8410 (p0) REVERT: 1 75 MET cc_start: 0.8959 (ptt) cc_final: 0.8206 (pmm) REVERT: 0 11 MET cc_start: 0.7591 (ptt) cc_final: 0.7380 (ptt) REVERT: 0 20 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8303 (mmm) REVERT: 0 77 MET cc_start: 0.5957 (tmm) cc_final: 0.5703 (tmm) REVERT: 0 100 MET cc_start: 0.2996 (tpp) cc_final: 0.2501 (tpp) outliers start: 194 outliers final: 142 residues processed: 934 average time/residue: 0.8919 time to fit residues: 1421.1067 Evaluate side-chains 919 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 768 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 207 LYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 75 ASN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 85 ILE Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 84 CYS Chi-restraints excluded: chain O residue 96 THR Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 57 LEU Chi-restraints excluded: chain P residue 70 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 106 ASN Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 57 HIS Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain S residue 2 ILE Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 60 ASP Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 43 PHE Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 63 LYS Chi-restraints excluded: chain T residue 106 LYS Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 29 VAL Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 65 ASP Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 80 PHE Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain c residue 48 LYS Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain d residue 56 VAL Chi-restraints excluded: chain f residue 7 ARG Chi-restraints excluded: chain f residue 8 THR Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 26 ASN Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain 1 residue 28 ILE Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 0 residue 20 MET Chi-restraints excluded: chain 0 residue 152 SER Chi-restraints excluded: chain 0 residue 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 537 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 9 optimal weight: 20.0000 chunk 480 optimal weight: 10.0000 chunk 266 optimal weight: 20.0000 chunk 550 optimal weight: 30.0000 chunk 446 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 329 optimal weight: 9.9990 chunk 579 optimal weight: 7.9990 chunk 162 optimal weight: 30.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 HIS ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 GLN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 29 HIS T 36 ASN ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 38 HIS ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 305 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 372 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 101964 Z= 0.274 Angle : 0.701 13.496 152487 Z= 0.361 Chirality : 0.039 0.537 19499 Planarity : 0.006 0.096 8177 Dihedral : 24.670 179.692 50819 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 28.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.03 % Favored : 92.86 % Rotamer: Outliers : 6.82 % Allowed : 23.62 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3742 helix: 0.10 (0.15), residues: 1142 sheet: -1.13 (0.18), residues: 740 loop : -1.74 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP G 83 HIS 0.010 0.002 HIS F 126 PHE 0.032 0.002 PHE H 99 TYR 0.019 0.002 TYR N 76 ARG 0.014 0.001 ARG H 150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1038 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 826 time to evaluate : 4.343 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: E 27 ASP cc_start: 0.8403 (p0) cc_final: 0.8153 (p0) REVERT: E 45 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7505 (p0) REVERT: F 207 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8189 (ptpp) REVERT: G 39 MET cc_start: 0.7552 (ppp) cc_final: 0.6996 (ppp) REVERT: G 132 ASP cc_start: 0.8342 (OUTLIER) cc_final: 0.8104 (p0) REVERT: K 40 LYS cc_start: 0.9361 (mmmt) cc_final: 0.8870 (mmtm) REVERT: L 23 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8589 (pptt) REVERT: L 36 SER cc_start: 0.9178 (m) cc_final: 0.8940 (p) REVERT: N 119 MET cc_start: 0.7983 (ppp) cc_final: 0.7416 (ppp) REVERT: O 6 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7245 (p) REVERT: O 12 ASP cc_start: 0.7013 (p0) cc_final: 0.6713 (p0) REVERT: O 66 LYS cc_start: 0.7917 (mtmm) cc_final: 0.7551 (mtmm) REVERT: O 107 ARG cc_start: 0.9127 (mmm-85) cc_final: 0.8887 (mmm-85) REVERT: P 58 PHE cc_start: 0.7652 (p90) cc_final: 0.7396 (p90) REVERT: T 89 TYR cc_start: 0.7836 (m-10) cc_final: 0.7370 (m-10) REVERT: T 98 TYR cc_start: 0.8436 (m-80) cc_final: 0.8215 (m-80) REVERT: T 113 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7361 (mt) REVERT: W 73 GLN cc_start: 0.8241 (pm20) cc_final: 0.8040 (pm20) REVERT: Y 89 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6943 (pmmt) REVERT: b 22 MET cc_start: 0.7680 (mmm) cc_final: 0.7442 (tpp) REVERT: c 17 LYS cc_start: 0.9211 (mmtp) cc_final: 0.9011 (mmtp) REVERT: c 54 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8490 (mtpp) REVERT: d 30 LYS cc_start: 0.7456 (tttp) cc_final: 0.6975 (tttp) REVERT: h 6 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8024 (mm110) REVERT: h 10 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7481 (ttp-170) REVERT: 1 74 ASN cc_start: 0.8744 (p0) cc_final: 0.8538 (p0) REVERT: 1 75 MET cc_start: 0.8801 (ptt) cc_final: 0.8346 (pmm) REVERT: 0 11 MET cc_start: 0.7786 (ptt) cc_final: 0.7314 (ptt) REVERT: 0 20 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8271 (mmm) REVERT: 0 77 MET cc_start: 0.5783 (tmm) cc_final: 0.5489 (tmm) REVERT: 0 100 MET cc_start: 0.3388 (tpp) cc_final: 0.2832 (tpp) outliers start: 212 outliers final: 146 residues processed: 936 average time/residue: 1.0000 time to fit residues: 1621.6661 Evaluate side-chains 900 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 744 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 207 LYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 177 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 75 ASN Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 65 SER Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 6 THR Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 32 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 65 THR Chi-restraints excluded: chain O residue 84 CYS Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 70 ASN Chi-restraints excluded: chain P residue 76 VAL Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 5 LYS Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 57 HIS Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain S residue 2 ILE Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain S residue 106 VAL Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 63 LYS Chi-restraints excluded: chain T residue 106 LYS Chi-restraints excluded: chain T residue 113 ILE Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain W residue 106 VAL Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 19 LYS Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 57 GLU Chi-restraints excluded: chain a residue 65 ASP Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain c residue 25 LEU Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain f residue 7 ARG Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain h residue 6 GLN Chi-restraints excluded: chain h residue 10 ARG Chi-restraints excluded: chain h residue 36 ARG Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain 1 residue 28 ILE Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 63 LEU Chi-restraints excluded: chain 0 residue 20 MET Chi-restraints excluded: chain 0 residue 149 SER Chi-restraints excluded: chain 0 residue 251 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 217 optimal weight: 20.0000 chunk 581 optimal weight: 0.0770 chunk 127 optimal weight: 20.0000 chunk 379 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 646 optimal weight: 30.0000 chunk 536 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 339 optimal weight: 20.0000 overall best weight: 7.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 8 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 16 ASN ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 101964 Z= 0.258 Angle : 0.689 14.387 152487 Z= 0.353 Chirality : 0.038 0.520 19499 Planarity : 0.005 0.060 8177 Dihedral : 24.697 179.527 50819 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 27.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.00 % Favored : 92.92 % Rotamer: Outliers : 6.44 % Allowed : 26.13 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.13), residues: 3742 helix: 0.00 (0.15), residues: 1139 sheet: -0.96 (0.19), residues: 709 loop : -1.70 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 93 HIS 0.011 0.002 HIS d 52 PHE 0.038 0.002 PHE L 99 TYR 0.015 0.002 TYR H 22 ARG 0.014 0.001 ARG H 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 800 time to evaluate : 4.402 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: E 27 ASP cc_start: 0.8449 (p0) cc_final: 0.8192 (p0) REVERT: E 45 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7701 (p0) REVERT: G 39 MET cc_start: 0.7511 (ppp) cc_final: 0.7004 (ppp) REVERT: G 49 HIS cc_start: 0.5386 (p-80) cc_final: 0.4868 (p-80) REVERT: G 132 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7971 (p0) REVERT: H 26 MET cc_start: 0.4497 (ptp) cc_final: 0.4094 (ptt) REVERT: I 76 MET cc_start: 0.8506 (tmm) cc_final: 0.8232 (tmm) REVERT: K 40 LYS cc_start: 0.9365 (mmmt) cc_final: 0.8860 (mmtm) REVERT: K 101 LYS cc_start: 0.9516 (tppt) cc_final: 0.9005 (tppt) REVERT: K 129 GLU cc_start: 0.9211 (pt0) cc_final: 0.8636 (tm-30) REVERT: L 36 SER cc_start: 0.9210 (OUTLIER) cc_final: 0.8988 (p) REVERT: N 119 MET cc_start: 0.8047 (ppp) cc_final: 0.7591 (ppp) REVERT: O 5 GLU cc_start: 0.8099 (mp0) cc_final: 0.7852 (mp0) REVERT: O 66 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7681 (mtmm) REVERT: O 105 GLU cc_start: 0.8172 (mp0) cc_final: 0.7941 (mp0) REVERT: R 3 TYR cc_start: 0.5783 (OUTLIER) cc_final: 0.3895 (p90) REVERT: R 69 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6155 (mm-30) REVERT: S 90 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7715 (tp) REVERT: T 63 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7060 (mtmm) REVERT: Y 89 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.7011 (pmmt) REVERT: b 4 LYS cc_start: 0.8217 (ttpt) cc_final: 0.8016 (ttmt) REVERT: b 22 MET cc_start: 0.7687 (mmm) cc_final: 0.7446 (tpp) REVERT: b 33 LEU cc_start: 0.7538 (tp) cc_final: 0.7184 (tp) REVERT: c 19 LYS cc_start: 0.8962 (ptpp) cc_final: 0.8748 (pttm) REVERT: c 54 LYS cc_start: 0.8710 (mtpp) cc_final: 0.8340 (mtpp) REVERT: d 15 ARG cc_start: 0.8470 (OUTLIER) cc_final: 0.8019 (tpp80) REVERT: d 30 LYS cc_start: 0.7418 (tttp) cc_final: 0.7079 (tttp) REVERT: h 10 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7557 (ttp-170) REVERT: 1 11 ARG cc_start: 0.8768 (ttm-80) cc_final: 0.8064 (ttm-80) REVERT: 0 11 MET cc_start: 0.7822 (ptt) cc_final: 0.7435 (ptt) REVERT: 0 20 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8440 (mmm) REVERT: 0 77 MET cc_start: 0.5945 (tmm) cc_final: 0.5633 (tmm) REVERT: 0 100 MET cc_start: 0.3371 (tpp) cc_final: 0.3013 (tpp) outliers start: 200 outliers final: 143 residues processed: 913 average time/residue: 0.8917 time to fit residues: 1396.6201 Evaluate side-chains 895 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 742 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 SER Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 132 ASP Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 9 ASN Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 177 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 28 LEU Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 49 ASN Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 70 ASN Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 3 TYR Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 57 HIS Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 80 LEU Chi-restraints excluded: chain S residue 2 ILE Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 43 PHE Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 63 LYS Chi-restraints excluded: chain T residue 106 LYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain Y residue 16 ASP Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 19 LYS Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 57 GLU Chi-restraints excluded: chain a residue 65 ASP Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain c residue 57 ILE Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 25 THR Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain f residue 7 ARG Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 25 ASN Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain h residue 10 ARG Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain 1 residue 28 ILE Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 0 residue 20 MET Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 149 SER Chi-restraints excluded: chain 0 residue 251 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 623 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 368 optimal weight: 6.9990 chunk 471 optimal weight: 20.0000 chunk 365 optimal weight: 7.9990 chunk 544 optimal weight: 20.0000 chunk 360 optimal weight: 20.0000 chunk 643 optimal weight: 5.9990 chunk 402 optimal weight: 30.0000 chunk 392 optimal weight: 20.0000 chunk 297 optimal weight: 0.5980 overall best weight: 6.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 8 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS P 54 GLN ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 12 GLN ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 81 ASN ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 HIS ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 101964 Z= 0.229 Angle : 0.674 16.179 152487 Z= 0.345 Chirality : 0.037 0.505 19499 Planarity : 0.005 0.123 8177 Dihedral : 24.675 179.709 50819 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 26.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.16 % Favored : 92.73 % Rotamer: Outliers : 5.66 % Allowed : 27.67 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.13), residues: 3742 helix: 0.06 (0.15), residues: 1148 sheet: -0.87 (0.19), residues: 713 loop : -1.65 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP G 83 HIS 0.015 0.001 HIS 0 33 PHE 0.037 0.002 PHE L 99 TYR 0.018 0.002 TYR T 98 ARG 0.018 0.001 ARG F 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 776 time to evaluate : 4.371 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: E 27 ASP cc_start: 0.8441 (p0) cc_final: 0.8195 (p0) REVERT: G 39 MET cc_start: 0.7526 (ppp) cc_final: 0.7049 (ppp) REVERT: H 26 MET cc_start: 0.4495 (ptp) cc_final: 0.4096 (ptt) REVERT: I 76 MET cc_start: 0.8693 (tmm) cc_final: 0.8197 (tmm) REVERT: K 40 LYS cc_start: 0.9381 (mmmt) cc_final: 0.8888 (mmtm) REVERT: K 125 MET cc_start: 0.9472 (ptp) cc_final: 0.9036 (ptp) REVERT: K 133 ARG cc_start: 0.8490 (mtp-110) cc_final: 0.7832 (mtp180) REVERT: L 36 SER cc_start: 0.9198 (OUTLIER) cc_final: 0.8983 (p) REVERT: N 61 GLU cc_start: 0.8103 (pm20) cc_final: 0.7497 (pm20) REVERT: N 119 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7589 (ppp) REVERT: O 66 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7490 (mtmm) REVERT: O 73 ASP cc_start: 0.7986 (p0) cc_final: 0.7668 (p0) REVERT: P 58 PHE cc_start: 0.7661 (p90) cc_final: 0.7341 (p90) REVERT: R 3 TYR cc_start: 0.5711 (OUTLIER) cc_final: 0.3804 (p90) REVERT: S 90 ILE cc_start: 0.8050 (OUTLIER) cc_final: 0.7795 (tp) REVERT: T 63 LYS cc_start: 0.8161 (OUTLIER) cc_final: 0.6992 (mtmm) REVERT: a 84 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7552 (mmm-85) REVERT: b 33 LEU cc_start: 0.7668 (tp) cc_final: 0.7307 (tp) REVERT: c 54 LYS cc_start: 0.8739 (mtpp) cc_final: 0.8367 (mtpp) REVERT: c 58 ARG cc_start: 0.8503 (tpt90) cc_final: 0.8079 (tpt90) REVERT: d 15 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7924 (tpp80) REVERT: d 30 LYS cc_start: 0.7444 (tttp) cc_final: 0.7070 (tttp) REVERT: g 23 LYS cc_start: 0.8856 (tppt) cc_final: 0.8582 (tppt) REVERT: h 10 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7468 (ttp-170) REVERT: 1 11 ARG cc_start: 0.8802 (ttm-80) cc_final: 0.8100 (ttm-80) REVERT: 0 11 MET cc_start: 0.7844 (ptt) cc_final: 0.7513 (ptt) REVERT: 0 20 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8408 (mmm) REVERT: 0 77 MET cc_start: 0.5923 (tmm) cc_final: 0.5589 (tmm) REVERT: 0 100 MET cc_start: 0.3172 (tpp) cc_final: 0.2897 (tpp) outliers start: 176 outliers final: 146 residues processed: 878 average time/residue: 0.9667 time to fit residues: 1465.3562 Evaluate side-chains 880 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 726 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 177 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 95 ASN Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 45 GLN Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain O residue 112 MET Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 70 ASN Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain Q residue 83 MET Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 3 TYR Chi-restraints excluded: chain R residue 12 GLN Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 43 PHE Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 63 LYS Chi-restraints excluded: chain T residue 106 LYS Chi-restraints excluded: chain U residue 64 ARG Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 16 ASP Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 57 GLU Chi-restraints excluded: chain a residue 65 ASP Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 40 ASN Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain f residue 7 ARG Chi-restraints excluded: chain f residue 10 LYS Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 33 LYS Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain h residue 10 ARG Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain 1 residue 28 ILE Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 ILE Chi-restraints excluded: chain 0 residue 20 MET Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 251 TYR Chi-restraints excluded: chain 0 residue 268 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 398 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 chunk 384 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 126 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 409 optimal weight: 8.9990 chunk 438 optimal weight: 20.0000 chunk 318 optimal weight: 0.6980 chunk 60 optimal weight: 20.0000 chunk 506 optimal weight: 0.6980 overall best weight: 5.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 10 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 101964 Z= 0.204 Angle : 0.663 17.993 152487 Z= 0.338 Chirality : 0.037 0.491 19499 Planarity : 0.005 0.076 8177 Dihedral : 24.645 179.878 50819 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 25.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 5.57 % Allowed : 28.83 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3742 helix: 0.09 (0.15), residues: 1149 sheet: -0.76 (0.19), residues: 715 loop : -1.62 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 83 HIS 0.013 0.001 HIS i 31 PHE 0.031 0.002 PHE L 99 TYR 0.041 0.002 TYR L 30 ARG 0.017 0.001 ARG F 153 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 771 time to evaluate : 4.359 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: E 27 ASP cc_start: 0.8421 (p0) cc_final: 0.8170 (p0) REVERT: G 39 MET cc_start: 0.7486 (ppp) cc_final: 0.7017 (ppp) REVERT: H 26 MET cc_start: 0.4617 (ptp) cc_final: 0.4300 (ptp) REVERT: I 76 MET cc_start: 0.8767 (tmm) cc_final: 0.8257 (tmm) REVERT: K 40 LYS cc_start: 0.9371 (mmmt) cc_final: 0.8887 (mmtm) REVERT: K 125 MET cc_start: 0.9464 (ptp) cc_final: 0.8942 (ptp) REVERT: K 129 GLU cc_start: 0.9213 (pt0) cc_final: 0.8828 (pp20) REVERT: K 133 ARG cc_start: 0.8516 (mtp-110) cc_final: 0.7815 (mtp180) REVERT: L 36 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8916 (p) REVERT: N 119 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7530 (ppp) REVERT: O 66 LYS cc_start: 0.8080 (mtmm) cc_final: 0.7534 (mtmm) REVERT: O 73 ASP cc_start: 0.8086 (p0) cc_final: 0.7659 (p0) REVERT: P 58 PHE cc_start: 0.7705 (p90) cc_final: 0.7389 (p90) REVERT: R 3 TYR cc_start: 0.5702 (OUTLIER) cc_final: 0.3779 (p90) REVERT: R 69 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6064 (mm-30) REVERT: S 90 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7769 (tp) REVERT: Y 87 ASP cc_start: 0.7873 (m-30) cc_final: 0.7587 (m-30) REVERT: Y 89 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6937 (pmmt) REVERT: a 54 TYR cc_start: 0.7609 (m-10) cc_final: 0.6652 (m-10) REVERT: b 33 LEU cc_start: 0.7622 (tp) cc_final: 0.7276 (pp) REVERT: b 48 TYR cc_start: 0.6239 (m-10) cc_final: 0.5744 (m-10) REVERT: c 25 LEU cc_start: 0.9173 (pp) cc_final: 0.8890 (pp) REVERT: c 34 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8729 (p) REVERT: c 54 LYS cc_start: 0.8724 (mtpp) cc_final: 0.8345 (mtpp) REVERT: c 58 ARG cc_start: 0.8519 (tpt90) cc_final: 0.8209 (tpt90) REVERT: d 15 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7961 (tpp80) REVERT: f 15 LEU cc_start: 0.8620 (mt) cc_final: 0.8364 (mp) REVERT: g 23 LYS cc_start: 0.8850 (tppt) cc_final: 0.8596 (tppt) REVERT: 1 11 ARG cc_start: 0.8753 (ttm-80) cc_final: 0.8113 (mtm-85) REVERT: 0 11 MET cc_start: 0.7878 (ptt) cc_final: 0.7590 (ptt) REVERT: 0 20 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8476 (mmm) REVERT: 0 77 MET cc_start: 0.5899 (tmm) cc_final: 0.5588 (tmm) REVERT: 0 100 MET cc_start: 0.3092 (tpp) cc_final: 0.2842 (tpp) outliers start: 173 outliers final: 139 residues processed: 875 average time/residue: 0.9185 time to fit residues: 1383.8909 Evaluate side-chains 884 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 737 time to evaluate : 4.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 177 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 70 ASN Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 3 TYR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 58 THR Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 63 LYS Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 106 LYS Chi-restraints excluded: chain U residue 64 ARG Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 22 ASP Chi-restraints excluded: chain W residue 33 VAL Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 16 ASP Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain b residue 16 ASN Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain f residue 7 ARG Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 30 VAL Chi-restraints excluded: chain g residue 33 LYS Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain h residue 10 ARG Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 24 SER Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 61 ASN Chi-restraints excluded: chain 1 residue 78 ILE Chi-restraints excluded: chain 0 residue 20 MET Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 251 TYR Chi-restraints excluded: chain 0 residue 268 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 585 optimal weight: 7.9990 chunk 616 optimal weight: 20.0000 chunk 562 optimal weight: 0.0370 chunk 599 optimal weight: 1.9990 chunk 361 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 471 optimal weight: 6.9990 chunk 184 optimal weight: 20.0000 chunk 542 optimal weight: 50.0000 chunk 567 optimal weight: 5.9990 chunk 597 optimal weight: 10.0000 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 8 ASN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 GLN I 66 HIS P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 ASN ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 36 ASN ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 101964 Z= 0.198 Angle : 0.667 17.971 152487 Z= 0.339 Chirality : 0.036 0.478 19499 Planarity : 0.005 0.061 8177 Dihedral : 24.606 179.776 50819 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 25.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.11 % Favored : 92.78 % Rotamer: Outliers : 4.95 % Allowed : 29.70 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.13), residues: 3742 helix: 0.12 (0.15), residues: 1145 sheet: -0.70 (0.19), residues: 736 loop : -1.56 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP G 83 HIS 0.011 0.001 HIS i 31 PHE 0.041 0.002 PHE T 74 TYR 0.039 0.002 TYR L 30 ARG 0.014 0.001 ARG d 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 763 time to evaluate : 4.388 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: E 27 ASP cc_start: 0.8402 (p0) cc_final: 0.8136 (p0) REVERT: E 183 MET cc_start: 0.7108 (ppp) cc_final: 0.6795 (ppp) REVERT: G 39 MET cc_start: 0.7440 (ppp) cc_final: 0.6945 (ppp) REVERT: H 26 MET cc_start: 0.4533 (ptp) cc_final: 0.4214 (ptp) REVERT: I 76 MET cc_start: 0.8786 (tmm) cc_final: 0.8297 (tmm) REVERT: K 40 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8850 (mmtm) REVERT: K 125 MET cc_start: 0.9469 (ptp) cc_final: 0.8952 (ptp) REVERT: K 129 GLU cc_start: 0.9220 (pt0) cc_final: 0.8829 (pp20) REVERT: L 36 SER cc_start: 0.9121 (OUTLIER) cc_final: 0.8886 (p) REVERT: N 119 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7489 (ppp) REVERT: O 66 LYS cc_start: 0.7999 (mtmm) cc_final: 0.7478 (mtmm) REVERT: O 73 ASP cc_start: 0.8101 (p0) cc_final: 0.7649 (p0) REVERT: P 58 PHE cc_start: 0.7672 (p90) cc_final: 0.7402 (p90) REVERT: R 69 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6068 (mm-30) REVERT: T 7 ASP cc_start: 0.8538 (p0) cc_final: 0.8122 (p0) REVERT: T 63 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6989 (mtmm) REVERT: T 113 ILE cc_start: 0.7562 (pt) cc_final: 0.7151 (mt) REVERT: Y 87 ASP cc_start: 0.7844 (m-30) cc_final: 0.7642 (m-30) REVERT: Y 89 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.6901 (pmmt) REVERT: a 57 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7349 (mm-30) REVERT: a 58 ASN cc_start: 0.8072 (m110) cc_final: 0.7661 (t0) REVERT: a 65 ASP cc_start: 0.6731 (m-30) cc_final: 0.6216 (m-30) REVERT: b 33 LEU cc_start: 0.7690 (tp) cc_final: 0.7271 (pp) REVERT: c 1 MET cc_start: 0.9178 (tpt) cc_final: 0.8770 (tpp) REVERT: c 25 LEU cc_start: 0.9158 (pp) cc_final: 0.8868 (pp) REVERT: c 54 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8345 (mtpp) REVERT: c 58 ARG cc_start: 0.8552 (tpt90) cc_final: 0.8242 (tpt90) REVERT: d 15 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7860 (tpp80) REVERT: f 15 LEU cc_start: 0.8591 (mt) cc_final: 0.8328 (mp) REVERT: g 23 LYS cc_start: 0.8871 (tppt) cc_final: 0.8638 (tppt) REVERT: 1 11 ARG cc_start: 0.8732 (ttm-80) cc_final: 0.8134 (mtm-85) REVERT: 0 11 MET cc_start: 0.7940 (ptt) cc_final: 0.7712 (ptt) REVERT: 0 20 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8436 (mmm) REVERT: 0 77 MET cc_start: 0.5894 (tmm) cc_final: 0.5584 (tmm) outliers start: 154 outliers final: 139 residues processed: 854 average time/residue: 0.8827 time to fit residues: 1297.1160 Evaluate side-chains 887 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 742 time to evaluate : 4.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 177 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 41 LEU Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 70 ASN Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain Q residue 120 LEU Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 63 LYS Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 106 LYS Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 64 ARG Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 22 ASP Chi-restraints excluded: chain W residue 44 SER Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 16 ASP Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain f residue 7 ARG Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 33 LYS Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain h residue 10 ARG Chi-restraints excluded: chain h residue 24 SER Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 78 ILE Chi-restraints excluded: chain 0 residue 20 MET Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 149 SER Chi-restraints excluded: chain 0 residue 251 TYR Chi-restraints excluded: chain 0 residue 268 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 393 optimal weight: 6.9990 chunk 634 optimal weight: 30.0000 chunk 387 optimal weight: 40.0000 chunk 300 optimal weight: 30.0000 chunk 441 optimal weight: 0.9990 chunk 665 optimal weight: 50.0000 chunk 612 optimal weight: 7.9990 chunk 529 optimal weight: 9.9990 chunk 55 optimal weight: 30.0000 chunk 409 optimal weight: 6.9990 chunk 324 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 153 GLN ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 HIS ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 101964 Z= 0.230 Angle : 0.688 18.373 152487 Z= 0.350 Chirality : 0.037 0.479 19499 Planarity : 0.005 0.117 8177 Dihedral : 24.617 179.450 50819 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.43 % Favored : 92.46 % Rotamer: Outliers : 5.08 % Allowed : 30.08 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.13), residues: 3742 helix: 0.06 (0.15), residues: 1142 sheet: -0.72 (0.19), residues: 735 loop : -1.57 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP G 83 HIS 0.062 0.002 HIS P 35 PHE 0.087 0.003 PHE T 43 TYR 0.047 0.002 TYR H 22 ARG 0.017 0.001 ARG d 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7484 Ramachandran restraints generated. 3742 Oldfield, 0 Emsley, 3742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 753 time to evaluate : 4.378 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: E 27 ASP cc_start: 0.8457 (p0) cc_final: 0.8207 (p0) REVERT: E 183 MET cc_start: 0.6957 (ppp) cc_final: 0.6699 (ppp) REVERT: G 39 MET cc_start: 0.7471 (ppp) cc_final: 0.6973 (ppp) REVERT: H 26 MET cc_start: 0.4542 (ptp) cc_final: 0.4212 (ptp) REVERT: I 76 MET cc_start: 0.8800 (tmm) cc_final: 0.8328 (tmm) REVERT: K 40 LYS cc_start: 0.9339 (mmmt) cc_final: 0.8847 (mmtm) REVERT: K 125 MET cc_start: 0.9479 (ptp) cc_final: 0.8968 (ptp) REVERT: K 129 GLU cc_start: 0.9072 (pt0) cc_final: 0.8837 (pp20) REVERT: K 135 MET cc_start: 0.6803 (mmm) cc_final: 0.6327 (mmm) REVERT: L 36 SER cc_start: 0.9133 (OUTLIER) cc_final: 0.8901 (p) REVERT: N 119 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7468 (ppp) REVERT: O 66 LYS cc_start: 0.8028 (mtmm) cc_final: 0.7490 (mtmm) REVERT: O 73 ASP cc_start: 0.8119 (p0) cc_final: 0.7683 (p0) REVERT: P 58 PHE cc_start: 0.7704 (p90) cc_final: 0.7390 (p90) REVERT: R 3 TYR cc_start: 0.5701 (OUTLIER) cc_final: 0.3712 (p90) REVERT: S 90 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7783 (tp) REVERT: T 63 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6626 (mtmm) REVERT: T 113 ILE cc_start: 0.7506 (pt) cc_final: 0.7070 (mt) REVERT: Y 87 ASP cc_start: 0.7879 (m-30) cc_final: 0.7660 (m-30) REVERT: Y 89 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6927 (pmmt) REVERT: a 57 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7348 (mm-30) REVERT: a 58 ASN cc_start: 0.8039 (m110) cc_final: 0.7635 (t0) REVERT: a 65 ASP cc_start: 0.6694 (m-30) cc_final: 0.6221 (m-30) REVERT: b 33 LEU cc_start: 0.7767 (tp) cc_final: 0.7288 (pp) REVERT: c 1 MET cc_start: 0.9196 (tpt) cc_final: 0.8788 (tpp) REVERT: c 25 LEU cc_start: 0.9158 (pp) cc_final: 0.8873 (pp) REVERT: c 54 LYS cc_start: 0.8780 (mtpp) cc_final: 0.8354 (mtpp) REVERT: c 58 ARG cc_start: 0.8562 (tpt90) cc_final: 0.8247 (tpt90) REVERT: d 15 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7901 (tpp80) REVERT: f 15 LEU cc_start: 0.8643 (mt) cc_final: 0.8372 (mp) REVERT: g 23 LYS cc_start: 0.8899 (tppt) cc_final: 0.8674 (tppt) REVERT: 1 11 ARG cc_start: 0.8711 (ttm-80) cc_final: 0.8116 (ttm-80) REVERT: 0 20 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8465 (mmm) REVERT: 0 77 MET cc_start: 0.5904 (tmm) cc_final: 0.5593 (tmm) REVERT: 0 100 MET cc_start: 0.2467 (tpt) cc_final: 0.2171 (tpt) outliers start: 158 outliers final: 143 residues processed: 845 average time/residue: 0.8730 time to fit residues: 1271.0883 Evaluate side-chains 893 residues out of total 3206 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 742 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 192 ILE Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 26 THR Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 109 ASP Chi-restraints excluded: chain F residue 110 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain G residue 3 LYS Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 65 TRP Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 80 SER Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 179 ASN Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 195 THR Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 107 SER Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 158 THR Chi-restraints excluded: chain H residue 161 ASN Chi-restraints excluded: chain H residue 162 THR Chi-restraints excluded: chain H residue 165 GLU Chi-restraints excluded: chain H residue 177 PHE Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 44 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain K residue 13 ILE Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 59 SER Chi-restraints excluded: chain K residue 115 ASP Chi-restraints excluded: chain K residue 120 ASP Chi-restraints excluded: chain L residue 5 ILE Chi-restraints excluded: chain L residue 14 GLU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain L residue 119 THR Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 119 MET Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 142 GLU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 9 LYS Chi-restraints excluded: chain O residue 10 VAL Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 31 LYS Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 37 ASP Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 109 ASN Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 30 THR Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 70 ASN Chi-restraints excluded: chain P residue 79 LEU Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 37 LEU Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain R residue 3 TYR Chi-restraints excluded: chain R residue 24 LEU Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 70 VAL Chi-restraints excluded: chain R residue 72 ASN Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain S residue 47 ASP Chi-restraints excluded: chain S residue 90 ILE Chi-restraints excluded: chain T residue 15 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 63 LYS Chi-restraints excluded: chain T residue 86 VAL Chi-restraints excluded: chain T residue 106 LYS Chi-restraints excluded: chain U residue 4 VAL Chi-restraints excluded: chain U residue 64 ARG Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 34 THR Chi-restraints excluded: chain V residue 37 ASP Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain V residue 86 GLN Chi-restraints excluded: chain W residue 11 ARG Chi-restraints excluded: chain W residue 39 THR Chi-restraints excluded: chain W residue 71 ILE Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 35 ASN Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 50 LYS Chi-restraints excluded: chain X residue 51 VAL Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain Y residue 16 ASP Chi-restraints excluded: chain Y residue 48 THR Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 39 VAL Chi-restraints excluded: chain a residue 43 SER Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 67 LEU Chi-restraints excluded: chain b residue 36 VAL Chi-restraints excluded: chain b residue 59 VAL Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain d residue 8 LEU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 15 ARG Chi-restraints excluded: chain d residue 40 ASN Chi-restraints excluded: chain d residue 50 VAL Chi-restraints excluded: chain d residue 53 LEU Chi-restraints excluded: chain f residue 7 ARG Chi-restraints excluded: chain f residue 38 LEU Chi-restraints excluded: chain g residue 19 SER Chi-restraints excluded: chain g residue 33 LYS Chi-restraints excluded: chain g residue 42 SER Chi-restraints excluded: chain h residue 10 ARG Chi-restraints excluded: chain h residue 23 SER Chi-restraints excluded: chain h residue 24 SER Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 54 ASP Chi-restraints excluded: chain i residue 64 ASN Chi-restraints excluded: chain 1 residue 30 ILE Chi-restraints excluded: chain 1 residue 78 ILE Chi-restraints excluded: chain 0 residue 20 MET Chi-restraints excluded: chain 0 residue 146 LEU Chi-restraints excluded: chain 0 residue 149 SER Chi-restraints excluded: chain 0 residue 251 TYR Chi-restraints excluded: chain 0 residue 268 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 668 random chunks: chunk 420 optimal weight: 5.9990 chunk 564 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 chunk 488 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 530 optimal weight: 5.9990 chunk 222 optimal weight: 30.0000 chunk 545 optimal weight: 0.0980 chunk 67 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 overall best weight: 8.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN P 35 HIS ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 GLN ** P 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 41 GLN ** U 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.035156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.027745 restraints weight = 696354.065| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 3.66 r_work: 0.2582 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 101964 Z= 0.288 Angle : 0.731 17.100 152487 Z= 0.373 Chirality : 0.039 0.573 19499 Planarity : 0.006 0.060 8177 Dihedral : 24.741 179.865 50819 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 32.27 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.88 % Favored : 91.98 % Rotamer: Outliers : 5.12 % Allowed : 29.99 % Favored : 64.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.13), residues: 3742 helix: -0.07 (0.15), residues: 1151 sheet: -0.91 (0.19), residues: 715 loop : -1.64 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.003 TRP G 83 HIS 0.023 0.002 HIS P 35 PHE 0.065 0.003 PHE L 99 TYR 0.034 0.002 TYR L 30 ARG 0.015 0.001 ARG T 109 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23667.50 seconds wall clock time: 418 minutes 34.44 seconds (25114.44 seconds total)