Starting phenix.real_space_refine on Tue Mar 19 08:11:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/03_2024/7as9_11890.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/03_2024/7as9_11890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/03_2024/7as9_11890.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/03_2024/7as9_11890.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/03_2024/7as9_11890.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7as9_11890/03_2024/7as9_11890.pdb" } resolution = 3.5 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 2996 5.49 5 S 100 5.16 5 C 46731 2.51 5 N 17303 2.21 5 O 26007 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 107": "NH1" <-> "NH2" Residue "0 ARG 116": "NH1" <-> "NH2" Residue "0 ARG 125": "NH1" <-> "NH2" Residue "0 ARG 183": "NH1" <-> "NH2" Residue "0 PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 238": "NH1" <-> "NH2" Residue "0 ARG 265": "NH1" <-> "NH2" Residue "0 ARG 276": "NH1" <-> "NH2" Residue "0 ARG 296": "NH1" <-> "NH2" Residue "0 ARG 302": "NH1" <-> "NH2" Residue "0 TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 395": "NH1" <-> "NH2" Residue "0 ARG 417": "NH1" <-> "NH2" Residue "0 ARG 433": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 217": "NH1" <-> "NH2" Residue "E ARG 221": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "E ARG 273": "NH1" <-> "NH2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "H ARG 125": "NH1" <-> "NH2" Residue "I ARG 3": "NH1" <-> "NH2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I ARG 172": "NH1" <-> "NH2" Residue "K ARG 45": "NH1" <-> "NH2" Residue "K ARG 94": "NH1" <-> "NH2" Residue "K ARG 106": "NH1" <-> "NH2" Residue "L TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 77": "NH1" <-> "NH2" Residue "N ARG 144": "NH1" <-> "NH2" Residue "O ARG 70": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "R ARG 108": "NH1" <-> "NH2" Residue "S ARG 97": "NH1" <-> "NH2" Residue "S ARG 114": "NH1" <-> "NH2" Residue "T ARG 39": "NH1" <-> "NH2" Residue "T ARG 93": "NH1" <-> "NH2" Residue "T ARG 109": "NH1" <-> "NH2" Residue "U ARG 3": "NH1" <-> "NH2" Residue "U ARG 58": "NH1" <-> "NH2" Residue "V ARG 67": "NH1" <-> "NH2" Residue "V ARG 75": "NH1" <-> "NH2" Residue "V ARG 89": "NH1" <-> "NH2" Residue "W ARG 86": "NH1" <-> "NH2" Residue "Y TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 28": "NH1" <-> "NH2" Residue "a ARG 79": "NH1" <-> "NH2" Residue "b ARG 27": "NH1" <-> "NH2" Residue "b ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 93137 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 3987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 3987 Classifications: {'peptide': 535} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 508} Chain breaks: 5 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 470 Unresolved non-hydrogen dihedrals: 299 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 Chain: "2" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1603 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 30, 'rna3p_pyr': 31} Link IDs: {'rna2p': 13, 'rna3p': 61} Chain: "A" Number of atoms: 60389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2812, 60389 Inner-chain residues flagged as termini: ['pdbres=" G A1220 "'] Classifications: {'RNA': 2812} Modifications used: {'5*END': 2, 'rna2p_pur': 284, 'rna2p_pyr': 145, 'rna3p_pur': 1350, 'rna3p_pyr': 1033} Link IDs: {'rna2p': 429, 'rna3p': 2382} Chain breaks: 5 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: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1284 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 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: 1123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1123 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "O" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 920 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "P" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1081 Classifications: {'peptide': 146} 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: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 953 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "S" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "T" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 944 Classifications: {'peptide': 115} 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: "a" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 585 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} 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: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 455 Classifications: {'peptide': 58} 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: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 367 Classifications: {'peptide': 44} 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: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Time building chain proxies: 35.88, per 1000 atoms: 0.39 Number of scatterers: 93137 At special positions: 0 Unit cell: (218.94, 247.64, 221.4, 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 100 16.00 P 2996 15.00 O 26007 8.00 N 17303 7.00 C 46731 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=2.03 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: 47.98 Conformation dependent library (CDL) restraints added in 4.6 seconds 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6820 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 55 sheets defined 31.0% alpha, 17.0% beta 1029 base pairs and 1514 stacking pairs defined. Time for finding SS restraints: 34.58 Creating SS restraints... Processing helix chain '0' and resid 5 through 20 removed outlier: 4.406A pdb=" N LYS 0 18 " --> pdb=" O GLU 0 14 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET 0 20 " --> pdb=" O ASN 0 16 " (cutoff:3.500A) Processing helix chain '0' and resid 73 through 83 Processing helix chain '0' and resid 180 through 185 removed outlier: 4.364A pdb=" N HIS 0 184 " --> pdb=" O ASP 0 180 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 200 removed outlier: 3.734A pdb=" N GLN 0 195 " --> pdb=" O ARG 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 204 through 214 Processing helix chain '0' and resid 223 through 237 Processing helix chain '0' and resid 269 through 274 removed outlier: 3.734A pdb=" N LEU 0 274 " --> pdb=" O LEU 0 270 " (cutoff:3.500A) Processing helix chain '0' and resid 274 through 317 removed outlier: 3.671A pdb=" N GLU 0 283 " --> pdb=" O PHE 0 279 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG 0 284 " --> pdb=" O GLY 0 280 " (cutoff:3.500A) Processing helix chain '0' and resid 322 through 335 removed outlier: 6.515A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 368 through 414 removed outlier: 3.967A pdb=" N SER 0 413 " --> pdb=" O GLN 0 409 " (cutoff:3.500A) Processing helix chain '0' and resid 415 through 429 Processing helix chain '0' and resid 466 through 474 Processing helix chain '0' and resid 503 through 518 Processing helix chain '0' and resid 532 through 536 Processing helix chain '0' and resid 561 through 565 Processing helix chain 'E' and resid 207 through 215 removed outlier: 4.120A pdb=" N SER E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 225 removed outlier: 3.705A pdb=" N VAL E 224 " --> pdb=" O ARG E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'F' and resid 62 through 72 removed outlier: 4.322A pdb=" N ALA F 72 " --> pdb=" O HIS F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 127 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 102 through 121 Processing helix chain 'G' and resid 135 through 146 removed outlier: 4.137A 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 183 through 189 Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'H' and resid 3 through 11 Processing helix chain 'H' and resid 11 through 21 removed outlier: 3.756A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 28 Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.519A pdb=" N VAL H 44 " --> pdb=" O GLY H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 61 removed outlier: 4.126A pdb=" N ASP H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ALA H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU H 56 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 57 " --> pdb=" O ALA H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 93 through 106 Processing helix chain 'H' and resid 106 through 111 removed outlier: 3.961A pdb=" N VAL H 111 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 174 Processing helix chain 'I' and resid 59 through 68 removed outlier: 3.727A pdb=" N ALA I 64 " --> pdb=" O LYS I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 153 removed outlier: 3.763A pdb=" N VAL I 152 " --> pdb=" O ASN I 148 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ARG I 153 " --> pdb=" O ILE I 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 28 removed outlier: 3.973A pdb=" N VAL K 24 " --> pdb=" O PRO K 20 " (cutoff:3.500A) Proline residue: K 26 - end of helix 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 135 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 66 Processing helix chain 'L' and resid 93 through 104 Processing helix chain 'L' and resid 119 through 127 Processing helix chain 'N' and resid 25 through 39 removed outlier: 4.172A pdb=" N GLU N 32 " --> pdb=" O ARG N 28 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA N 35 " --> pdb=" O SER N 31 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 63 removed outlier: 3.917A pdb=" N ILE N 63 " --> pdb=" O ALA N 60 " (cutoff:3.500A) 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: 3.791A pdb=" N MET N 101 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 122 removed outlier: 3.727A pdb=" N LYS N 122 " --> pdb=" O GLN N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 137 Processing helix chain 'O' and resid 111 through 118 Processing helix chain 'P' and resid 92 through 100 Processing helix chain 'P' and resid 129 through 140 Processing helix chain 'Q' and resid 43 through 58 Processing helix chain 'Q' and resid 110 through 123 Processing helix chain 'R' and resid 9 through 28 Processing helix chain 'R' and resid 34 through 54 removed outlier: 3.609A pdb=" N GLU R 39 " --> pdb=" O THR R 35 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER R 42 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 4.105A 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 8 through 21 Processing helix chain 'U' and resid 26 through 31 Processing helix chain 'U' and resid 32 through 72 removed outlier: 3.818A pdb=" N LYS U 41 " --> pdb=" O GLN U 37 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS U 54 " --> pdb=" O ARG U 50 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG U 55 " --> pdb=" O ARG U 51 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ARG U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.732A 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 Processing helix chain 'W' and resid 13 through 23 removed outlier: 3.763A pdb=" N ALA W 17 " --> pdb=" O ALA W 13 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 43 through 62 Processing helix chain 'X' and resid 3 through 7 Processing helix chain 'X' and resid 14 through 22 Processing helix chain 'X' and resid 35 through 47 Processing helix chain 'b' and resid 19 through 23 removed outlier: 4.097A pdb=" N ASN b 23 " --> pdb=" O HIS b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 55 Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 12 through 35 Processing helix chain 'c' and resid 40 through 65 removed outlier: 3.973A pdb=" N ARG c 44 " --> pdb=" O THR c 40 " (cutoff:3.500A) removed outlier: 3.532A 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 18 Processing helix chain 'h' and resid 8 through 16 Processing helix chain 'h' and resid 24 through 36 removed outlier: 3.661A pdb=" N LEU h 29 " --> pdb=" O LYS h 25 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL h 30 " --> pdb=" O ASN h 26 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU h 31 " --> pdb=" O GLY h 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 14 Processing helix chain 'i' and resid 18 through 20 No H-bonds generated for 'chain 'i' and resid 18 through 20' Processing helix chain 'i' and resid 37 through 46 removed outlier: 3.973A pdb=" N LYS i 46 " --> pdb=" O ARG i 42 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 59 Processing helix chain 'i' and resid 60 through 63 removed outlier: 4.233A 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 sheet with id=AA1, first strand: chain '0' and resid 24 through 28 removed outlier: 6.493A pdb=" N ILE 0 24 " --> pdb=" O ARG 0 40 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ARG 0 40 " --> pdb=" O ILE 0 24 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '0' and resid 86 through 88 Processing sheet with id=AA3, first strand: chain '0' and resid 92 through 93 Processing sheet with id=AA4, first strand: chain '0' and resid 119 through 120 Processing sheet with id=AA5, first strand: chain '0' and resid 132 through 133 Processing sheet with id=AA6, first strand: chain '0' and resid 242 through 244 Processing sheet with id=AA7, first strand: chain '0' and resid 451 through 454 removed outlier: 4.350A pdb=" N GLU 0 451 " --> pdb=" O VAL 0 463 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE 0 483 " --> pdb=" O ILE 0 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '0' and resid 526 through 530 Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AB2, first strand: chain 'E' and resid 101 through 105 removed outlier: 3.804A pdb=" N ARG E 102 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 91 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N VAL E 81 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU E 93 " --> pdb=" O ALA E 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 130 through 131 removed outlier: 7.903A pdb=" N ARG E 189 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE E 144 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 164 through 167 removed outlier: 5.809A pdb=" N VAL E 164 " --> pdb=" O ARG E 175 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG E 175 " --> pdb=" O VAL E 164 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 16 removed outlier: 5.921A pdb=" N LYS F 9 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLU F 29 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY F 11 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU F 185 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL F 179 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU F 187 " --> pdb=" O VAL F 177 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N GLU F 175 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL F 108 " --> pdb=" O ASN F 173 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL F 113 " --> pdb=" O LEU F 199 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU F 199 " --> pdb=" O VAL F 113 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 82 through 83 removed outlier: 3.604A pdb=" N LEU F 83 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 49 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLN F 50 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 118 through 120 removed outlier: 3.899A pdb=" N GLY F 118 " --> pdb=" O MET F 164 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 3 through 7 removed outlier: 6.240A pdb=" N VAL G 4 " --> pdb=" O ASP G 16 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP G 16 " --> pdb=" O VAL G 4 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU G 6 " --> pdb=" O ALA G 14 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 123 through 125 removed outlier: 6.338A pdb=" N LEU G 153 " --> pdb=" O LEU G 193 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 31 through 37 removed outlier: 9.922A pdb=" N ILE H 34 " --> pdb=" O THR H 158 " (cutoff:3.500A) removed outlier: 10.113A pdb=" N THR H 158 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE H 36 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 66 through 70 removed outlier: 6.462A pdb=" N VAL H 66 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY H 86 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N THR H 68 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 9 through 10 removed outlier: 3.501A pdb=" N LEU I 9 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 16 through 19 Processing sheet with id=AC5, first strand: chain 'I' and resid 84 through 89 Processing sheet with id=AC6, first strand: chain 'I' and resid 96 through 98 Processing sheet with id=AC7, first strand: chain 'K' and resid 10 through 13 removed outlier: 3.716A pdb=" N SER K 65 " --> pdb=" O TYR K 61 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 99 through 101 Processing sheet with id=AC9, first strand: chain 'L' and resid 51 through 54 removed outlier: 6.944A pdb=" N ASP L 29 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE L 108 " --> pdb=" O ASP L 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 124 through 125 removed outlier: 6.503A pdb=" N VAL N 55 " --> pdb=" O ASN N 124 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TRP N 16 " --> pdb=" O GLU N 139 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 74 through 78 Processing sheet with id=AD3, first strand: chain 'O' and resid 7 through 10 removed outlier: 6.687A pdb=" N ARG O 17 " --> pdb=" O VAL O 10 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA O 16 " --> pdb=" O ALA O 46 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA O 46 " --> pdb=" O ALA O 16 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU O 18 " --> pdb=" O LYS O 44 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL O 40 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL O 24 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N VAL O 38 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA O 83 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N CYS O 84 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS O 9 " --> pdb=" O CYS O 84 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE O 86 " --> pdb=" O LYS O 9 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 76 through 79 removed outlier: 6.751A pdb=" N THR T 58 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG T 50 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR T 60 " --> pdb=" O ILE T 48 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE T 64 " --> pdb=" O GLU T 44 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N GLU T 44 " --> pdb=" O ILE T 64 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR T 25 " --> pdb=" O VAL T 86 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N VAL T 86 " --> pdb=" O THR T 25 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ARG T 27 " --> pdb=" O ILE T 84 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE T 84 " --> pdb=" O ARG T 27 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N HIS T 29 " --> pdb=" O ALA T 82 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 101 through 102 Processing sheet with id=AD6, first strand: chain 'P' and resid 75 through 77 removed outlier: 5.605A pdb=" N ALA P 75 " --> pdb=" O LYS P 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'Q' and resid 102 through 104 removed outlier: 6.969A pdb=" N ILE Q 34 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Q' and resid 41 through 42 Processing sheet with id=AD9, first strand: chain 'R' and resid 29 through 33 removed outlier: 3.979A pdb=" N MET R 114 " --> pdb=" O LEU R 104 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'R' and resid 70 through 72 removed outlier: 6.309A pdb=" N GLN R 77 " --> pdb=" O ALA R 71 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 30 through 34 removed outlier: 6.495A pdb=" N ALA S 42 " --> pdb=" O SER S 55 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER S 55 " --> pdb=" O ALA S 42 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE S 44 " --> pdb=" O LEU S 53 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'V' and resid 11 through 14 removed outlier: 3.866A pdb=" N ILE V 4 " --> pdb=" O LEU V 39 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU V 39 " --> pdb=" O ILE V 4 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'V' and resid 19 through 23 removed outlier: 7.586A pdb=" N VAL V 82 " --> pdb=" O TYR V 76 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TYR V 76 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS V 84 " --> pdb=" O PHE V 74 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE V 74 " --> pdb=" O LYS V 84 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN V 86 " --> pdb=" O THR V 72 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR V 72 " --> pdb=" O GLN V 86 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N HIS V 88 " --> pdb=" O LYS V 70 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LYS V 70 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN V 90 " --> pdb=" O ALA V 68 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS V 64 " --> pdb=" O LYS V 94 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR V 96 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL V 62 " --> pdb=" O THR V 96 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU V 98 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA V 60 " --> pdb=" O GLU V 98 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'W' and resid 3 through 11 removed outlier: 5.949A pdb=" N SER W 101 " --> pdb=" O THR W 9 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ARG W 11 " --> pdb=" O ARG W 99 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG W 99 " --> pdb=" O ARG W 11 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE W 96 " --> pdb=" O LEU W 82 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU W 82 " --> pdb=" O ILE W 96 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N LYS W 98 " --> pdb=" O PRO W 80 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR W 100 " --> pdb=" O GLU W 78 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLU W 78 " --> pdb=" O THR W 100 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS W 102 " --> pdb=" O VAL W 76 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL W 76 " --> pdb=" O HIS W 102 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR W 104 " --> pdb=" O ALA W 74 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA W 74 " --> pdb=" O THR W 104 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL W 106 " --> pdb=" O SER W 72 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'X' and resid 8 through 11 removed outlier: 3.542A pdb=" N LYS X 9 " --> pdb=" O GLU X 29 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N GLU X 29 " --> pdb=" O LYS X 9 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N THR X 27 " --> pdb=" O PRO X 11 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG X 77 " --> pdb=" O VAL X 30 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 9 through 11 Processing sheet with id=AE8, first strand: chain 'Y' and resid 23 through 27 removed outlier: 3.986A pdb=" N ALA Y 25 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Y' and resid 40 through 43 Processing sheet with id=AF1, first strand: chain 'Y' and resid 81 through 85 Processing sheet with id=AF2, first strand: chain 'a' and resid 30 through 31 removed outlier: 5.683A pdb=" N ILE a 44 " --> pdb=" O ALA a 69 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ALA a 69 " --> pdb=" O ILE a 44 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'a' and resid 38 through 39 removed outlier: 3.782A pdb=" N TYR a 54 " --> pdb=" O LYS a 85 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL a 87 " --> pdb=" O TYR a 54 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'b' and resid 34 through 36 Processing sheet with id=AF5, first strand: chain 'd' and resid 35 through 38 Processing sheet with id=AF6, first strand: chain 'f' and resid 27 through 29 Processing sheet with id=AF7, first strand: chain 'f' and resid 48 through 49 Processing sheet with id=AF8, first strand: chain 'g' and resid 18 through 22 Processing sheet with id=AF9, first strand: chain 'i' and resid 15 through 16 removed outlier: 3.729A pdb=" N LYS i 15 " --> pdb=" O LYS i 23 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'j' and resid 15 through 19 1079 hydrogen bonds defined for protein. 3015 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2618 hydrogen bonds 4240 hydrogen bond angles 0 basepair planarities 1029 basepair parallelities 1514 stacking parallelities Total time for adding SS restraints: 151.88 Time building geometry restraints manager: 51.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 13902 1.33 - 1.45: 42374 1.45 - 1.57: 38787 1.57 - 1.70: 5989 1.70 - 1.82: 184 Bond restraints: 101236 Sorted by residual: bond pdb=" C VAL H 155 " pdb=" N ILE H 156 " ideal model delta sigma weight residual 1.333 1.460 -0.127 1.20e-02 6.94e+03 1.13e+02 bond pdb=" CA VAL H 35 " pdb=" CB VAL H 35 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.36e-02 5.41e+03 1.96e+01 bond pdb=" N VAL H 155 " pdb=" CA VAL H 155 " ideal model delta sigma weight residual 1.459 1.514 -0.055 1.25e-02 6.40e+03 1.92e+01 bond pdb=" C TYR V 76 " pdb=" N LYS V 77 " ideal model delta sigma weight residual 1.330 1.271 0.059 1.47e-02 4.63e+03 1.62e+01 bond pdb=" CA ASP U 102 " pdb=" CB ASP U 102 " ideal model delta sigma weight residual 1.523 1.475 0.049 1.27e-02 6.20e+03 1.46e+01 ... (remaining 101231 not shown) Histogram of bond angle deviations from ideal: 94.28 - 107.00: 19852 107.00 - 119.71: 89267 119.71 - 132.43: 42153 132.43 - 145.15: 250 145.15 - 157.86: 1 Bond angle restraints: 151523 Sorted by residual: angle pdb=" CA LEU I 72 " pdb=" CB LEU I 72 " pdb=" CG LEU I 72 " ideal model delta sigma weight residual 116.30 157.86 -41.56 3.50e+00 8.16e-02 1.41e+02 angle pdb=" N VAL I 80 " pdb=" CA VAL I 80 " pdb=" CB VAL I 80 " ideal model delta sigma weight residual 110.62 119.28 -8.66 1.05e+00 9.07e-01 6.81e+01 angle pdb=" N THR I 69 " pdb=" CA THR I 69 " pdb=" C THR I 69 " ideal model delta sigma weight residual 112.93 122.06 -9.13 1.12e+00 7.97e-01 6.65e+01 angle pdb=" N PRO 0 544 " pdb=" CA PRO 0 544 " pdb=" CB PRO 0 544 " ideal model delta sigma weight residual 103.25 111.56 -8.31 1.05e+00 9.07e-01 6.27e+01 angle pdb=" N PRO 0 491 " pdb=" CA PRO 0 491 " pdb=" CB PRO 0 491 " ideal model delta sigma weight residual 103.25 111.03 -7.78 1.05e+00 9.07e-01 5.49e+01 ... (remaining 151518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 56180 35.98 - 71.97: 7761 71.97 - 107.95: 856 107.95 - 143.94: 38 143.94 - 179.92: 42 Dihedral angle restraints: 64877 sinusoidal: 54290 harmonic: 10587 Sorted by residual: dihedral pdb=" CB CYS f 33 " pdb=" SG CYS f 33 " pdb=" SG CYS f 46 " pdb=" CB CYS f 46 " ideal model delta sinusoidal sigma weight residual -86.00 -175.78 89.78 1 1.00e+01 1.00e-02 9.56e+01 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 180.00 132.84 47.16 0 5.00e+00 4.00e-02 8.90e+01 dihedral pdb=" CA VAL 0 203 " pdb=" C VAL 0 203 " pdb=" N SER 0 204 " pdb=" CA SER 0 204 " ideal model delta harmonic sigma weight residual 180.00 133.10 46.90 0 5.00e+00 4.00e-02 8.80e+01 ... (remaining 64874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 18183 0.088 - 0.175: 1123 0.175 - 0.263: 72 0.263 - 0.350: 8 0.350 - 0.438: 3 Chirality restraints: 19389 Sorted by residual: chirality pdb=" C1' G A1757 " pdb=" O4' G A1757 " pdb=" C2' G A1757 " pdb=" N9 G A1757 " both_signs ideal model delta sigma weight residual False 2.46 2.02 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA VAL H 35 " pdb=" N VAL H 35 " pdb=" C VAL H 35 " pdb=" CB VAL H 35 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" C3' G A1828 " pdb=" C4' G A1828 " pdb=" O3' G A1828 " pdb=" C2' G A1828 " both_signs ideal model delta sigma weight residual False -2.74 -2.36 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 19386 not shown) Planarity restraints: 8035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 68 " 0.022 2.00e-02 2.50e+03 4.48e-02 2.01e+01 pdb=" C THR I 68 " -0.077 2.00e-02 2.50e+03 pdb=" O THR I 68 " 0.029 2.00e-02 2.50e+03 pdb=" N THR I 69 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN H 9 " -0.020 2.00e-02 2.50e+03 4.09e-02 1.68e+01 pdb=" C ASN H 9 " 0.071 2.00e-02 2.50e+03 pdb=" O ASN H 9 " -0.027 2.00e-02 2.50e+03 pdb=" N LYS H 10 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G A1304 " 0.047 2.00e-02 2.50e+03 2.05e-02 1.26e+01 pdb=" N9 G A1304 " -0.048 2.00e-02 2.50e+03 pdb=" C8 G A1304 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G A1304 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G A1304 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G A1304 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G A1304 " 0.016 2.00e-02 2.50e+03 pdb=" N1 G A1304 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G A1304 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G A1304 " 0.004 2.00e-02 2.50e+03 pdb=" N3 G A1304 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G A1304 " -0.007 2.00e-02 2.50e+03 ... (remaining 8032 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 1528 2.56 - 3.15: 79508 3.15 - 3.73: 207099 3.73 - 4.32: 259190 4.32 - 4.90: 351402 Nonbonded interactions: 898727 Sorted by model distance: nonbonded pdb=" O2 C A2841 " pdb=" O2' A A2908 " model vdw 1.976 2.440 nonbonded pdb=" O4 U A1058 " pdb=" OG SER N 31 " model vdw 1.995 2.440 nonbonded pdb=" O LYS R 46 " pdb=" OG1 THR R 49 " model vdw 2.001 2.440 nonbonded pdb=" O ALA G 109 " pdb=" OG SER G 112 " model vdw 2.005 2.440 nonbonded pdb=" O2 U A1081 " pdb=" O6 G A1166 " model vdw 2.009 2.432 ... (remaining 898722 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 17.720 Check model and map are aligned: 1.010 Set scattering table: 0.650 Process input model: 338.490 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.210 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:2.200 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 365.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 101236 Z= 0.430 Angle : 0.982 41.562 151523 Z= 0.510 Chirality : 0.048 0.438 19389 Planarity : 0.007 0.086 8035 Dihedral : 24.571 179.922 58051 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.03 % Favored : 86.62 % Rotamer: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.76 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.11), residues: 3646 helix: -2.86 (0.12), residues: 1018 sheet: -3.43 (0.17), residues: 562 loop : -3.47 (0.11), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP U 61 HIS 0.016 0.004 HIS I 66 PHE 0.028 0.004 PHE I 38 TYR 0.034 0.003 TYR H 128 ARG 0.021 0.002 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1230 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1228 time to evaluate : 4.076 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: 0 100 MET cc_start: 0.9494 (mtp) cc_final: 0.8763 (tpp) REVERT: 0 102 PHE cc_start: 0.9466 (m-80) cc_final: 0.8723 (m-80) REVERT: 0 118 LEU cc_start: 0.9597 (tt) cc_final: 0.9366 (tp) REVERT: 0 123 MET cc_start: 0.2767 (mmt) cc_final: 0.2245 (mmt) REVERT: 0 286 ARG cc_start: 0.9311 (tmm160) cc_final: 0.8906 (tpm170) REVERT: E 11 ASN cc_start: 0.8179 (m-40) cc_final: 0.7299 (t0) REVERT: E 216 ILE cc_start: 0.8876 (mt) cc_final: 0.8612 (tt) REVERT: E 229 ASP cc_start: 0.8900 (m-30) cc_final: 0.8654 (m-30) REVERT: E 246 PRO cc_start: 0.8682 (Cg_exo) cc_final: 0.8195 (Cg_endo) REVERT: E 269 PHE cc_start: 0.7654 (m-80) cc_final: 0.7356 (m-80) REVERT: F 16 PHE cc_start: 0.8232 (m-80) cc_final: 0.7957 (m-80) REVERT: F 79 PHE cc_start: 0.8654 (m-80) cc_final: 0.8182 (m-10) REVERT: F 91 TYR cc_start: 0.9160 (m-80) cc_final: 0.8918 (m-80) REVERT: F 109 ASP cc_start: 0.7164 (p0) cc_final: 0.6528 (p0) REVERT: F 134 SER cc_start: 0.8250 (p) cc_final: 0.7880 (m) REVERT: F 176 ILE cc_start: 0.8653 (mt) cc_final: 0.8306 (mt) REVERT: F 203 LYS cc_start: 0.8509 (mttt) cc_final: 0.8289 (tttm) REVERT: G 34 PHE cc_start: 0.8783 (t80) cc_final: 0.8446 (t80) REVERT: G 50 LYS cc_start: 0.8923 (tmtp) cc_final: 0.8546 (tmmt) REVERT: G 82 GLN cc_start: 0.8170 (tt0) cc_final: 0.7151 (tp-100) REVERT: G 107 ARG cc_start: 0.9411 (mtt180) cc_final: 0.8944 (ttm110) REVERT: G 189 HIS cc_start: 0.8760 (m-70) cc_final: 0.8158 (m-70) REVERT: H 22 TYR cc_start: 0.8422 (m-80) cc_final: 0.8108 (m-80) REVERT: H 96 MET cc_start: 0.7961 (mpp) cc_final: 0.7501 (mpp) REVERT: H 110 ARG cc_start: 0.8342 (ppt-90) cc_final: 0.7979 (ptm-80) REVERT: H 125 ARG cc_start: 0.8831 (mmt180) cc_final: 0.8561 (mmm-85) REVERT: H 169 LEU cc_start: 0.9358 (tt) cc_final: 0.9068 (tp) REVERT: I 14 ASP cc_start: 0.9267 (m-30) cc_final: 0.8991 (t0) REVERT: I 35 THR cc_start: 0.9005 (p) cc_final: 0.8633 (m) REVERT: I 49 ASN cc_start: 0.9549 (t0) cc_final: 0.9325 (t0) REVERT: K 19 ASN cc_start: 0.8789 (t0) cc_final: 0.7988 (m-40) REVERT: K 61 TYR cc_start: 0.9123 (t80) cc_final: 0.8902 (t80) REVERT: K 99 THR cc_start: 0.8992 (t) cc_final: 0.8553 (m) REVERT: L 15 ILE cc_start: 0.9425 (mt) cc_final: 0.8749 (mt) REVERT: L 18 LYS cc_start: 0.9042 (ptpp) cc_final: 0.8768 (ptpp) REVERT: L 128 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7338 (pt0) REVERT: N 30 SER cc_start: 0.8578 (p) cc_final: 0.7805 (p) REVERT: N 42 LYS cc_start: 0.8146 (mttt) cc_final: 0.7792 (mttm) REVERT: N 81 HIS cc_start: 0.7835 (m-70) cc_final: 0.7143 (m-70) REVERT: N 92 GLU cc_start: 0.9221 (tt0) cc_final: 0.8955 (tm-30) REVERT: N 93 MET cc_start: 0.8943 (mmm) cc_final: 0.7935 (mpp) REVERT: N 100 LYS cc_start: 0.8916 (mttt) cc_final: 0.8281 (tttt) REVERT: N 101 MET cc_start: 0.9026 (ppp) cc_final: 0.8695 (ppp) REVERT: N 117 ARG cc_start: 0.8721 (mtm-85) cc_final: 0.8484 (mtt90) REVERT: O 7 ARG cc_start: 0.9004 (mtt-85) cc_final: 0.8394 (mmt90) REVERT: O 9 LYS cc_start: 0.9002 (ptpp) cc_final: 0.8782 (ptmm) REVERT: O 18 GLU cc_start: 0.8888 (tt0) cc_final: 0.8398 (tm-30) REVERT: O 20 LEU cc_start: 0.9023 (tt) cc_final: 0.8440 (tp) REVERT: O 44 LYS cc_start: 0.7684 (mmtt) cc_final: 0.6322 (mmtt) REVERT: O 45 GLN cc_start: 0.8621 (mm110) cc_final: 0.8258 (mm110) REVERT: O 64 ARG cc_start: 0.8245 (ptt-90) cc_final: 0.7964 (ttp80) REVERT: O 76 TYR cc_start: 0.8009 (m-10) cc_final: 0.7770 (m-10) REVERT: O 107 ARG cc_start: 0.9299 (mtt180) cc_final: 0.8950 (mmm160) REVERT: O 112 MET cc_start: 0.8815 (pmm) cc_final: 0.8098 (pmm) REVERT: O 113 LYS cc_start: 0.9584 (tppp) cc_final: 0.9371 (tppt) REVERT: P 50 PHE cc_start: 0.8152 (t80) cc_final: 0.7590 (t80) REVERT: P 74 TYR cc_start: 0.8797 (m-80) cc_final: 0.8450 (m-80) REVERT: P 85 PHE cc_start: 0.8333 (m-80) cc_final: 0.7984 (m-80) REVERT: Q 3 LEU cc_start: 0.8576 (mt) cc_final: 0.8317 (tp) REVERT: Q 29 PHE cc_start: 0.8808 (m-80) cc_final: 0.8379 (m-10) REVERT: Q 37 LEU cc_start: 0.9503 (mt) cc_final: 0.9204 (mt) REVERT: Q 38 GLU cc_start: 0.8215 (mt-10) cc_final: 0.8009 (mp0) REVERT: Q 57 TYR cc_start: 0.9204 (t80) cc_final: 0.7846 (t80) REVERT: Q 75 THR cc_start: 0.8357 (p) cc_final: 0.7804 (p) REVERT: Q 83 MET cc_start: 0.8589 (mmm) cc_final: 0.7716 (mmt) REVERT: Q 104 PHE cc_start: 0.8156 (m-10) cc_final: 0.7903 (m-10) REVERT: R 8 ARG cc_start: 0.8398 (mmt90) cc_final: 0.8044 (mtt-85) REVERT: R 14 LYS cc_start: 0.9573 (ptmt) cc_final: 0.9307 (ptmm) REVERT: R 16 MET cc_start: 0.9186 (ttm) cc_final: 0.8713 (ttp) REVERT: R 31 GLU cc_start: 0.8680 (pp20) cc_final: 0.8088 (tm-30) REVERT: R 52 LYS cc_start: 0.8855 (mttt) cc_final: 0.8470 (mmtt) REVERT: R 76 ASN cc_start: 0.9386 (m110) cc_final: 0.9070 (t0) REVERT: R 78 ASP cc_start: 0.9016 (p0) cc_final: 0.8711 (p0) REVERT: R 99 THR cc_start: 0.9077 (p) cc_final: 0.8865 (t) REVERT: R 114 MET cc_start: 0.8734 (mtm) cc_final: 0.8047 (mtt) REVERT: R 117 ILE cc_start: 0.9615 (tt) cc_final: 0.9273 (tt) REVERT: S 41 TYR cc_start: 0.8277 (m-10) cc_final: 0.7956 (m-10) REVERT: S 90 ILE cc_start: 0.7840 (pt) cc_final: 0.7543 (tt) REVERT: T 26 LEU cc_start: 0.9320 (tt) cc_final: 0.8782 (tt) REVERT: T 48 ILE cc_start: 0.8764 (mm) cc_final: 0.8456 (tt) REVERT: T 74 PHE cc_start: 0.9132 (m-80) cc_final: 0.8928 (m-80) REVERT: T 91 LYS cc_start: 0.8537 (ptmm) cc_final: 0.8237 (mtmm) REVERT: U 38 GLN cc_start: 0.8899 (tp40) cc_final: 0.8559 (tp40) REVERT: U 45 TYR cc_start: 0.8684 (m-10) cc_final: 0.8354 (m-10) REVERT: U 47 PHE cc_start: 0.8735 (t80) cc_final: 0.8331 (t80) REVERT: U 56 ASP cc_start: 0.9085 (m-30) cc_final: 0.8858 (m-30) REVERT: U 74 LEU cc_start: 0.9054 (mt) cc_final: 0.8756 (mt) REVERT: U 80 MET cc_start: 0.8085 (mtt) cc_final: 0.7685 (mtt) REVERT: V 40 PHE cc_start: 0.8014 (t80) cc_final: 0.6340 (t80) REVERT: V 75 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8238 (mtt-85) REVERT: V 76 TYR cc_start: 0.8516 (p90) cc_final: 0.7862 (p90) REVERT: V 97 ILE cc_start: 0.9301 (mm) cc_final: 0.9072 (mt) REVERT: W 48 GLU cc_start: 0.9209 (pt0) cc_final: 0.8689 (pp20) REVERT: W 49 LYS cc_start: 0.8868 (tppp) cc_final: 0.8443 (tptt) REVERT: W 52 LYS cc_start: 0.9526 (mttt) cc_final: 0.9207 (mttp) REVERT: W 68 ASN cc_start: 0.9146 (t0) cc_final: 0.8700 (t0) REVERT: W 94 SER cc_start: 0.7713 (p) cc_final: 0.7202 (p) REVERT: X 16 ARG cc_start: 0.9310 (mmm-85) cc_final: 0.8884 (mtm-85) REVERT: X 20 LEU cc_start: 0.9823 (mt) cc_final: 0.9616 (mt) REVERT: X 21 MET cc_start: 0.9425 (ptp) cc_final: 0.9153 (ppp) REVERT: X 38 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7984 (mt-10) REVERT: X 55 ASN cc_start: 0.8546 (m110) cc_final: 0.8345 (m-40) REVERT: X 57 MET cc_start: 0.5076 (mtp) cc_final: 0.4579 (mtp) REVERT: Y 10 MET cc_start: 0.8390 (tpt) cc_final: 0.7720 (tpt) REVERT: Y 11 VAL cc_start: 0.8914 (t) cc_final: 0.8637 (t) REVERT: Y 20 GLN cc_start: 0.9309 (pt0) cc_final: 0.9096 (pm20) REVERT: Y 27 PHE cc_start: 0.8990 (m-80) cc_final: 0.8662 (m-80) REVERT: Y 64 HIS cc_start: 0.8722 (t-90) cc_final: 0.8245 (t-90) REVERT: Y 69 MET cc_start: 0.6972 (mtp) cc_final: 0.6622 (mmm) REVERT: Y 83 TYR cc_start: 0.8411 (m-80) cc_final: 0.8077 (m-80) REVERT: Y 92 ARG cc_start: 0.8513 (mtm180) cc_final: 0.8290 (ptp-170) REVERT: a 25 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8231 (tm-30) REVERT: a 85 LYS cc_start: 0.9069 (mttm) cc_final: 0.8735 (mttt) REVERT: b 27 ARG cc_start: 0.7581 (ptm160) cc_final: 0.6973 (ptm160) REVERT: b 48 TYR cc_start: 0.8121 (m-80) cc_final: 0.7648 (m-10) REVERT: c 21 LEU cc_start: 0.9607 (mp) cc_final: 0.9396 (pp) REVERT: c 25 LEU cc_start: 0.9066 (tp) cc_final: 0.8587 (tp) REVERT: c 26 PHE cc_start: 0.9020 (t80) cc_final: 0.8093 (t80) REVERT: c 30 PHE cc_start: 0.8779 (m-10) cc_final: 0.8008 (m-80) REVERT: c 37 LEU cc_start: 0.7476 (tt) cc_final: 0.6686 (tt) REVERT: c 38 GLU cc_start: 0.8075 (mp0) cc_final: 0.7726 (mp0) REVERT: c 54 LYS cc_start: 0.9497 (ttmp) cc_final: 0.9286 (mtpp) REVERT: d 18 ASP cc_start: 0.9280 (m-30) cc_final: 0.8898 (m-30) REVERT: d 24 ARG cc_start: 0.8393 (tpt90) cc_final: 0.7946 (tpt90) REVERT: d 37 HIS cc_start: 0.8516 (m-70) cc_final: 0.8199 (m90) REVERT: d 49 LYS cc_start: 0.8579 (tttt) cc_final: 0.8034 (tppt) REVERT: f 5 PHE cc_start: 0.9373 (t80) cc_final: 0.9115 (t80) REVERT: f 14 ARG cc_start: 0.9181 (mtt180) cc_final: 0.8879 (mtt180) REVERT: f 25 PRO cc_start: 0.8062 (Cg_exo) cc_final: 0.7829 (Cg_endo) REVERT: f 36 MET cc_start: 0.9372 (mmm) cc_final: 0.9131 (mmp) REVERT: g 25 ASN cc_start: 0.8962 (m-40) cc_final: 0.8120 (t0) REVERT: g 28 ASP cc_start: 0.8851 (p0) cc_final: 0.8555 (p0) REVERT: g 30 VAL cc_start: 0.9389 (p) cc_final: 0.9101 (t) REVERT: g 38 ARG cc_start: 0.8778 (mtp180) cc_final: 0.8382 (mtp180) REVERT: h 8 ASN cc_start: 0.8438 (t0) cc_final: 0.8122 (t0) REVERT: h 13 SER cc_start: 0.9282 (m) cc_final: 0.8610 (t) REVERT: h 19 ARG cc_start: 0.9311 (mmm160) cc_final: 0.8536 (mmm160) REVERT: h 21 ARG cc_start: 0.9115 (mmt90) cc_final: 0.8417 (mmt180) REVERT: i 59 LYS cc_start: 0.9247 (ptpt) cc_final: 0.8925 (ptpp) REVERT: j 26 ILE cc_start: 0.8285 (mm) cc_final: 0.7997 (mm) REVERT: j 33 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8858 (ttpp) outliers start: 2 outliers final: 0 residues processed: 1230 average time/residue: 0.9946 time to fit residues: 1982.6652 Evaluate side-chains 777 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 777 time to evaluate : 4.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 555 optimal weight: 20.0000 chunk 498 optimal weight: 8.9990 chunk 276 optimal weight: 20.0000 chunk 170 optimal weight: 50.0000 chunk 336 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 chunk 515 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 383 optimal weight: 5.9990 chunk 597 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN F 50 GLN F 135 HIS G 9 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 102 ASN I 107 ASN I 129 GLN L 44 GLN L 49 ASN L 73 ASN L 103 HIS N 8 ASN O 45 GLN O 109 ASN P 59 GLN Q 28 HIS Q 123 HIS ** R 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 ASN ** T 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 GLN W 2 GLN Y 59 GLN ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 101236 Z= 0.293 Angle : 0.816 20.177 151523 Z= 0.415 Chirality : 0.042 0.481 19389 Planarity : 0.006 0.075 8035 Dihedral : 25.563 179.730 50770 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 24.66 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.50 % Favored : 89.41 % Rotamer: Outliers : 3.68 % Allowed : 15.45 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.34 % 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: -3.73 (0.12), residues: 3646 helix: -1.60 (0.14), residues: 1033 sheet: -2.86 (0.18), residues: 595 loop : -2.92 (0.12), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP Q 65 HIS 0.011 0.002 HIS T 29 PHE 0.034 0.003 PHE R 84 TYR 0.045 0.003 TYR I 165 ARG 0.012 0.001 ARG b 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 913 time to evaluate : 3.979 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: 0 100 MET cc_start: 0.9509 (mtp) cc_final: 0.8931 (tmm) REVERT: 0 102 PHE cc_start: 0.9487 (m-80) cc_final: 0.8785 (m-80) REVERT: 0 118 LEU cc_start: 0.9631 (tt) cc_final: 0.9352 (tp) REVERT: 0 123 MET cc_start: 0.3045 (mmt) cc_final: 0.2360 (mmt) REVERT: 0 286 ARG cc_start: 0.9242 (tmm160) cc_final: 0.8806 (tpm170) REVERT: E 183 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8686 (mpp) REVERT: E 216 ILE cc_start: 0.8896 (mt) cc_final: 0.8486 (tp) REVERT: E 246 PRO cc_start: 0.8630 (Cg_exo) cc_final: 0.8362 (Cg_endo) REVERT: E 269 PHE cc_start: 0.8104 (m-80) cc_final: 0.7785 (m-80) REVERT: F 8 ARG cc_start: 0.8903 (ttm170) cc_final: 0.8625 (ttp-170) REVERT: F 16 PHE cc_start: 0.8481 (m-80) cc_final: 0.7529 (m-80) REVERT: F 79 PHE cc_start: 0.8724 (m-80) cc_final: 0.8217 (m-10) REVERT: F 109 ASP cc_start: 0.7232 (p0) cc_final: 0.6000 (p0) REVERT: F 133 MET cc_start: 0.8840 (mmm) cc_final: 0.8508 (mmm) REVERT: F 134 SER cc_start: 0.8120 (p) cc_final: 0.7790 (m) REVERT: F 152 ASN cc_start: 0.8890 (m-40) cc_final: 0.8562 (t0) REVERT: F 178 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8286 (ttpt) REVERT: F 203 LYS cc_start: 0.8514 (mttt) cc_final: 0.8265 (ttpt) REVERT: G 40 GLN cc_start: 0.9067 (OUTLIER) cc_final: 0.8400 (tp40) REVERT: G 50 LYS cc_start: 0.9208 (tmtp) cc_final: 0.8669 (ttpt) REVERT: G 82 GLN cc_start: 0.8148 (tt0) cc_final: 0.7291 (tp40) REVERT: G 83 TRP cc_start: 0.8743 (m100) cc_final: 0.8394 (m100) REVERT: G 149 GLU cc_start: 0.8958 (pm20) cc_final: 0.8544 (pm20) REVERT: G 150 LYS cc_start: 0.9297 (mmmt) cc_final: 0.8786 (mmmt) REVERT: G 153 LEU cc_start: 0.9200 (tp) cc_final: 0.8958 (pp) REVERT: H 22 TYR cc_start: 0.8569 (m-80) cc_final: 0.8358 (m-10) REVERT: H 125 ARG cc_start: 0.8662 (mmt180) cc_final: 0.8416 (mmm-85) REVERT: H 152 MET cc_start: 0.8589 (ptt) cc_final: 0.8117 (mpp) REVERT: I 14 ASP cc_start: 0.9336 (m-30) cc_final: 0.8905 (t0) REVERT: K 61 TYR cc_start: 0.9114 (t80) cc_final: 0.8793 (t80) REVERT: K 93 ASN cc_start: 0.9558 (m110) cc_final: 0.9048 (p0) REVERT: K 125 MET cc_start: 0.8427 (mmt) cc_final: 0.8210 (mmt) REVERT: N 45 TYR cc_start: 0.8710 (t80) cc_final: 0.8467 (t80) REVERT: N 81 HIS cc_start: 0.7787 (m-70) cc_final: 0.7449 (m90) REVERT: N 88 ARG cc_start: 0.7932 (mmm-85) cc_final: 0.7684 (mtt180) REVERT: N 93 MET cc_start: 0.9142 (mmm) cc_final: 0.8476 (mmm) REVERT: N 96 ASN cc_start: 0.9168 (m110) cc_final: 0.8788 (m110) REVERT: N 100 LYS cc_start: 0.8979 (mttt) cc_final: 0.8504 (tmtt) REVERT: N 101 MET cc_start: 0.9079 (ppp) cc_final: 0.8811 (ppp) REVERT: N 109 MET cc_start: 0.8335 (mtm) cc_final: 0.8111 (mtm) REVERT: N 117 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8485 (mtt90) REVERT: N 133 HIS cc_start: 0.7398 (m-70) cc_final: 0.7071 (m-70) REVERT: O 7 ARG cc_start: 0.9013 (mtt-85) cc_final: 0.8386 (mmt90) REVERT: O 9 LYS cc_start: 0.9318 (ptpp) cc_final: 0.8991 (ptmm) REVERT: O 18 GLU cc_start: 0.9038 (tt0) cc_final: 0.8645 (tt0) REVERT: O 20 LEU cc_start: 0.9035 (tt) cc_final: 0.8604 (tp) REVERT: O 44 LYS cc_start: 0.7807 (mmtt) cc_final: 0.6532 (mmtt) REVERT: O 53 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8480 (mppt) REVERT: O 112 MET cc_start: 0.8840 (pmm) cc_final: 0.8593 (mpp) REVERT: O 113 LYS cc_start: 0.9610 (tppp) cc_final: 0.9396 (tppt) REVERT: O 120 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: P 50 PHE cc_start: 0.8219 (t80) cc_final: 0.7642 (t80) REVERT: P 85 PHE cc_start: 0.8359 (m-80) cc_final: 0.7985 (m-80) REVERT: Q 1 MET cc_start: 0.7511 (mmm) cc_final: 0.7290 (ptt) REVERT: Q 37 LEU cc_start: 0.9524 (mt) cc_final: 0.9250 (mt) REVERT: Q 38 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7925 (mp0) REVERT: Q 72 LYS cc_start: 0.9279 (ttmm) cc_final: 0.9068 (tppp) REVERT: Q 83 MET cc_start: 0.8657 (mmm) cc_final: 0.8171 (mmt) REVERT: Q 103 LEU cc_start: 0.9227 (mm) cc_final: 0.9026 (mm) REVERT: Q 104 PHE cc_start: 0.8417 (m-10) cc_final: 0.8115 (m-10) REVERT: R 3 TYR cc_start: 0.7417 (p90) cc_final: 0.7198 (p90) REVERT: R 28 GLU cc_start: 0.8315 (tm-30) cc_final: 0.8114 (tp30) REVERT: R 31 GLU cc_start: 0.8700 (pp20) cc_final: 0.8490 (tm-30) REVERT: R 39 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8544 (mp0) REVERT: R 52 LYS cc_start: 0.8739 (mttt) cc_final: 0.8395 (mmtt) REVERT: R 78 ASP cc_start: 0.9157 (p0) cc_final: 0.8934 (p0) REVERT: R 114 MET cc_start: 0.8581 (mtm) cc_final: 0.8367 (mtm) REVERT: R 117 ILE cc_start: 0.9481 (tt) cc_final: 0.9224 (tt) REVERT: R 119 LEU cc_start: 0.9222 (mt) cc_final: 0.8785 (mt) REVERT: S 90 ILE cc_start: 0.8199 (pt) cc_final: 0.7974 (tp) REVERT: T 10 LYS cc_start: 0.9491 (mtmt) cc_final: 0.9048 (ptpp) REVERT: T 48 ILE cc_start: 0.8874 (mm) cc_final: 0.8535 (tt) REVERT: T 74 PHE cc_start: 0.9099 (m-80) cc_final: 0.8894 (m-80) REVERT: T 106 LYS cc_start: 0.9368 (mmmt) cc_final: 0.9030 (mmmt) REVERT: U 45 TYR cc_start: 0.8737 (m-10) cc_final: 0.8370 (m-10) REVERT: U 94 MET cc_start: 0.9181 (mmm) cc_final: 0.8839 (mmm) REVERT: V 2 TYR cc_start: 0.7780 (p90) cc_final: 0.7075 (p90) REVERT: V 40 PHE cc_start: 0.8293 (t80) cc_final: 0.7401 (t80) REVERT: V 75 ARG cc_start: 0.8508 (mtp85) cc_final: 0.8234 (mtt-85) REVERT: V 76 TYR cc_start: 0.8469 (p90) cc_final: 0.8089 (p90) REVERT: V 97 ILE cc_start: 0.9286 (mm) cc_final: 0.9025 (mt) REVERT: W 48 GLU cc_start: 0.9224 (pt0) cc_final: 0.8749 (pp20) REVERT: W 49 LYS cc_start: 0.8835 (tppp) cc_final: 0.8354 (tptt) REVERT: W 52 LYS cc_start: 0.9604 (mttt) cc_final: 0.9240 (mttp) REVERT: W 78 GLU cc_start: 0.7488 (pp20) cc_final: 0.7238 (pp20) REVERT: X 16 ARG cc_start: 0.9347 (mmm-85) cc_final: 0.8903 (mtm-85) REVERT: X 40 LYS cc_start: 0.9340 (tttt) cc_final: 0.9126 (tptt) REVERT: X 44 GLU cc_start: 0.8282 (mp0) cc_final: 0.7840 (mm-30) REVERT: X 57 MET cc_start: 0.5351 (mtp) cc_final: 0.5134 (mtp) REVERT: Y 27 PHE cc_start: 0.9051 (m-80) cc_final: 0.8752 (m-80) REVERT: Y 32 ARG cc_start: 0.8885 (mtt-85) cc_final: 0.8514 (mtt180) REVERT: Y 83 TYR cc_start: 0.8387 (m-80) cc_final: 0.8090 (m-80) REVERT: Y 92 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8358 (ptp-170) REVERT: a 25 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8209 (tm-30) REVERT: a 49 ARG cc_start: 0.7908 (mmt90) cc_final: 0.7480 (mmt90) REVERT: a 85 LYS cc_start: 0.9102 (mttm) cc_final: 0.8847 (mttt) REVERT: c 18 VAL cc_start: 0.9614 (t) cc_final: 0.9236 (m) REVERT: c 26 PHE cc_start: 0.9071 (t80) cc_final: 0.8360 (t80) REVERT: c 30 PHE cc_start: 0.8786 (m-10) cc_final: 0.8142 (m-80) REVERT: c 38 GLU cc_start: 0.8292 (mp0) cc_final: 0.7873 (mp0) REVERT: c 44 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7780 (tpp-160) REVERT: c 45 GLU cc_start: 0.8786 (tt0) cc_final: 0.8557 (tm-30) REVERT: c 47 ARG cc_start: 0.8110 (mtp180) cc_final: 0.7558 (ttm-80) REVERT: c 53 MET cc_start: 0.9157 (mtp) cc_final: 0.8750 (ptp) REVERT: c 54 LYS cc_start: 0.9563 (ttmp) cc_final: 0.9344 (mtpp) REVERT: d 19 GLN cc_start: 0.9069 (mp10) cc_final: 0.8668 (mp10) REVERT: d 24 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8189 (tpt170) REVERT: f 16 ARG cc_start: 0.8490 (ttp-170) cc_final: 0.7823 (ttp-170) REVERT: f 17 ARG cc_start: 0.8688 (mtt180) cc_final: 0.8411 (mtt180) REVERT: f 21 LYS cc_start: 0.9149 (pttt) cc_final: 0.8912 (pttt) REVERT: g 25 ASN cc_start: 0.9132 (m-40) cc_final: 0.8651 (t0) REVERT: g 26 ASN cc_start: 0.8033 (m110) cc_final: 0.7532 (p0) REVERT: g 28 ASP cc_start: 0.9242 (p0) cc_final: 0.8793 (p0) REVERT: g 30 VAL cc_start: 0.9278 (p) cc_final: 0.8843 (t) REVERT: g 38 ARG cc_start: 0.8855 (mtp180) cc_final: 0.8279 (mtp180) REVERT: g 40 LYS cc_start: 0.9441 (mmmm) cc_final: 0.9216 (mmmm) REVERT: g 46 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8119 (tpp80) REVERT: h 8 ASN cc_start: 0.8553 (t0) cc_final: 0.8262 (t0) REVERT: h 9 ASN cc_start: 0.8628 (m-40) cc_final: 0.8336 (m110) REVERT: h 12 ARG cc_start: 0.9280 (ttm-80) cc_final: 0.8715 (tpp80) REVERT: h 13 SER cc_start: 0.9444 (m) cc_final: 0.8782 (t) REVERT: i 32 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8337 (mt) REVERT: j 17 ILE cc_start: 0.9315 (pp) cc_final: 0.9045 (pp) REVERT: j 18 ARG cc_start: 0.8812 (ttm170) cc_final: 0.8421 (ttm170) REVERT: j 24 MET cc_start: 0.9142 (mtp) cc_final: 0.8908 (tmm) REVERT: j 33 LYS cc_start: 0.8946 (ttmt) cc_final: 0.8736 (ttpt) outliers start: 111 outliers final: 64 residues processed: 960 average time/residue: 0.9772 time to fit residues: 1556.5145 Evaluate side-chains 819 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 750 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 113 ILE Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 123 HIS Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 116 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 25 THR Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain W residue 2 GLN Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 62 TYR Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 76 ARG Chi-restraints excluded: chain Y residue 87 ASP Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 34 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 332 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 497 optimal weight: 0.6980 chunk 406 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 598 optimal weight: 5.9990 chunk 646 optimal weight: 10.0000 chunk 533 optimal weight: 10.0000 chunk 593 optimal weight: 9.9990 chunk 204 optimal weight: 30.0000 chunk 480 optimal weight: 20.0000 overall best weight: 6.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 247 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 GLN F 184 ASN ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 75 ASN I 107 ASN ** O 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 123 HIS ** R 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 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** V 101 ASN ** W 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 95 GLN ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 101236 Z= 0.275 Angle : 0.767 14.163 151523 Z= 0.392 Chirality : 0.040 0.465 19389 Planarity : 0.006 0.069 8035 Dihedral : 25.419 179.949 50770 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 25.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.78 % Favored : 89.11 % Rotamer: Outliers : 4.87 % Allowed : 18.53 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.12), residues: 3646 helix: -1.25 (0.14), residues: 1053 sheet: -2.55 (0.19), residues: 590 loop : -2.72 (0.12), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 93 HIS 0.032 0.002 HIS Q 123 PHE 0.031 0.003 PHE R 84 TYR 0.020 0.002 TYR I 165 ARG 0.011 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 839 time to evaluate : 4.054 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: 0 100 MET cc_start: 0.9503 (mtp) cc_final: 0.8966 (tmm) REVERT: 0 102 PHE cc_start: 0.9529 (m-80) cc_final: 0.8863 (m-80) REVERT: 0 118 LEU cc_start: 0.9645 (tt) cc_final: 0.9400 (tp) REVERT: 0 123 MET cc_start: 0.3376 (mmt) cc_final: 0.2726 (mmt) REVERT: 0 286 ARG cc_start: 0.9255 (tmm160) cc_final: 0.8892 (tpm170) REVERT: 0 327 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8711 (pt) REVERT: E 180 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7106 (mt-10) REVERT: E 183 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8597 (mpp) REVERT: E 216 ILE cc_start: 0.8954 (mt) cc_final: 0.8519 (tp) REVERT: E 247 MET cc_start: 0.8641 (mmp) cc_final: 0.8263 (tpp) REVERT: E 269 PHE cc_start: 0.8194 (m-80) cc_final: 0.7865 (m-80) REVERT: F 16 PHE cc_start: 0.8430 (m-80) cc_final: 0.7643 (m-80) REVERT: F 50 GLN cc_start: 0.7424 (mm-40) cc_final: 0.6700 (mm110) REVERT: F 79 PHE cc_start: 0.8723 (m-80) cc_final: 0.8195 (m-80) REVERT: F 109 ASP cc_start: 0.7389 (p0) cc_final: 0.6410 (p0) REVERT: F 128 GLN cc_start: 0.8383 (mp10) cc_final: 0.8004 (mp10) REVERT: F 134 SER cc_start: 0.8063 (p) cc_final: 0.7771 (m) REVERT: F 203 LYS cc_start: 0.8456 (mttt) cc_final: 0.8184 (tttm) REVERT: G 39 MET cc_start: 0.9192 (tmm) cc_final: 0.8512 (tmm) REVERT: G 40 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8263 (tp40) REVERT: G 50 LYS cc_start: 0.9251 (tmtp) cc_final: 0.8711 (ttpt) REVERT: G 82 GLN cc_start: 0.8159 (tt0) cc_final: 0.7597 (tp-100) REVERT: G 83 TRP cc_start: 0.8853 (m100) cc_final: 0.8382 (m100) REVERT: G 107 ARG cc_start: 0.9461 (mtt180) cc_final: 0.9070 (mtm110) REVERT: G 153 LEU cc_start: 0.9305 (tp) cc_final: 0.9073 (pp) REVERT: H 22 TYR cc_start: 0.8450 (m-80) cc_final: 0.8216 (m-10) REVERT: H 94 GLU cc_start: 0.9304 (mm-30) cc_final: 0.9074 (tp30) REVERT: H 152 MET cc_start: 0.8299 (ptt) cc_final: 0.8001 (mpp) REVERT: I 14 ASP cc_start: 0.9333 (m-30) cc_final: 0.8867 (t0) REVERT: I 49 ASN cc_start: 0.9491 (t0) cc_final: 0.9229 (t0) REVERT: I 110 TYR cc_start: 0.8624 (m-80) cc_final: 0.8403 (m-80) REVERT: K 61 TYR cc_start: 0.9101 (t80) cc_final: 0.8743 (t80) REVERT: K 125 MET cc_start: 0.8421 (mmt) cc_final: 0.8028 (mmt) REVERT: L 59 MET cc_start: 0.2804 (mpp) cc_final: 0.1797 (ppp) REVERT: N 26 LEU cc_start: 0.9158 (pt) cc_final: 0.8919 (pp) REVERT: N 45 TYR cc_start: 0.8674 (t80) cc_final: 0.8436 (t80) REVERT: N 81 HIS cc_start: 0.7878 (m-70) cc_final: 0.7497 (m90) REVERT: N 96 ASN cc_start: 0.9017 (m110) cc_final: 0.8735 (m110) REVERT: N 100 LYS cc_start: 0.9058 (mttt) cc_final: 0.8614 (tmtt) REVERT: N 101 MET cc_start: 0.9107 (ppp) cc_final: 0.8804 (ppp) REVERT: N 133 HIS cc_start: 0.7448 (m-70) cc_final: 0.7021 (m-70) REVERT: O 1 MET cc_start: 0.5398 (mmm) cc_final: 0.5028 (tpt) REVERT: O 4 GLN cc_start: 0.8926 (pp30) cc_final: 0.8349 (pp30) REVERT: O 5 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8808 (mm-30) REVERT: O 7 ARG cc_start: 0.9074 (mtt-85) cc_final: 0.8679 (mmt90) REVERT: O 9 LYS cc_start: 0.9400 (ptpp) cc_final: 0.9035 (ptmm) REVERT: O 20 LEU cc_start: 0.9017 (tt) cc_final: 0.8511 (tp) REVERT: O 23 LYS cc_start: 0.8615 (ttmm) cc_final: 0.8405 (ttpp) REVERT: O 45 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8337 (mm110) REVERT: O 59 LYS cc_start: 0.8861 (pttm) cc_final: 0.8637 (tmmt) REVERT: O 105 GLU cc_start: 0.9064 (mp0) cc_final: 0.8764 (mp0) REVERT: O 112 MET cc_start: 0.8853 (pmm) cc_final: 0.8544 (mpp) REVERT: O 113 LYS cc_start: 0.9629 (tppp) cc_final: 0.9393 (tppt) REVERT: O 120 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: P 3 LEU cc_start: 0.9628 (mt) cc_final: 0.9381 (tt) REVERT: P 58 PHE cc_start: 0.8435 (p90) cc_final: 0.8103 (p90) REVERT: P 59 GLN cc_start: 0.9058 (pt0) cc_final: 0.8164 (tp-100) REVERT: P 60 ARG cc_start: 0.8410 (ptp-170) cc_final: 0.7944 (ptp-170) REVERT: P 85 PHE cc_start: 0.8376 (m-80) cc_final: 0.8020 (m-80) REVERT: Q 1 MET cc_start: 0.7469 (mmm) cc_final: 0.7265 (ptt) REVERT: Q 17 MET cc_start: 0.7783 (tpp) cc_final: 0.7568 (mpp) REVERT: Q 37 LEU cc_start: 0.9521 (mt) cc_final: 0.9282 (mt) REVERT: Q 38 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8213 (mp0) REVERT: Q 57 TYR cc_start: 0.9256 (t80) cc_final: 0.7903 (t80) REVERT: Q 83 MET cc_start: 0.8633 (mmm) cc_final: 0.7681 (tpp) REVERT: Q 103 LEU cc_start: 0.9232 (mm) cc_final: 0.9007 (mm) REVERT: Q 104 PHE cc_start: 0.8520 (m-10) cc_final: 0.8231 (m-10) REVERT: R 3 TYR cc_start: 0.7525 (p90) cc_final: 0.7186 (p90) REVERT: R 28 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7469 (tp30) REVERT: R 31 GLU cc_start: 0.8755 (pp20) cc_final: 0.8437 (tm-30) REVERT: R 39 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8624 (mp0) REVERT: R 46 LYS cc_start: 0.9015 (mmtp) cc_final: 0.8783 (mmtm) REVERT: R 52 LYS cc_start: 0.8781 (mttt) cc_final: 0.8486 (mmtt) REVERT: R 55 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.7936 (p0) REVERT: R 74 GLU cc_start: 0.9471 (OUTLIER) cc_final: 0.9035 (pt0) REVERT: R 119 LEU cc_start: 0.9257 (mt) cc_final: 0.8798 (mt) REVERT: S 90 ILE cc_start: 0.8484 (pt) cc_final: 0.8093 (tp) REVERT: T 3 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8630 (pttm) REVERT: T 6 GLU cc_start: 0.9425 (tp30) cc_final: 0.8993 (tm-30) REVERT: T 7 ASP cc_start: 0.9235 (p0) cc_final: 0.8864 (p0) REVERT: T 48 ILE cc_start: 0.8987 (mm) cc_final: 0.8573 (tt) REVERT: T 74 PHE cc_start: 0.9078 (m-80) cc_final: 0.8844 (m-80) REVERT: T 80 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8130 (mtmm) REVERT: T 109 ARG cc_start: 0.8304 (ptp-110) cc_final: 0.8004 (ttm110) REVERT: U 76 TYR cc_start: 0.8514 (t80) cc_final: 0.8298 (t80) REVERT: U 80 MET cc_start: 0.8093 (mtt) cc_final: 0.7736 (mtp) REVERT: U 94 MET cc_start: 0.9117 (mmm) cc_final: 0.8699 (mmm) REVERT: V 2 TYR cc_start: 0.7526 (p90) cc_final: 0.6959 (p90) REVERT: V 23 GLU cc_start: 0.8057 (pm20) cc_final: 0.7535 (pp20) REVERT: V 40 PHE cc_start: 0.8463 (t80) cc_final: 0.8064 (t80) REVERT: V 73 VAL cc_start: 0.9179 (t) cc_final: 0.8731 (p) REVERT: V 75 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8126 (mtt-85) REVERT: V 76 TYR cc_start: 0.8617 (p90) cc_final: 0.8192 (p90) REVERT: V 86 GLN cc_start: 0.8856 (tt0) cc_final: 0.8353 (tt0) REVERT: W 4 LYS cc_start: 0.9407 (ttpt) cc_final: 0.9087 (tppp) REVERT: W 48 GLU cc_start: 0.9230 (pt0) cc_final: 0.8739 (tt0) REVERT: W 78 GLU cc_start: 0.7590 (pp20) cc_final: 0.7357 (pp20) REVERT: W 83 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8437 (mmmm) REVERT: W 105 ILE cc_start: 0.9144 (mm) cc_final: 0.8494 (pt) REVERT: X 15 GLU cc_start: 0.9385 (mp0) cc_final: 0.9146 (pm20) REVERT: X 16 ARG cc_start: 0.9382 (mmm-85) cc_final: 0.9034 (mmm-85) REVERT: X 21 MET cc_start: 0.9503 (ptp) cc_final: 0.9288 (ppp) REVERT: X 57 MET cc_start: 0.5589 (mtp) cc_final: 0.4977 (mtp) REVERT: X 59 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.5238 (m-10) REVERT: Y 11 VAL cc_start: 0.9030 (t) cc_final: 0.8753 (t) REVERT: Y 27 PHE cc_start: 0.9111 (m-80) cc_final: 0.8817 (m-80) REVERT: Y 69 MET cc_start: 0.7793 (mtp) cc_final: 0.7495 (mtp) REVERT: Y 83 TYR cc_start: 0.8370 (m-80) cc_final: 0.7921 (m-80) REVERT: Y 90 LYS cc_start: 0.8628 (mtpt) cc_final: 0.8347 (tttt) REVERT: Y 92 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8312 (ptp-170) REVERT: a 25 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8358 (tm-30) REVERT: a 52 LYS cc_start: 0.8448 (mmtt) cc_final: 0.7996 (mmmt) REVERT: a 85 LYS cc_start: 0.9054 (mttm) cc_final: 0.8799 (mttt) REVERT: a 90 TYR cc_start: 0.8551 (m-80) cc_final: 0.8319 (m-80) REVERT: c 1 MET cc_start: 0.9457 (tpp) cc_final: 0.9035 (tpp) REVERT: c 5 GLU cc_start: 0.9379 (mp0) cc_final: 0.8952 (mp0) REVERT: c 25 LEU cc_start: 0.8944 (mt) cc_final: 0.8619 (mt) REVERT: c 26 PHE cc_start: 0.9047 (t80) cc_final: 0.8811 (t80) REVERT: c 38 GLU cc_start: 0.8309 (mp0) cc_final: 0.8041 (mp0) REVERT: c 45 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8451 (tm-30) REVERT: d 19 GLN cc_start: 0.9073 (mp10) cc_final: 0.8824 (mp10) REVERT: d 24 ARG cc_start: 0.8493 (tpt90) cc_final: 0.8092 (tpt90) REVERT: d 46 MET cc_start: 0.9017 (ptp) cc_final: 0.8663 (ptp) REVERT: d 49 LYS cc_start: 0.8745 (tttt) cc_final: 0.8300 (mtpp) REVERT: d 55 SER cc_start: 0.8982 (m) cc_final: 0.8734 (m) REVERT: f 14 ARG cc_start: 0.8970 (mtt-85) cc_final: 0.8729 (mpp80) REVERT: f 16 ARG cc_start: 0.8422 (ttp-170) cc_final: 0.7868 (ttp-170) REVERT: f 17 ARG cc_start: 0.8730 (mtt180) cc_final: 0.8342 (mtt180) REVERT: f 27 MET cc_start: 0.8806 (ttm) cc_final: 0.7982 (tpp) REVERT: f 37 LYS cc_start: 0.7821 (ttpt) cc_final: 0.7562 (tppt) REVERT: f 44 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8892 (mmmt) REVERT: g 25 ASN cc_start: 0.9196 (m-40) cc_final: 0.8686 (t0) REVERT: g 26 ASN cc_start: 0.8119 (m110) cc_final: 0.7535 (p0) REVERT: g 28 ASP cc_start: 0.9300 (p0) cc_final: 0.8924 (p0) REVERT: h 8 ASN cc_start: 0.8670 (t0) cc_final: 0.8433 (t0) REVERT: h 9 ASN cc_start: 0.8595 (m-40) cc_final: 0.8349 (m110) REVERT: h 13 SER cc_start: 0.9488 (m) cc_final: 0.8815 (t) REVERT: h 14 LYS cc_start: 0.9377 (ttmm) cc_final: 0.8970 (ttpt) REVERT: h 22 MET cc_start: 0.9227 (mmm) cc_final: 0.8982 (mmm) REVERT: h 25 LYS cc_start: 0.9339 (tppt) cc_final: 0.8620 (tptt) REVERT: h 28 ARG cc_start: 0.9403 (mpp80) cc_final: 0.9038 (mpp80) REVERT: h 37 LYS cc_start: 0.9387 (ttmm) cc_final: 0.9095 (tttp) REVERT: i 4 MET cc_start: 0.8377 (mmm) cc_final: 0.7883 (mmm) REVERT: i 32 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8391 (mt) REVERT: i 38 GLN cc_start: 0.8322 (tp40) cc_final: 0.8032 (tp40) REVERT: i 60 GLN cc_start: 0.8202 (tt0) cc_final: 0.7725 (tm-30) REVERT: j 2 LYS cc_start: 0.7674 (mttt) cc_final: 0.7464 (mttt) REVERT: j 17 ILE cc_start: 0.9389 (pp) cc_final: 0.9098 (pp) REVERT: j 18 ARG cc_start: 0.8804 (ttm170) cc_final: 0.8452 (ttm-80) REVERT: j 24 MET cc_start: 0.9186 (mtp) cc_final: 0.8927 (tmm) REVERT: j 33 LYS cc_start: 0.8873 (ttmt) cc_final: 0.8560 (ttpt) REVERT: j 36 GLN cc_start: 0.7450 (tt0) cc_final: 0.7222 (tt0) outliers start: 147 outliers final: 85 residues processed: 904 average time/residue: 0.9645 time to fit residues: 1459.5817 Evaluate side-chains 828 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 732 time to evaluate : 4.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 LYS Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 200 HIS Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 18 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 58 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain V residue 35 PHE Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 62 TYR Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 3 ASP Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 59 TYR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 76 ARG Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 49 GLN Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain d residue 9 LYS Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain g residue 39 ASP Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 61 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 591 optimal weight: 8.9990 chunk 450 optimal weight: 7.9990 chunk 310 optimal weight: 20.0000 chunk 66 optimal weight: 30.0000 chunk 285 optimal weight: 20.0000 chunk 401 optimal weight: 2.9990 chunk 600 optimal weight: 8.9990 chunk 636 optimal weight: 6.9990 chunk 313 optimal weight: 20.0000 chunk 569 optimal weight: 10.0000 chunk 171 optimal weight: 50.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 182 ASN ** H 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 45 GLN ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 57 HIS R 61 GLN V 86 GLN ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 101236 Z= 0.278 Angle : 0.753 18.488 151523 Z= 0.384 Chirality : 0.040 0.452 19389 Planarity : 0.006 0.066 8035 Dihedral : 25.358 179.557 50770 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 27.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.56 % Favored : 89.39 % Rotamer: Outliers : 5.27 % Allowed : 20.26 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.20 % 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: -3.07 (0.13), residues: 3646 helix: -1.02 (0.15), residues: 1054 sheet: -2.36 (0.19), residues: 594 loop : -2.57 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP Q 93 HIS 0.010 0.002 HIS Y 64 PHE 0.031 0.003 PHE R 84 TYR 0.030 0.002 TYR F 46 ARG 0.011 0.001 ARG N 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 798 time to evaluate : 4.102 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: 0 20 MET cc_start: 0.7915 (mmm) cc_final: 0.7505 (mmm) REVERT: 0 100 MET cc_start: 0.9503 (mtp) cc_final: 0.8947 (tmm) REVERT: 0 102 PHE cc_start: 0.9543 (m-80) cc_final: 0.8845 (m-80) REVERT: 0 118 LEU cc_start: 0.9645 (tt) cc_final: 0.9338 (tp) REVERT: 0 123 MET cc_start: 0.3363 (mmt) cc_final: 0.2705 (mmt) REVERT: 0 286 ARG cc_start: 0.9297 (tmm160) cc_final: 0.8911 (tpm170) REVERT: 0 327 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8788 (pt) REVERT: E 6 TYR cc_start: 0.8000 (m-10) cc_final: 0.7773 (m-10) REVERT: E 216 ILE cc_start: 0.8984 (mt) cc_final: 0.8537 (tp) REVERT: F 16 PHE cc_start: 0.8355 (m-80) cc_final: 0.7608 (m-80) REVERT: F 79 PHE cc_start: 0.8766 (m-80) cc_final: 0.8270 (m-80) REVERT: F 109 ASP cc_start: 0.7249 (p0) cc_final: 0.6263 (p0) REVERT: F 128 GLN cc_start: 0.8323 (mp10) cc_final: 0.8108 (mp10) REVERT: F 134 SER cc_start: 0.8028 (p) cc_final: 0.7673 (m) REVERT: F 152 ASN cc_start: 0.8846 (m-40) cc_final: 0.8544 (t0) REVERT: F 160 LEU cc_start: 0.9081 (mt) cc_final: 0.8879 (mt) REVERT: F 203 LYS cc_start: 0.8427 (mttt) cc_final: 0.8140 (tttm) REVERT: G 39 MET cc_start: 0.9215 (tmm) cc_final: 0.8644 (tmm) REVERT: G 40 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8258 (tp40) REVERT: G 75 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7491 (mp10) REVERT: G 82 GLN cc_start: 0.8117 (tt0) cc_final: 0.7683 (tp-100) REVERT: G 83 TRP cc_start: 0.8909 (m100) cc_final: 0.8473 (m100) REVERT: G 107 ARG cc_start: 0.9448 (mtt180) cc_final: 0.9109 (mtm110) REVERT: H 94 GLU cc_start: 0.9306 (mm-30) cc_final: 0.9077 (tp30) REVERT: H 172 GLN cc_start: 0.9092 (tt0) cc_final: 0.8841 (tt0) REVERT: I 14 ASP cc_start: 0.9331 (m-30) cc_final: 0.8826 (t0) REVERT: I 41 ASP cc_start: 0.9099 (m-30) cc_final: 0.8733 (t0) REVERT: I 76 MET cc_start: 0.7765 (ptt) cc_final: 0.6667 (mmt) REVERT: I 110 TYR cc_start: 0.8573 (m-80) cc_final: 0.8352 (m-80) REVERT: K 40 LYS cc_start: 0.9269 (mmmt) cc_final: 0.9017 (mmtm) REVERT: K 61 TYR cc_start: 0.9115 (t80) cc_final: 0.8757 (t80) REVERT: K 120 ASP cc_start: 0.8623 (p0) cc_final: 0.8385 (p0) REVERT: K 125 MET cc_start: 0.8477 (mmp) cc_final: 0.8176 (mmt) REVERT: N 26 LEU cc_start: 0.9206 (pt) cc_final: 0.8914 (pp) REVERT: N 45 TYR cc_start: 0.8764 (t80) cc_final: 0.8347 (t80) REVERT: N 81 HIS cc_start: 0.7942 (m-70) cc_final: 0.7523 (m90) REVERT: N 88 ARG cc_start: 0.6981 (mtt180) cc_final: 0.6770 (mtt180) REVERT: N 100 LYS cc_start: 0.9028 (mttt) cc_final: 0.8605 (tmtt) REVERT: N 133 HIS cc_start: 0.7418 (m-70) cc_final: 0.6768 (m170) REVERT: N 143 LEU cc_start: 0.9082 (mt) cc_final: 0.8822 (tp) REVERT: O 5 GLU cc_start: 0.9171 (mm-30) cc_final: 0.8769 (mm-30) REVERT: O 7 ARG cc_start: 0.8996 (mtt-85) cc_final: 0.8698 (mmt90) REVERT: O 9 LYS cc_start: 0.9334 (ptpp) cc_final: 0.9015 (ptmm) REVERT: O 18 GLU cc_start: 0.8810 (mp0) cc_final: 0.8567 (mp0) REVERT: O 20 LEU cc_start: 0.9124 (tt) cc_final: 0.8630 (tp) REVERT: O 23 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8436 (ttpp) REVERT: O 104 ARG cc_start: 0.8712 (ptm160) cc_final: 0.7837 (ptm160) REVERT: O 112 MET cc_start: 0.8823 (pmm) cc_final: 0.8494 (mmm) REVERT: P 3 LEU cc_start: 0.9641 (mt) cc_final: 0.9409 (tt) REVERT: P 50 PHE cc_start: 0.8294 (t80) cc_final: 0.8059 (t80) REVERT: P 58 PHE cc_start: 0.8451 (p90) cc_final: 0.8062 (p90) REVERT: P 59 GLN cc_start: 0.9221 (pt0) cc_final: 0.8285 (tp-100) REVERT: P 85 PHE cc_start: 0.8386 (m-80) cc_final: 0.8029 (m-80) REVERT: Q 17 MET cc_start: 0.7856 (tpp) cc_final: 0.7501 (mpp) REVERT: Q 37 LEU cc_start: 0.9543 (mt) cc_final: 0.9334 (mt) REVERT: Q 38 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8138 (mp0) REVERT: Q 57 TYR cc_start: 0.8970 (t80) cc_final: 0.8084 (t80) REVERT: Q 83 MET cc_start: 0.8661 (mmm) cc_final: 0.7809 (tpp) REVERT: Q 103 LEU cc_start: 0.9223 (mm) cc_final: 0.8956 (mm) REVERT: Q 104 PHE cc_start: 0.8599 (m-80) cc_final: 0.8376 (m-10) REVERT: R 3 TYR cc_start: 0.7519 (p90) cc_final: 0.7227 (p90) REVERT: R 8 ARG cc_start: 0.8064 (mmt180) cc_final: 0.7640 (mtt180) REVERT: R 10 SER cc_start: 0.8823 (p) cc_final: 0.8427 (m) REVERT: R 27 ASN cc_start: 0.9175 (m-40) cc_final: 0.8968 (m-40) REVERT: R 28 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7987 (tp30) REVERT: R 46 LYS cc_start: 0.9043 (mmtp) cc_final: 0.8835 (mmtm) REVERT: R 52 LYS cc_start: 0.8784 (mttt) cc_final: 0.8472 (mmtt) REVERT: R 55 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8140 (p0) REVERT: R 114 MET cc_start: 0.8187 (mtm) cc_final: 0.7689 (mpp) REVERT: R 119 LEU cc_start: 0.9224 (mt) cc_final: 0.8788 (mt) REVERT: S 62 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8077 (p0) REVERT: S 90 ILE cc_start: 0.8519 (pt) cc_final: 0.8133 (tp) REVERT: T 6 GLU cc_start: 0.9425 (tp30) cc_final: 0.9021 (tm-30) REVERT: T 7 ASP cc_start: 0.9224 (p0) cc_final: 0.8941 (p0) REVERT: T 20 PHE cc_start: 0.8358 (p90) cc_final: 0.7918 (p90) REVERT: T 48 ILE cc_start: 0.9041 (mm) cc_final: 0.8726 (tt) REVERT: T 80 LYS cc_start: 0.8452 (mtmm) cc_final: 0.8213 (mtmm) REVERT: T 110 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6239 (mp) REVERT: U 32 TYR cc_start: 0.8986 (t80) cc_final: 0.8733 (t80) REVERT: U 52 GLN cc_start: 0.9240 (tp40) cc_final: 0.8648 (mm-40) REVERT: U 80 MET cc_start: 0.8144 (mtt) cc_final: 0.7820 (mtp) REVERT: U 94 MET cc_start: 0.9159 (mmm) cc_final: 0.8792 (mmm) REVERT: V 2 TYR cc_start: 0.7128 (p90) cc_final: 0.6836 (p90) REVERT: V 36 GLU cc_start: 0.8670 (mp0) cc_final: 0.8329 (mp0) REVERT: V 40 PHE cc_start: 0.8651 (t80) cc_final: 0.8089 (t80) REVERT: V 76 TYR cc_start: 0.8656 (p90) cc_final: 0.8166 (p90) REVERT: V 84 LYS cc_start: 0.8143 (tptt) cc_final: 0.7262 (tptt) REVERT: V 86 GLN cc_start: 0.9051 (tt0) cc_final: 0.8743 (mt0) REVERT: W 48 GLU cc_start: 0.9232 (pt0) cc_final: 0.8593 (tt0) REVERT: W 52 LYS cc_start: 0.9595 (mttm) cc_final: 0.9151 (mttp) REVERT: W 78 GLU cc_start: 0.7639 (pp20) cc_final: 0.7422 (pp20) REVERT: W 104 THR cc_start: 0.9315 (m) cc_final: 0.9061 (p) REVERT: X 10 ARG cc_start: 0.9013 (ptp-170) cc_final: 0.8686 (ptm160) REVERT: X 16 ARG cc_start: 0.9397 (mmm-85) cc_final: 0.8953 (mmm-85) REVERT: X 57 MET cc_start: 0.5928 (mtp) cc_final: 0.5091 (mtp) REVERT: X 59 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.5347 (m-10) REVERT: Y 27 PHE cc_start: 0.9155 (m-80) cc_final: 0.8887 (m-80) REVERT: Y 69 MET cc_start: 0.7800 (mtp) cc_final: 0.7338 (mtp) REVERT: Y 83 TYR cc_start: 0.8361 (m-80) cc_final: 0.8084 (m-80) REVERT: Y 92 ARG cc_start: 0.8585 (mtm180) cc_final: 0.8247 (ptp-170) REVERT: a 25 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8392 (tm-30) REVERT: a 64 ASP cc_start: 0.8180 (p0) cc_final: 0.7708 (p0) REVERT: a 76 LYS cc_start: 0.9071 (mppt) cc_final: 0.8384 (mppt) REVERT: c 1 MET cc_start: 0.9448 (tpp) cc_final: 0.9075 (tpp) REVERT: c 5 GLU cc_start: 0.9451 (mp0) cc_final: 0.8930 (mp0) REVERT: c 26 PHE cc_start: 0.9065 (t80) cc_final: 0.8825 (t80) REVERT: c 38 GLU cc_start: 0.8347 (mp0) cc_final: 0.7979 (mp0) REVERT: c 45 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8461 (tm-30) REVERT: c 53 MET cc_start: 0.9285 (OUTLIER) cc_final: 0.9040 (ptp) REVERT: c 54 LYS cc_start: 0.9475 (mtpp) cc_final: 0.9270 (mtpt) REVERT: d 19 GLN cc_start: 0.9091 (mp10) cc_final: 0.8727 (mp10) REVERT: d 24 ARG cc_start: 0.8473 (tpt90) cc_final: 0.8165 (tpt90) REVERT: d 38 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7861 (pm20) REVERT: d 46 MET cc_start: 0.9016 (ptp) cc_final: 0.8540 (ptp) REVERT: d 49 LYS cc_start: 0.8768 (tttt) cc_final: 0.8334 (mtpp) REVERT: f 16 ARG cc_start: 0.8426 (ttp-170) cc_final: 0.7973 (ttp-170) REVERT: f 17 ARG cc_start: 0.8794 (mtt180) cc_final: 0.8491 (mtt180) REVERT: f 27 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8113 (ttm) REVERT: g 1 MET cc_start: 0.8818 (tpt) cc_final: 0.8409 (tpt) REVERT: g 25 ASN cc_start: 0.9244 (m-40) cc_final: 0.8743 (t0) REVERT: g 26 ASN cc_start: 0.8266 (m110) cc_final: 0.7661 (p0) REVERT: g 28 ASP cc_start: 0.9427 (p0) cc_final: 0.9103 (p0) REVERT: h 1 MET cc_start: 0.8381 (tpt) cc_final: 0.8159 (tpt) REVERT: h 8 ASN cc_start: 0.8694 (t0) cc_final: 0.8454 (t0) REVERT: h 9 ASN cc_start: 0.8616 (m-40) cc_final: 0.8382 (m110) REVERT: h 13 SER cc_start: 0.9500 (m) cc_final: 0.8801 (t) REVERT: h 14 LYS cc_start: 0.9389 (ttmm) cc_final: 0.9186 (tppt) REVERT: h 28 ARG cc_start: 0.9400 (mpp80) cc_final: 0.8842 (mpp80) REVERT: h 37 LYS cc_start: 0.9450 (ttmm) cc_final: 0.9193 (tttp) REVERT: i 4 MET cc_start: 0.8311 (mmm) cc_final: 0.7889 (mmt) REVERT: i 32 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8457 (mt) REVERT: i 59 LYS cc_start: 0.9362 (ptpt) cc_final: 0.8994 (ptpp) REVERT: i 60 GLN cc_start: 0.8215 (tt0) cc_final: 0.7769 (tm-30) REVERT: j 13 LYS cc_start: 0.9674 (mtpp) cc_final: 0.9448 (mtmm) REVERT: j 17 ILE cc_start: 0.9357 (pp) cc_final: 0.8481 (pp) REVERT: j 18 ARG cc_start: 0.8816 (ttm170) cc_final: 0.8535 (ttm-80) REVERT: j 33 LYS cc_start: 0.8811 (ttmt) cc_final: 0.8531 (ttpt) outliers start: 159 outliers final: 100 residues processed: 873 average time/residue: 0.9217 time to fit residues: 1347.3138 Evaluate side-chains 848 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 736 time to evaluate : 4.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 LYS Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 49 HIS Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 156 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 23 LYS Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 61 GLN Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 35 PHE Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 31 GLU Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 3 ASP Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 52 ASP Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 59 TYR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 76 ARG Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 49 GLN Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 53 MET Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain f residue 15 LEU Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 27 MET Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 61 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 529 optimal weight: 20.0000 chunk 361 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 473 optimal weight: 40.0000 chunk 262 optimal weight: 10.0000 chunk 542 optimal weight: 5.9990 chunk 439 optimal weight: 30.0000 chunk 0 optimal weight: 50.0000 chunk 324 optimal weight: 20.0000 chunk 570 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 160 GLN ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 ASN ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 GLN ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 ASN Y 59 GLN ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 101236 Z= 0.374 Angle : 0.839 16.062 151523 Z= 0.426 Chirality : 0.044 0.425 19389 Planarity : 0.006 0.071 8035 Dihedral : 25.476 179.562 50770 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 36.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.15 % Favored : 87.79 % Rotamer: Outliers : 6.53 % Allowed : 21.55 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.14 % 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: -3.10 (0.13), residues: 3646 helix: -1.05 (0.15), residues: 1054 sheet: -2.24 (0.19), residues: 584 loop : -2.63 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP Q 93 HIS 0.011 0.002 HIS 0 60 PHE 0.047 0.003 PHE O 79 TYR 0.032 0.003 TYR H 22 ARG 0.009 0.001 ARG i 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 950 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 753 time to evaluate : 4.110 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: 0 60 HIS cc_start: 0.6713 (OUTLIER) cc_final: 0.3725 (t70) REVERT: 0 100 MET cc_start: 0.9509 (mtp) cc_final: 0.9081 (tpp) REVERT: 0 102 PHE cc_start: 0.9536 (m-80) cc_final: 0.8993 (m-80) REVERT: 0 118 LEU cc_start: 0.9652 (tt) cc_final: 0.9403 (tp) REVERT: 0 123 MET cc_start: 0.3803 (mmt) cc_final: 0.3128 (mmt) REVERT: 0 238 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7829 (ptt90) REVERT: 0 327 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8771 (pt) REVERT: E 183 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7719 (mpp) REVERT: E 216 ILE cc_start: 0.9002 (mt) cc_final: 0.8586 (tp) REVERT: F 16 PHE cc_start: 0.8205 (m-80) cc_final: 0.7344 (m-80) REVERT: F 79 PHE cc_start: 0.8823 (m-80) cc_final: 0.8276 (m-80) REVERT: F 134 SER cc_start: 0.8039 (p) cc_final: 0.7711 (m) REVERT: F 152 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8536 (t0) REVERT: F 203 LYS cc_start: 0.8411 (mttt) cc_final: 0.8065 (tttm) REVERT: G 39 MET cc_start: 0.9181 (tmm) cc_final: 0.8684 (tmm) REVERT: G 40 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8215 (tp40) REVERT: G 75 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7796 (mp10) REVERT: G 82 GLN cc_start: 0.8072 (tt0) cc_final: 0.7746 (tp-100) REVERT: G 83 TRP cc_start: 0.9024 (m100) cc_final: 0.8509 (m100) REVERT: H 22 TYR cc_start: 0.7885 (m-10) cc_final: 0.7594 (m-10) REVERT: H 94 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9030 (tp30) REVERT: H 152 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7578 (mpp) REVERT: H 172 GLN cc_start: 0.9177 (tt0) cc_final: 0.8937 (tt0) REVERT: I 41 ASP cc_start: 0.9126 (m-30) cc_final: 0.8851 (t70) REVERT: I 49 ASN cc_start: 0.9496 (t0) cc_final: 0.9278 (t0) REVERT: I 76 MET cc_start: 0.7944 (ptt) cc_final: 0.7620 (ptt) REVERT: I 110 TYR cc_start: 0.8476 (m-80) cc_final: 0.8261 (m-80) REVERT: K 61 TYR cc_start: 0.9075 (t80) cc_final: 0.8729 (t80) REVERT: K 120 ASP cc_start: 0.8576 (p0) cc_final: 0.8300 (p0) REVERT: K 125 MET cc_start: 0.8539 (mmp) cc_final: 0.8221 (mmt) REVERT: N 45 TYR cc_start: 0.8695 (t80) cc_final: 0.8223 (t80) REVERT: N 81 HIS cc_start: 0.7975 (m-70) cc_final: 0.7450 (m90) REVERT: N 86 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8230 (mmtm) REVERT: N 93 MET cc_start: 0.9402 (mmm) cc_final: 0.9102 (mmm) REVERT: N 100 LYS cc_start: 0.9126 (mttt) cc_final: 0.8640 (tmtt) REVERT: N 133 HIS cc_start: 0.7529 (m-70) cc_final: 0.7174 (m90) REVERT: O 5 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8932 (mm-30) REVERT: O 9 LYS cc_start: 0.9347 (ptpp) cc_final: 0.9007 (ptmm) REVERT: O 18 GLU cc_start: 0.8980 (mp0) cc_final: 0.8707 (mp0) REVERT: O 110 ASN cc_start: 0.9464 (t0) cc_final: 0.8806 (t0) REVERT: P 59 GLN cc_start: 0.9253 (pt0) cc_final: 0.8293 (tp-100) REVERT: P 60 ARG cc_start: 0.8371 (ptp-170) cc_final: 0.8143 (ptp-170) REVERT: P 85 PHE cc_start: 0.8397 (m-80) cc_final: 0.8020 (m-80) REVERT: Q 17 MET cc_start: 0.7894 (tpp) cc_final: 0.7589 (mpp) REVERT: Q 38 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8191 (mp0) REVERT: Q 57 TYR cc_start: 0.9070 (t80) cc_final: 0.8824 (t80) REVERT: Q 83 MET cc_start: 0.8669 (mmm) cc_final: 0.8264 (tpp) REVERT: Q 104 PHE cc_start: 0.8697 (m-80) cc_final: 0.8356 (m-10) REVERT: R 3 TYR cc_start: 0.7460 (p90) cc_final: 0.7242 (p90) REVERT: R 28 GLU cc_start: 0.8310 (tm-30) cc_final: 0.7863 (tp30) REVERT: R 39 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8668 (mp0) REVERT: R 52 LYS cc_start: 0.8817 (mttt) cc_final: 0.8465 (mmtt) REVERT: R 55 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8270 (p0) REVERT: R 82 LYS cc_start: 0.9548 (tttt) cc_final: 0.9342 (ttpt) REVERT: R 114 MET cc_start: 0.8298 (mtm) cc_final: 0.7671 (mtm) REVERT: R 119 LEU cc_start: 0.9048 (mt) cc_final: 0.8470 (mt) REVERT: S 62 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8216 (p0) REVERT: S 90 ILE cc_start: 0.8698 (pt) cc_final: 0.8338 (tp) REVERT: T 1 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7972 (pmm) REVERT: T 6 GLU cc_start: 0.9433 (tp30) cc_final: 0.9014 (tm-30) REVERT: T 7 ASP cc_start: 0.9223 (p0) cc_final: 0.8855 (p0) REVERT: T 20 PHE cc_start: 0.8487 (p90) cc_final: 0.8134 (p90) REVERT: T 22 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.7981 (Cg_endo) REVERT: T 57 GLU cc_start: 0.8297 (tp30) cc_final: 0.8019 (mp0) REVERT: T 60 THR cc_start: 0.8888 (m) cc_final: 0.8353 (p) REVERT: T 103 LEU cc_start: 0.8830 (tp) cc_final: 0.8600 (tp) REVERT: U 32 TYR cc_start: 0.9141 (t80) cc_final: 0.8869 (t80) REVERT: U 80 MET cc_start: 0.8185 (mtt) cc_final: 0.7632 (mtp) REVERT: U 94 MET cc_start: 0.9216 (mmm) cc_final: 0.8715 (mmm) REVERT: V 40 PHE cc_start: 0.8869 (t80) cc_final: 0.8295 (t80) REVERT: V 76 TYR cc_start: 0.8739 (p90) cc_final: 0.8417 (p90) REVERT: W 48 GLU cc_start: 0.9252 (pt0) cc_final: 0.8768 (tt0) REVERT: W 52 LYS cc_start: 0.9632 (mttm) cc_final: 0.9356 (mtpp) REVERT: W 78 GLU cc_start: 0.7606 (pp20) cc_final: 0.7388 (pp20) REVERT: X 16 ARG cc_start: 0.9220 (mmm-85) cc_final: 0.8884 (mmm-85) REVERT: X 57 MET cc_start: 0.6057 (mtp) cc_final: 0.5099 (mtp) REVERT: X 59 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.5400 (m-10) REVERT: Y 10 MET cc_start: 0.8269 (tpp) cc_final: 0.7937 (tpp) REVERT: Y 27 PHE cc_start: 0.9193 (m-80) cc_final: 0.8904 (m-80) REVERT: Y 30 LYS cc_start: 0.9532 (mttt) cc_final: 0.9175 (mtmm) REVERT: Y 69 MET cc_start: 0.7687 (mtp) cc_final: 0.7269 (mtp) REVERT: Y 92 ARG cc_start: 0.8622 (mtm180) cc_final: 0.8398 (mtt180) REVERT: a 76 LYS cc_start: 0.9066 (mppt) cc_final: 0.8395 (mppt) REVERT: a 80 PHE cc_start: 0.8593 (m-80) cc_final: 0.8391 (m-10) REVERT: b 22 MET cc_start: 0.7291 (mtt) cc_final: 0.6948 (mtt) REVERT: b 23 ASN cc_start: 0.4895 (OUTLIER) cc_final: 0.4674 (p0) REVERT: c 1 MET cc_start: 0.9454 (tpp) cc_final: 0.9096 (tpp) REVERT: c 5 GLU cc_start: 0.9503 (mp0) cc_final: 0.9223 (mp0) REVERT: c 25 LEU cc_start: 0.8784 (mt) cc_final: 0.8531 (mt) REVERT: c 38 GLU cc_start: 0.8332 (mp0) cc_final: 0.7973 (mp0) REVERT: c 45 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: c 53 MET cc_start: 0.9349 (ptp) cc_final: 0.9121 (ptp) REVERT: c 54 LYS cc_start: 0.9376 (mtpp) cc_final: 0.9156 (mtpt) REVERT: d 46 MET cc_start: 0.9061 (ptp) cc_final: 0.8726 (ptp) REVERT: d 49 LYS cc_start: 0.8865 (tttt) cc_final: 0.8415 (tppt) REVERT: f 7 ARG cc_start: 0.8485 (ppp80) cc_final: 0.7279 (ptp90) REVERT: f 27 MET cc_start: 0.8516 (ttm) cc_final: 0.8100 (ttm) REVERT: g 1 MET cc_start: 0.9137 (tpt) cc_final: 0.8828 (tpt) REVERT: g 25 ASN cc_start: 0.9209 (m-40) cc_final: 0.8706 (t0) REVERT: g 26 ASN cc_start: 0.8397 (m110) cc_final: 0.7868 (p0) REVERT: g 28 ASP cc_start: 0.9397 (p0) cc_final: 0.9060 (p0) REVERT: g 38 ARG cc_start: 0.8749 (mtp180) cc_final: 0.8303 (mtp180) REVERT: h 8 ASN cc_start: 0.8738 (t0) cc_final: 0.8386 (t0) REVERT: h 9 ASN cc_start: 0.8676 (m-40) cc_final: 0.8351 (m110) REVERT: h 13 SER cc_start: 0.9520 (m) cc_final: 0.8871 (t) REVERT: h 14 LYS cc_start: 0.9411 (ttmm) cc_final: 0.9189 (tppt) REVERT: i 4 MET cc_start: 0.8328 (mmm) cc_final: 0.7892 (mmt) REVERT: i 32 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8491 (mt) REVERT: i 57 ARG cc_start: 0.9430 (OUTLIER) cc_final: 0.8175 (mtm110) REVERT: i 59 LYS cc_start: 0.9404 (ptpt) cc_final: 0.8968 (ptpt) REVERT: i 60 GLN cc_start: 0.8209 (tt0) cc_final: 0.7962 (tm-30) REVERT: j 13 LYS cc_start: 0.9674 (mtpp) cc_final: 0.9441 (mtmm) REVERT: j 18 ARG cc_start: 0.8818 (ttm170) cc_final: 0.8489 (ttm-80) REVERT: j 33 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8421 (ttmt) outliers start: 197 outliers final: 134 residues processed: 859 average time/residue: 0.9205 time to fit residues: 1326.9566 Evaluate side-chains 849 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 699 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 LYS Chi-restraints excluded: chain 0 residue 60 HIS Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 238 ARG Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 149 VAL Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 49 HIS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 152 MET Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 86 LYS Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 35 HIS Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 34 PHE Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 GLU Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 109 ARG Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 106 PHE Chi-restraints excluded: chain V residue 35 PHE Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 31 GLU Chi-restraints excluded: chain W residue 34 SER Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 62 TYR Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 76 VAL Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 3 ASP Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 59 TYR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 40 MET Chi-restraints excluded: chain Y residue 49 GLN Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 9 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 55 THR Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 15 LEU Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain g residue 23 LYS Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 57 ARG Chi-restraints excluded: chain i residue 61 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 3 VAL Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 213 optimal weight: 30.0000 chunk 572 optimal weight: 6.9990 chunk 125 optimal weight: 20.0000 chunk 373 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 636 optimal weight: 8.9990 chunk 528 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 52 optimal weight: 50.0000 chunk 210 optimal weight: 20.0000 chunk 334 optimal weight: 20.0000 overall best weight: 10.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN Y 59 GLN ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 39 ASN ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 101236 Z= 0.364 Angle : 0.827 15.564 151523 Z= 0.420 Chirality : 0.043 0.395 19389 Planarity : 0.006 0.084 8035 Dihedral : 25.513 179.072 50770 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 36.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.88 % Favored : 88.01 % Rotamer: Outliers : 7.13 % Allowed : 23.34 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.13), residues: 3646 helix: -0.98 (0.15), residues: 1043 sheet: -2.33 (0.19), residues: 625 loop : -2.64 (0.13), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP Q 93 HIS 0.010 0.002 HIS N 131 PHE 0.050 0.003 PHE O 79 TYR 0.022 0.003 TYR I 95 ARG 0.015 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 733 time to evaluate : 4.125 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: 0 20 MET cc_start: 0.7665 (mmm) cc_final: 0.7398 (mmm) REVERT: 0 102 PHE cc_start: 0.9519 (m-80) cc_final: 0.9183 (m-10) REVERT: 0 123 MET cc_start: 0.3667 (mmt) cc_final: 0.2924 (mmt) REVERT: 0 238 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7937 (ppt170) REVERT: 0 327 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8770 (pt) REVERT: E 183 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7763 (mpp) REVERT: E 216 ILE cc_start: 0.8973 (mt) cc_final: 0.8595 (tp) REVERT: F 16 PHE cc_start: 0.8131 (m-80) cc_final: 0.7362 (m-80) REVERT: F 44 ASP cc_start: 0.8335 (m-30) cc_final: 0.8066 (t0) REVERT: F 79 PHE cc_start: 0.8879 (m-80) cc_final: 0.8396 (m-80) REVERT: F 134 SER cc_start: 0.8109 (p) cc_final: 0.7739 (m) REVERT: F 152 ASN cc_start: 0.8832 (m-40) cc_final: 0.8565 (t0) REVERT: F 203 LYS cc_start: 0.8414 (mttt) cc_final: 0.8081 (tttm) REVERT: G 39 MET cc_start: 0.9156 (tmm) cc_final: 0.8659 (tmm) REVERT: G 40 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8216 (tp40) REVERT: G 75 GLN cc_start: 0.8079 (mm-40) cc_final: 0.7825 (mp10) REVERT: G 82 GLN cc_start: 0.8093 (tt0) cc_final: 0.7836 (tp-100) REVERT: G 83 TRP cc_start: 0.9052 (m100) cc_final: 0.8659 (m100) REVERT: H 22 TYR cc_start: 0.7977 (m-10) cc_final: 0.7637 (m-10) REVERT: H 172 GLN cc_start: 0.9169 (tt0) cc_final: 0.8898 (tt0) REVERT: I 41 ASP cc_start: 0.9153 (m-30) cc_final: 0.8904 (t70) REVERT: I 76 MET cc_start: 0.8004 (ptt) cc_final: 0.7673 (ptt) REVERT: I 110 TYR cc_start: 0.8456 (m-80) cc_final: 0.8163 (m-80) REVERT: K 54 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9181 (mt) REVERT: K 61 TYR cc_start: 0.9061 (t80) cc_final: 0.8718 (t80) REVERT: K 120 ASP cc_start: 0.8402 (p0) cc_final: 0.8025 (p0) REVERT: K 125 MET cc_start: 0.8559 (mmp) cc_final: 0.8251 (mmt) REVERT: N 45 TYR cc_start: 0.8725 (t80) cc_final: 0.8519 (t80) REVERT: N 81 HIS cc_start: 0.8045 (m-70) cc_final: 0.7691 (m170) REVERT: N 100 LYS cc_start: 0.9126 (mttt) cc_final: 0.8650 (tmtt) REVERT: N 133 HIS cc_start: 0.7517 (m-70) cc_final: 0.7113 (m90) REVERT: O 1 MET cc_start: 0.5480 (tpt) cc_final: 0.5270 (tpt) REVERT: O 5 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8985 (mm-30) REVERT: O 9 LYS cc_start: 0.9339 (ptpp) cc_final: 0.9030 (ptmm) REVERT: O 110 ASN cc_start: 0.9452 (t0) cc_final: 0.8660 (t0) REVERT: P 59 GLN cc_start: 0.9274 (pt0) cc_final: 0.8370 (tp-100) REVERT: P 85 PHE cc_start: 0.8387 (m-80) cc_final: 0.8016 (m-80) REVERT: P 111 ILE cc_start: 0.7829 (mm) cc_final: 0.7228 (tp) REVERT: Q 17 MET cc_start: 0.7933 (tpp) cc_final: 0.7540 (mpp) REVERT: Q 57 TYR cc_start: 0.9101 (t80) cc_final: 0.8445 (t80) REVERT: Q 83 MET cc_start: 0.8674 (mmm) cc_final: 0.8379 (tpp) REVERT: R 46 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8846 (mmtt) REVERT: R 52 LYS cc_start: 0.8813 (mttt) cc_final: 0.8389 (mmtt) REVERT: R 55 ASP cc_start: 0.8722 (OUTLIER) cc_final: 0.8174 (p0) REVERT: R 114 MET cc_start: 0.8367 (mtm) cc_final: 0.7844 (mtm) REVERT: S 62 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.8199 (p0) REVERT: S 63 LEU cc_start: 0.8942 (tt) cc_final: 0.8728 (pp) REVERT: T 6 GLU cc_start: 0.9433 (tp30) cc_final: 0.9120 (tm-30) REVERT: T 10 LYS cc_start: 0.9390 (mtmt) cc_final: 0.9022 (mtmt) REVERT: T 20 PHE cc_start: 0.8690 (p90) cc_final: 0.8397 (p90) REVERT: T 22 PRO cc_start: 0.8142 (Cg_exo) cc_final: 0.7830 (Cg_endo) REVERT: T 60 THR cc_start: 0.8977 (m) cc_final: 0.8449 (p) REVERT: T 103 LEU cc_start: 0.8917 (tp) cc_final: 0.8669 (tp) REVERT: T 110 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6583 (mp) REVERT: U 36 ASN cc_start: 0.9455 (t0) cc_final: 0.9203 (t0) REVERT: U 37 GLN cc_start: 0.9332 (pt0) cc_final: 0.8548 (pm20) REVERT: U 52 GLN cc_start: 0.9305 (tp40) cc_final: 0.9070 (mm-40) REVERT: U 80 MET cc_start: 0.8111 (mtt) cc_final: 0.7628 (mtp) REVERT: U 94 MET cc_start: 0.9237 (mmm) cc_final: 0.8735 (mmm) REVERT: V 40 PHE cc_start: 0.8957 (t80) cc_final: 0.8723 (t80) REVERT: V 76 TYR cc_start: 0.8732 (p90) cc_final: 0.8515 (p90) REVERT: V 97 ILE cc_start: 0.9059 (mp) cc_final: 0.8558 (tp) REVERT: W 52 LYS cc_start: 0.9646 (mttm) cc_final: 0.9197 (mttp) REVERT: X 10 ARG cc_start: 0.9021 (ptp-170) cc_final: 0.8707 (ptm160) REVERT: X 16 ARG cc_start: 0.9178 (mmm-85) cc_final: 0.8853 (mmm-85) REVERT: X 57 MET cc_start: 0.6166 (mtp) cc_final: 0.5290 (mtp) REVERT: X 59 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.5491 (m-10) REVERT: Y 27 PHE cc_start: 0.9221 (m-80) cc_final: 0.8956 (m-80) REVERT: Y 30 LYS cc_start: 0.9523 (mttt) cc_final: 0.9161 (mtmm) REVERT: Y 69 MET cc_start: 0.7536 (mtp) cc_final: 0.7153 (mtp) REVERT: a 76 LYS cc_start: 0.9115 (mppt) cc_final: 0.8533 (mppt) REVERT: b 22 MET cc_start: 0.7233 (mtt) cc_final: 0.6923 (mtt) REVERT: c 1 MET cc_start: 0.9415 (tpp) cc_final: 0.9161 (tpp) REVERT: c 5 GLU cc_start: 0.9504 (mp0) cc_final: 0.8881 (mp0) REVERT: c 30 PHE cc_start: 0.8907 (m-10) cc_final: 0.8406 (m-80) REVERT: c 37 LEU cc_start: 0.8328 (pt) cc_final: 0.7693 (tt) REVERT: c 38 GLU cc_start: 0.8302 (mp0) cc_final: 0.7981 (mp0) REVERT: c 40 THR cc_start: 0.8912 (p) cc_final: 0.8683 (t) REVERT: c 54 LYS cc_start: 0.9379 (mtpp) cc_final: 0.9162 (mtpt) REVERT: d 19 GLN cc_start: 0.9297 (mp10) cc_final: 0.8890 (mp10) REVERT: d 38 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8013 (pm20) REVERT: d 49 LYS cc_start: 0.8919 (tttt) cc_final: 0.8456 (tppt) REVERT: f 7 ARG cc_start: 0.8503 (ppp80) cc_final: 0.7238 (ptp90) REVERT: f 10 LYS cc_start: 0.7867 (ttmt) cc_final: 0.7521 (tttt) REVERT: f 16 ARG cc_start: 0.8482 (ttp-170) cc_final: 0.7919 (ttp-170) REVERT: f 27 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8249 (ttm) REVERT: g 25 ASN cc_start: 0.9240 (m-40) cc_final: 0.8366 (t0) REVERT: g 26 ASN cc_start: 0.8509 (m110) cc_final: 0.7673 (m110) REVERT: g 28 ASP cc_start: 0.9420 (p0) cc_final: 0.9010 (p0) REVERT: g 38 ARG cc_start: 0.8721 (mtp180) cc_final: 0.8339 (mtp180) REVERT: h 8 ASN cc_start: 0.8786 (t0) cc_final: 0.8493 (t0) REVERT: h 9 ASN cc_start: 0.8696 (m-40) cc_final: 0.8382 (m110) REVERT: h 13 SER cc_start: 0.9524 (m) cc_final: 0.8468 (t) REVERT: h 14 LYS cc_start: 0.9416 (ttmm) cc_final: 0.9179 (mmtt) REVERT: i 4 MET cc_start: 0.8394 (mmm) cc_final: 0.8009 (mmt) REVERT: i 32 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8620 (mt) REVERT: j 2 LYS cc_start: 0.7616 (mttt) cc_final: 0.7378 (mttt) REVERT: j 33 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8299 (ttmt) outliers start: 215 outliers final: 161 residues processed: 859 average time/residue: 0.9156 time to fit residues: 1335.8936 Evaluate side-chains 855 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 682 time to evaluate : 4.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 LYS Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 238 ARG Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 361 ILE Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 133 MET 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 F residue 201 THR Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 49 HIS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain K residue 35 ILE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 75 TYR Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 38 VAL Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 78 ASP Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 34 PHE Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 87 GLU Chi-restraints excluded: chain S residue 94 VAL Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 24 ASP Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 109 ARG Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 34 VAL Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 35 PHE Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 31 GLU Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 62 TYR Chi-restraints excluded: chain W residue 64 MET Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 3 ASP Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 29 GLU Chi-restraints excluded: chain X residue 30 VAL Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 54 VAL Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 59 TYR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 40 MET Chi-restraints excluded: chain Y residue 49 GLN Chi-restraints excluded: chain Y residue 67 ASN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 48 GLN Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 4 ASN Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain c residue 55 THR Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 48 ASN Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 15 LEU Chi-restraints excluded: chain f residue 24 VAL Chi-restraints excluded: chain f residue 27 MET Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 51 SER Chi-restraints excluded: chain i residue 61 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 34 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 613 optimal weight: 8.9990 chunk 71 optimal weight: 20.0000 chunk 362 optimal weight: 7.9990 chunk 464 optimal weight: 30.0000 chunk 360 optimal weight: 6.9990 chunk 535 optimal weight: 10.0000 chunk 355 optimal weight: 9.9990 chunk 634 optimal weight: 8.9990 chunk 396 optimal weight: 3.9990 chunk 386 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 HIS O 109 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 GLN ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 101236 Z= 0.282 Angle : 0.762 15.581 151523 Z= 0.389 Chirality : 0.040 0.398 19389 Planarity : 0.006 0.061 8035 Dihedral : 25.438 179.705 50770 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 32.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.60 % Favored : 88.32 % Rotamer: Outliers : 6.40 % Allowed : 25.33 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.08 % 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: -2.99 (0.13), residues: 3646 helix: -0.93 (0.15), residues: 1054 sheet: -2.31 (0.19), residues: 616 loop : -2.53 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 65 HIS 0.008 0.002 HIS Q 13 PHE 0.054 0.003 PHE O 79 TYR 0.030 0.002 TYR T 98 ARG 0.009 0.001 ARG W 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 746 time to evaluate : 4.083 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: 0 20 MET cc_start: 0.7616 (mmm) cc_final: 0.7302 (mmm) REVERT: 0 53 HIS cc_start: 0.9076 (t-90) cc_final: 0.8811 (t70) REVERT: 0 60 HIS cc_start: 0.6507 (OUTLIER) cc_final: 0.5472 (t-170) REVERT: 0 100 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8705 (mmp) REVERT: 0 102 PHE cc_start: 0.9537 (m-80) cc_final: 0.9098 (m-10) REVERT: 0 123 MET cc_start: 0.3544 (mmt) cc_final: 0.2872 (mmt) REVERT: 0 238 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7872 (ppt170) REVERT: 0 327 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8744 (pt) REVERT: E 183 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.7752 (mpp) REVERT: E 216 ILE cc_start: 0.8960 (mt) cc_final: 0.8622 (tp) REVERT: E 225 MET cc_start: 0.8161 (mtt) cc_final: 0.7626 (mmt) REVERT: F 16 PHE cc_start: 0.8130 (m-80) cc_final: 0.7369 (m-10) REVERT: F 79 PHE cc_start: 0.8838 (m-80) cc_final: 0.8259 (m-80) REVERT: F 80 VAL cc_start: 0.8108 (p) cc_final: 0.7862 (t) REVERT: F 128 GLN cc_start: 0.8793 (pm20) cc_final: 0.8534 (pm20) REVERT: F 134 SER cc_start: 0.8128 (p) cc_final: 0.7739 (m) REVERT: F 152 ASN cc_start: 0.8823 (m-40) cc_final: 0.8545 (t0) REVERT: G 39 MET cc_start: 0.9132 (tmm) cc_final: 0.8649 (tmm) REVERT: G 40 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8222 (tp40) REVERT: G 83 TRP cc_start: 0.9050 (m100) cc_final: 0.8562 (m100) REVERT: H 152 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7544 (mpp) REVERT: H 172 GLN cc_start: 0.9189 (tt0) cc_final: 0.8935 (tt0) REVERT: I 41 ASP cc_start: 0.9186 (m-30) cc_final: 0.8936 (t70) REVERT: I 76 MET cc_start: 0.7904 (ptt) cc_final: 0.7619 (ptt) REVERT: I 110 TYR cc_start: 0.8466 (m-80) cc_final: 0.8173 (m-80) REVERT: K 54 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9154 (mt) REVERT: K 61 TYR cc_start: 0.9046 (t80) cc_final: 0.8708 (t80) REVERT: K 120 ASP cc_start: 0.8279 (p0) cc_final: 0.7862 (p0) REVERT: K 125 MET cc_start: 0.8605 (mmp) cc_final: 0.8343 (mmp) REVERT: N 45 TYR cc_start: 0.8755 (t80) cc_final: 0.8178 (t80) REVERT: N 81 HIS cc_start: 0.7830 (m90) cc_final: 0.7576 (m170) REVERT: N 100 LYS cc_start: 0.9245 (mttt) cc_final: 0.8716 (tmmt) REVERT: N 133 HIS cc_start: 0.7445 (m-70) cc_final: 0.6730 (m-70) REVERT: O 1 MET cc_start: 0.5460 (tpt) cc_final: 0.5253 (tpt) REVERT: O 5 GLU cc_start: 0.9180 (mm-30) cc_final: 0.8955 (mm-30) REVERT: O 9 LYS cc_start: 0.9367 (ptpp) cc_final: 0.9053 (ptmm) REVERT: O 34 ASN cc_start: 0.8849 (p0) cc_final: 0.8537 (p0) REVERT: O 42 THR cc_start: 0.9089 (p) cc_final: 0.8841 (t) REVERT: O 110 ASN cc_start: 0.9481 (t0) cc_final: 0.8722 (t0) REVERT: O 120 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7962 (tm-30) REVERT: P 54 GLN cc_start: 0.8254 (tt0) cc_final: 0.7992 (tt0) REVERT: P 58 PHE cc_start: 0.8528 (p90) cc_final: 0.8050 (p90) REVERT: P 59 GLN cc_start: 0.9236 (pt0) cc_final: 0.8325 (tp-100) REVERT: P 85 PHE cc_start: 0.8315 (m-80) cc_final: 0.7961 (m-80) REVERT: P 111 ILE cc_start: 0.7775 (mm) cc_final: 0.7204 (tp) REVERT: Q 1 MET cc_start: 0.7485 (tpp) cc_final: 0.7190 (tpp) REVERT: Q 3 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8976 (tt) REVERT: Q 17 MET cc_start: 0.7954 (tpp) cc_final: 0.7701 (tpp) REVERT: Q 26 GLU cc_start: 0.7825 (pp20) cc_final: 0.7607 (tm-30) REVERT: Q 38 GLU cc_start: 0.8181 (mp0) cc_final: 0.7975 (mp0) REVERT: Q 57 TYR cc_start: 0.8982 (t80) cc_final: 0.8622 (t80) REVERT: R 10 SER cc_start: 0.8892 (p) cc_final: 0.8506 (m) REVERT: R 46 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8805 (mmtt) REVERT: R 52 LYS cc_start: 0.8802 (mttt) cc_final: 0.8393 (mmtt) REVERT: R 82 LYS cc_start: 0.9551 (tttt) cc_final: 0.9324 (ttpt) REVERT: R 114 MET cc_start: 0.8324 (mtm) cc_final: 0.7844 (mtm) REVERT: S 62 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8244 (p0) REVERT: T 6 GLU cc_start: 0.9396 (tp30) cc_final: 0.9042 (tm-30) REVERT: T 7 ASP cc_start: 0.9286 (p0) cc_final: 0.8854 (p0) REVERT: T 20 PHE cc_start: 0.8673 (p90) cc_final: 0.8422 (p90) REVERT: T 22 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7800 (Cg_endo) REVERT: T 57 GLU cc_start: 0.8338 (tp30) cc_final: 0.8007 (mp0) REVERT: T 60 THR cc_start: 0.8998 (m) cc_final: 0.8495 (p) REVERT: T 103 LEU cc_start: 0.8911 (tp) cc_final: 0.8685 (tp) REVERT: T 110 ILE cc_start: 0.6914 (OUTLIER) cc_final: 0.6577 (mp) REVERT: U 36 ASN cc_start: 0.9468 (t0) cc_final: 0.9265 (t0) REVERT: U 52 GLN cc_start: 0.9300 (tp40) cc_final: 0.9040 (mm-40) REVERT: U 80 MET cc_start: 0.7979 (mtt) cc_final: 0.7482 (mtp) REVERT: U 94 MET cc_start: 0.9194 (mmm) cc_final: 0.8578 (mmm) REVERT: V 2 TYR cc_start: 0.7100 (p90) cc_final: 0.6819 (p90) REVERT: V 35 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: V 40 PHE cc_start: 0.8940 (t80) cc_final: 0.8638 (t80) REVERT: V 86 GLN cc_start: 0.9099 (tt0) cc_final: 0.8725 (mt0) REVERT: V 97 ILE cc_start: 0.9063 (mp) cc_final: 0.8629 (tp) REVERT: W 52 LYS cc_start: 0.9637 (mttm) cc_final: 0.9172 (mttp) REVERT: X 10 ARG cc_start: 0.9029 (ptp-170) cc_final: 0.8711 (ptm160) REVERT: X 57 MET cc_start: 0.6229 (mtp) cc_final: 0.5429 (mtp) REVERT: X 59 TYR cc_start: 0.7386 (OUTLIER) cc_final: 0.5455 (m-10) REVERT: Y 10 MET cc_start: 0.8083 (tpp) cc_final: 0.7846 (tpp) REVERT: Y 27 PHE cc_start: 0.9219 (m-80) cc_final: 0.9010 (m-80) REVERT: Y 30 LYS cc_start: 0.9504 (mttt) cc_final: 0.9127 (mtmm) REVERT: Y 69 MET cc_start: 0.7531 (mtp) cc_final: 0.7153 (mtp) REVERT: a 76 LYS cc_start: 0.9118 (mppt) cc_final: 0.8527 (mppt) REVERT: b 22 MET cc_start: 0.7191 (mtt) cc_final: 0.6886 (mtt) REVERT: c 1 MET cc_start: 0.9505 (tpp) cc_final: 0.9243 (tpp) REVERT: c 26 PHE cc_start: 0.9053 (t80) cc_final: 0.8228 (t80) REVERT: c 30 PHE cc_start: 0.8880 (m-10) cc_final: 0.8348 (m-80) REVERT: c 37 LEU cc_start: 0.8332 (pt) cc_final: 0.7997 (tp) REVERT: c 38 GLU cc_start: 0.8247 (mp0) cc_final: 0.7887 (mp0) REVERT: c 45 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8356 (tm-30) REVERT: c 54 LYS cc_start: 0.9317 (mtpp) cc_final: 0.9059 (mtpp) REVERT: d 19 GLN cc_start: 0.9293 (mp10) cc_final: 0.8901 (mp10) REVERT: d 38 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7922 (pm20) REVERT: d 49 LYS cc_start: 0.8909 (tttt) cc_final: 0.8444 (tppt) REVERT: f 7 ARG cc_start: 0.8440 (ppp80) cc_final: 0.7355 (ptp90) REVERT: f 10 LYS cc_start: 0.7849 (ttmt) cc_final: 0.7526 (tttt) REVERT: f 22 LEU cc_start: 0.9151 (tp) cc_final: 0.8754 (pt) REVERT: f 27 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8081 (ttm) REVERT: f 37 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7675 (tppt) REVERT: f 42 VAL cc_start: 0.8583 (t) cc_final: 0.8261 (t) REVERT: g 24 ARG cc_start: 0.9019 (mmp80) cc_final: 0.8752 (mmp80) REVERT: g 25 ASN cc_start: 0.9246 (m-40) cc_final: 0.8194 (t0) REVERT: g 26 ASN cc_start: 0.8576 (m110) cc_final: 0.8107 (m-40) REVERT: g 28 ASP cc_start: 0.9385 (p0) cc_final: 0.9157 (p0) REVERT: g 38 ARG cc_start: 0.8660 (mtp180) cc_final: 0.8228 (mtp180) REVERT: h 8 ASN cc_start: 0.8747 (t0) cc_final: 0.8409 (t0) REVERT: h 9 ASN cc_start: 0.8678 (m-40) cc_final: 0.8348 (m110) REVERT: h 13 SER cc_start: 0.9515 (m) cc_final: 0.8437 (t) REVERT: h 14 LYS cc_start: 0.9402 (ttmm) cc_final: 0.9146 (mmtt) REVERT: h 25 LYS cc_start: 0.9439 (tppt) cc_final: 0.9142 (tppp) REVERT: i 4 MET cc_start: 0.8342 (mmm) cc_final: 0.8057 (mmt) REVERT: i 32 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8592 (mt) REVERT: j 33 LYS cc_start: 0.8482 (ttmt) cc_final: 0.8174 (ttmt) outliers start: 193 outliers final: 147 residues processed: 850 average time/residue: 0.9208 time to fit residues: 1323.0768 Evaluate side-chains 864 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 699 time to evaluate : 4.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 LYS Chi-restraints excluded: chain 0 residue 60 HIS Chi-restraints excluded: chain 0 residue 76 CYS Chi-restraints excluded: chain 0 residue 100 MET Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 238 ARG Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 361 ILE Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 133 MET 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 F residue 169 ILE Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 49 HIS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 152 MET Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 12 GLU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 103 LEU Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 8 ASN Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 24 ASP Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 35 PHE Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 31 GLU Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 62 TYR Chi-restraints excluded: chain W residue 64 MET Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 97 ASN Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 8 LEU Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 59 TYR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 74 SER Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 40 MET Chi-restraints excluded: chain Y residue 49 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 48 GLN Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 38 GLU Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 15 LEU Chi-restraints excluded: chain f residue 21 LYS Chi-restraints excluded: chain f residue 27 MET Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain i residue 22 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 61 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 16 VAL Chi-restraints excluded: chain j residue 34 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 392 optimal weight: 0.4980 chunk 253 optimal weight: 20.0000 chunk 378 optimal weight: 8.9990 chunk 191 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 403 optimal weight: 30.0000 chunk 432 optimal weight: 0.3980 chunk 313 optimal weight: 20.0000 chunk 59 optimal weight: 30.0000 chunk 498 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 305 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 ASN ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 10 ASN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 ASN ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 16 ASN ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 31 GLN ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 101236 Z= 0.224 Angle : 0.718 15.947 151523 Z= 0.366 Chirality : 0.038 0.399 19389 Planarity : 0.005 0.055 8035 Dihedral : 25.316 179.973 50770 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 28.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.42 % Favored : 89.52 % Rotamer: Outliers : 5.84 % Allowed : 26.43 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.14 % 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: -2.80 (0.13), residues: 3646 helix: -0.77 (0.15), residues: 1065 sheet: -2.14 (0.19), residues: 600 loop : -2.44 (0.13), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Q 65 HIS 0.008 0.002 HIS Q 13 PHE 0.046 0.003 PHE S 34 TYR 0.030 0.002 TYR T 98 ARG 0.007 0.001 ARG V 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 754 time to evaluate : 4.113 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: 0 20 MET cc_start: 0.7728 (mmm) cc_final: 0.7441 (mmm) REVERT: 0 53 HIS cc_start: 0.9038 (t-90) cc_final: 0.8770 (t70) REVERT: 0 55 SER cc_start: 0.7616 (t) cc_final: 0.7200 (t) REVERT: 0 60 HIS cc_start: 0.6097 (OUTLIER) cc_final: 0.5080 (t-170) REVERT: 0 76 CYS cc_start: 0.5780 (OUTLIER) cc_final: 0.5232 (m) REVERT: 0 102 PHE cc_start: 0.9542 (m-80) cc_final: 0.9157 (m-10) REVERT: 0 123 MET cc_start: 0.3207 (mmt) cc_final: 0.2597 (mmt) REVERT: 0 327 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8745 (pt) REVERT: E 123 ASP cc_start: 0.8534 (t0) cc_final: 0.8020 (p0) REVERT: E 183 MET cc_start: 0.8723 (mpp) cc_final: 0.7756 (mpp) REVERT: E 216 ILE cc_start: 0.8948 (mt) cc_final: 0.8589 (tp) REVERT: E 225 MET cc_start: 0.8409 (mtt) cc_final: 0.8002 (mmm) REVERT: F 16 PHE cc_start: 0.8163 (m-80) cc_final: 0.7532 (m-10) REVERT: F 39 LYS cc_start: 0.8772 (mtpp) cc_final: 0.8366 (mttm) REVERT: F 50 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6868 (mm110) REVERT: F 79 PHE cc_start: 0.8823 (m-80) cc_final: 0.8360 (m-80) REVERT: F 134 SER cc_start: 0.8211 (p) cc_final: 0.7807 (m) REVERT: F 152 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8495 (t0) REVERT: G 40 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8587 (tp40) REVERT: G 82 GLN cc_start: 0.6503 (tp40) cc_final: 0.6043 (tp-100) REVERT: G 83 TRP cc_start: 0.8946 (m100) cc_final: 0.8516 (m100) REVERT: H 152 MET cc_start: 0.7866 (mpp) cc_final: 0.7458 (mpp) REVERT: H 161 ASN cc_start: 0.9259 (m110) cc_final: 0.8609 (m110) REVERT: H 172 GLN cc_start: 0.9174 (tt0) cc_final: 0.8919 (tt0) REVERT: I 41 ASP cc_start: 0.9158 (m-30) cc_final: 0.8922 (t70) REVERT: I 42 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.5218 (mmt) REVERT: I 76 MET cc_start: 0.7734 (ptt) cc_final: 0.7471 (ptt) REVERT: I 110 TYR cc_start: 0.8428 (m-80) cc_final: 0.8186 (m-80) REVERT: K 38 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8455 (m-80) REVERT: K 61 TYR cc_start: 0.9041 (t80) cc_final: 0.8685 (t80) REVERT: K 125 MET cc_start: 0.8619 (mmp) cc_final: 0.8398 (mmp) REVERT: K 135 MET cc_start: 0.8650 (mmp) cc_final: 0.8383 (mmt) REVERT: N 26 LEU cc_start: 0.9214 (pt) cc_final: 0.8873 (pp) REVERT: N 45 TYR cc_start: 0.8783 (t80) cc_final: 0.8179 (t80) REVERT: N 81 HIS cc_start: 0.7744 (m90) cc_final: 0.7397 (m90) REVERT: N 93 MET cc_start: 0.9378 (mmm) cc_final: 0.9073 (mmm) REVERT: N 100 LYS cc_start: 0.9164 (mttt) cc_final: 0.8582 (tmmt) REVERT: N 133 HIS cc_start: 0.7368 (m-70) cc_final: 0.6910 (m90) REVERT: O 1 MET cc_start: 0.5546 (tpt) cc_final: 0.5246 (tpt) REVERT: O 5 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8912 (mm-30) REVERT: O 9 LYS cc_start: 0.9376 (ptpp) cc_final: 0.9105 (ptmm) REVERT: O 34 ASN cc_start: 0.8819 (p0) cc_final: 0.8602 (p0) REVERT: O 42 THR cc_start: 0.9103 (p) cc_final: 0.8859 (t) REVERT: O 84 CYS cc_start: 0.8655 (p) cc_final: 0.8112 (t) REVERT: O 91 LYS cc_start: 0.8615 (tptt) cc_final: 0.8384 (tptt) REVERT: O 110 ASN cc_start: 0.9461 (t0) cc_final: 0.8667 (t0) REVERT: O 120 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7919 (tm-30) REVERT: P 33 LYS cc_start: 0.9174 (mmmt) cc_final: 0.8920 (mmmt) REVERT: P 58 PHE cc_start: 0.8468 (p90) cc_final: 0.8180 (p90) REVERT: P 59 GLN cc_start: 0.9029 (pt0) cc_final: 0.8186 (tp-100) REVERT: P 60 ARG cc_start: 0.8365 (ptp-170) cc_final: 0.8028 (ptp-170) REVERT: P 85 PHE cc_start: 0.8315 (m-80) cc_final: 0.7933 (m-80) REVERT: P 111 ILE cc_start: 0.7774 (mm) cc_final: 0.7197 (tp) REVERT: Q 1 MET cc_start: 0.7389 (tpp) cc_final: 0.7085 (tpp) REVERT: Q 57 TYR cc_start: 0.8979 (t80) cc_final: 0.8485 (t80) REVERT: R 8 ARG cc_start: 0.8196 (mmt180) cc_final: 0.7775 (mtt180) REVERT: R 10 SER cc_start: 0.8915 (p) cc_final: 0.8506 (m) REVERT: R 46 LYS cc_start: 0.9100 (mmtm) cc_final: 0.8775 (mmtt) REVERT: R 52 LYS cc_start: 0.8810 (mttt) cc_final: 0.8399 (mmtt) REVERT: R 114 MET cc_start: 0.8240 (mtm) cc_final: 0.8010 (mtm) REVERT: S 1 MET cc_start: 0.8510 (mpp) cc_final: 0.8211 (mmm) REVERT: S 62 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8105 (p0) REVERT: S 63 LEU cc_start: 0.8906 (tt) cc_final: 0.8670 (pp) REVERT: T 6 GLU cc_start: 0.9368 (tp30) cc_final: 0.8835 (tm-30) REVERT: T 7 ASP cc_start: 0.9150 (p0) cc_final: 0.8910 (p0) REVERT: T 20 PHE cc_start: 0.8748 (p90) cc_final: 0.8487 (p90) REVERT: T 22 PRO cc_start: 0.8120 (Cg_exo) cc_final: 0.7770 (Cg_endo) REVERT: T 57 GLU cc_start: 0.8245 (tp30) cc_final: 0.7888 (mp0) REVERT: T 60 THR cc_start: 0.9051 (m) cc_final: 0.8546 (p) REVERT: T 103 LEU cc_start: 0.8905 (tp) cc_final: 0.8704 (tp) REVERT: T 110 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6560 (mp) REVERT: U 52 GLN cc_start: 0.9313 (tp40) cc_final: 0.9042 (mm-40) REVERT: U 80 MET cc_start: 0.7936 (mtt) cc_final: 0.7444 (mtp) REVERT: U 94 MET cc_start: 0.9279 (mmm) cc_final: 0.8733 (mmm) REVERT: V 2 TYR cc_start: 0.7044 (p90) cc_final: 0.6755 (p90) REVERT: V 35 PHE cc_start: 0.8521 (OUTLIER) cc_final: 0.8076 (m-80) REVERT: V 40 PHE cc_start: 0.8921 (t80) cc_final: 0.8647 (t80) REVERT: V 97 ILE cc_start: 0.9033 (mp) cc_final: 0.8634 (tp) REVERT: W 51 LEU cc_start: 0.9613 (mm) cc_final: 0.9384 (mm) REVERT: W 52 LYS cc_start: 0.9613 (mttm) cc_final: 0.9141 (mttp) REVERT: W 83 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8407 (mmmm) REVERT: X 10 ARG cc_start: 0.9029 (ptp-170) cc_final: 0.8750 (ptm160) REVERT: X 16 ARG cc_start: 0.9046 (mmm-85) cc_final: 0.8832 (mmm-85) REVERT: X 57 MET cc_start: 0.6151 (mtp) cc_final: 0.5446 (mtp) REVERT: X 59 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.5559 (m-10) REVERT: Y 27 PHE cc_start: 0.9211 (m-80) cc_final: 0.8945 (m-80) REVERT: Y 30 LYS cc_start: 0.9495 (mttt) cc_final: 0.9116 (mtmm) REVERT: Y 69 MET cc_start: 0.7520 (mtp) cc_final: 0.7109 (mtp) REVERT: a 76 LYS cc_start: 0.9182 (mppt) cc_final: 0.8543 (mppt) REVERT: b 22 MET cc_start: 0.7100 (mtt) cc_final: 0.6888 (mtt) REVERT: c 1 MET cc_start: 0.9523 (tpp) cc_final: 0.9195 (tpp) REVERT: c 21 LEU cc_start: 0.9641 (mt) cc_final: 0.9402 (pp) REVERT: c 30 PHE cc_start: 0.8876 (m-10) cc_final: 0.8441 (m-80) REVERT: c 31 GLN cc_start: 0.9376 (OUTLIER) cc_final: 0.9114 (tp-100) REVERT: c 38 GLU cc_start: 0.8058 (mp0) cc_final: 0.7721 (mp0) REVERT: c 42 ARG cc_start: 0.9113 (ptp90) cc_final: 0.8783 (ptp90) REVERT: c 45 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: d 19 GLN cc_start: 0.9325 (mp10) cc_final: 0.9083 (mp10) REVERT: d 29 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.7935 (mmmt) REVERT: d 46 MET cc_start: 0.8930 (ptp) cc_final: 0.8686 (ptp) REVERT: d 49 LYS cc_start: 0.8891 (tttt) cc_final: 0.8465 (tppt) REVERT: f 7 ARG cc_start: 0.8654 (ppp80) cc_final: 0.7372 (ptp90) REVERT: f 10 LYS cc_start: 0.7994 (ttmt) cc_final: 0.7415 (tttt) REVERT: f 14 ARG cc_start: 0.9155 (mpt-90) cc_final: 0.8852 (mpt-90) REVERT: f 22 LEU cc_start: 0.9110 (tp) cc_final: 0.8789 (pt) REVERT: f 27 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7879 (ttm) REVERT: f 36 MET cc_start: 0.9050 (mmm) cc_final: 0.8737 (tpt) REVERT: f 37 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7762 (tppt) REVERT: f 42 VAL cc_start: 0.8595 (t) cc_final: 0.8238 (t) REVERT: g 24 ARG cc_start: 0.9127 (mmp80) cc_final: 0.8716 (mmp80) REVERT: g 25 ASN cc_start: 0.9223 (m-40) cc_final: 0.8066 (t0) REVERT: g 26 ASN cc_start: 0.8611 (m110) cc_final: 0.8170 (m-40) REVERT: g 28 ASP cc_start: 0.9489 (p0) cc_final: 0.9282 (p0) REVERT: g 38 ARG cc_start: 0.8628 (mtp180) cc_final: 0.8169 (mtp180) REVERT: h 8 ASN cc_start: 0.8788 (t0) cc_final: 0.8431 (t0) REVERT: h 9 ASN cc_start: 0.8635 (m-40) cc_final: 0.8292 (m110) REVERT: h 13 SER cc_start: 0.9522 (m) cc_final: 0.8450 (t) REVERT: h 14 LYS cc_start: 0.9396 (ttmm) cc_final: 0.9123 (mmtt) REVERT: h 25 LYS cc_start: 0.9435 (tppt) cc_final: 0.9143 (tppp) REVERT: i 4 MET cc_start: 0.8289 (mmm) cc_final: 0.8013 (mmt) REVERT: i 32 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8590 (mt) REVERT: j 4 ARG cc_start: 0.8304 (ptp-170) cc_final: 0.7903 (mpp80) REVERT: j 33 LYS cc_start: 0.8519 (ttmt) cc_final: 0.8297 (ttmt) REVERT: j 35 LYS cc_start: 0.9187 (ptmm) cc_final: 0.8955 (pttt) outliers start: 176 outliers final: 136 residues processed: 849 average time/residue: 0.8982 time to fit residues: 1292.1447 Evaluate side-chains 864 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 711 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 LYS Chi-restraints excluded: chain 0 residue 60 HIS Chi-restraints excluded: chain 0 residue 76 CYS Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 361 ILE Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 170 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 49 HIS Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 38 MET Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 19 ASN Chi-restraints excluded: chain K residue 38 PHE Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 29 LEU Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 129 THR Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 34 GLU Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 37 ASN Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 24 ASP Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 74 PHE Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 22 ILE Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 35 PHE Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 31 GLU Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 62 TYR Chi-restraints excluded: chain W residue 64 MET Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 59 TYR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 80 ILE Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 40 MET Chi-restraints excluded: chain Y residue 49 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain a residue 45 LEU Chi-restraints excluded: chain a residue 48 GLN Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 11 THR Chi-restraints excluded: chain c residue 31 GLN Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 21 LYS Chi-restraints excluded: chain f residue 27 MET Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 61 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 16 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 576 optimal weight: 1.9990 chunk 607 optimal weight: 20.0000 chunk 554 optimal weight: 10.0000 chunk 590 optimal weight: 30.0000 chunk 355 optimal weight: 9.9990 chunk 257 optimal weight: 20.0000 chunk 464 optimal weight: 30.0000 chunk 181 optimal weight: 20.0000 chunk 534 optimal weight: 6.9990 chunk 558 optimal weight: 6.9990 chunk 588 optimal weight: 1.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 13 HIS ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 ASN ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 101236 Z= 0.236 Angle : 0.719 14.513 151523 Z= 0.367 Chirality : 0.038 0.429 19389 Planarity : 0.005 0.056 8035 Dihedral : 25.286 179.472 50770 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 29.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.97 % Favored : 88.95 % Rotamer: Outliers : 5.74 % Allowed : 27.79 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.13), residues: 3646 helix: -0.66 (0.15), residues: 1067 sheet: -2.02 (0.20), residues: 614 loop : -2.41 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP Q 65 HIS 0.008 0.002 HIS Q 13 PHE 0.070 0.003 PHE S 34 TYR 0.032 0.002 TYR T 98 ARG 0.013 0.001 ARG X 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 730 time to evaluate : 4.076 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: 0 20 MET cc_start: 0.7674 (mmm) cc_final: 0.7434 (mmm) REVERT: 0 53 HIS cc_start: 0.9023 (t-90) cc_final: 0.8747 (t70) REVERT: 0 55 SER cc_start: 0.7619 (t) cc_final: 0.7175 (t) REVERT: 0 60 HIS cc_start: 0.5955 (OUTLIER) cc_final: 0.4976 (t-170) REVERT: 0 76 CYS cc_start: 0.5619 (OUTLIER) cc_final: 0.5113 (m) REVERT: 0 100 MET cc_start: 0.9049 (mpp) cc_final: 0.8807 (mmp) REVERT: 0 102 PHE cc_start: 0.9556 (m-80) cc_final: 0.9160 (m-10) REVERT: 0 123 MET cc_start: 0.3288 (mmt) cc_final: 0.2639 (mmt) REVERT: 0 238 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7711 (ppt170) REVERT: 0 327 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8726 (pt) REVERT: E 183 MET cc_start: 0.8730 (mpp) cc_final: 0.7773 (mpp) REVERT: E 216 ILE cc_start: 0.8942 (mt) cc_final: 0.8581 (tp) REVERT: E 225 MET cc_start: 0.8441 (mtt) cc_final: 0.8018 (mmm) REVERT: F 16 PHE cc_start: 0.8265 (m-80) cc_final: 0.7597 (m-80) REVERT: F 51 LEU cc_start: 0.8687 (mm) cc_final: 0.7569 (tp) REVERT: F 79 PHE cc_start: 0.8772 (m-80) cc_final: 0.8291 (m-80) REVERT: F 134 SER cc_start: 0.8227 (p) cc_final: 0.7830 (m) REVERT: F 152 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8471 (t0) REVERT: G 40 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8718 (tp40) REVERT: G 83 TRP cc_start: 0.8990 (m100) cc_final: 0.8522 (m100) REVERT: H 152 MET cc_start: 0.7725 (mpp) cc_final: 0.7289 (mpp) REVERT: H 161 ASN cc_start: 0.9256 (m110) cc_final: 0.8747 (m110) REVERT: H 172 GLN cc_start: 0.9185 (tt0) cc_final: 0.8927 (tt0) REVERT: I 41 ASP cc_start: 0.9170 (m-30) cc_final: 0.8935 (t70) REVERT: I 42 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.5281 (mmt) REVERT: I 76 MET cc_start: 0.7729 (ptt) cc_final: 0.7436 (ptt) REVERT: I 110 TYR cc_start: 0.8427 (m-80) cc_final: 0.8141 (m-80) REVERT: K 54 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9157 (mt) REVERT: K 61 TYR cc_start: 0.9058 (t80) cc_final: 0.8705 (t80) REVERT: K 120 ASP cc_start: 0.8154 (p0) cc_final: 0.7751 (p0) REVERT: K 125 MET cc_start: 0.8559 (mmp) cc_final: 0.8296 (mmp) REVERT: K 135 MET cc_start: 0.8652 (mmp) cc_final: 0.8350 (mmt) REVERT: N 19 VAL cc_start: 0.8867 (OUTLIER) cc_final: 0.8631 (m) REVERT: N 26 LEU cc_start: 0.9195 (pt) cc_final: 0.8866 (pp) REVERT: N 45 TYR cc_start: 0.8783 (t80) cc_final: 0.8146 (t80) REVERT: N 81 HIS cc_start: 0.7773 (m90) cc_final: 0.7548 (m170) REVERT: N 93 MET cc_start: 0.9355 (mmm) cc_final: 0.8526 (tpp) REVERT: N 100 LYS cc_start: 0.9160 (mttt) cc_final: 0.8588 (tmmt) REVERT: O 1 MET cc_start: 0.5583 (tpt) cc_final: 0.5293 (tpt) REVERT: O 5 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8919 (mm-30) REVERT: O 9 LYS cc_start: 0.9402 (ptpp) cc_final: 0.9192 (pptt) REVERT: O 25 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8222 (tp) REVERT: O 34 ASN cc_start: 0.8879 (p0) cc_final: 0.8670 (p0) REVERT: O 91 LYS cc_start: 0.8654 (tptt) cc_final: 0.8360 (tptt) REVERT: O 110 ASN cc_start: 0.9469 (t0) cc_final: 0.8662 (t0) REVERT: O 120 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7916 (tm-30) REVERT: P 33 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8961 (mmmt) REVERT: P 55 MET cc_start: 0.7136 (ttm) cc_final: 0.6842 (ttm) REVERT: P 58 PHE cc_start: 0.8467 (p90) cc_final: 0.7976 (p90) REVERT: P 59 GLN cc_start: 0.9095 (pt0) cc_final: 0.8169 (tm-30) REVERT: P 60 ARG cc_start: 0.8311 (ptp-170) cc_final: 0.7902 (ptp-170) REVERT: P 85 PHE cc_start: 0.8305 (m-80) cc_final: 0.7928 (m-80) REVERT: P 111 ILE cc_start: 0.7762 (mm) cc_final: 0.7175 (tp) REVERT: Q 1 MET cc_start: 0.7402 (tpp) cc_final: 0.7010 (tpp) REVERT: Q 57 TYR cc_start: 0.8969 (t80) cc_final: 0.8710 (t80) REVERT: R 8 ARG cc_start: 0.8238 (mmt180) cc_final: 0.7816 (mtt180) REVERT: R 10 SER cc_start: 0.8896 (p) cc_final: 0.8488 (m) REVERT: R 46 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8792 (mmtt) REVERT: R 52 LYS cc_start: 0.8816 (mttt) cc_final: 0.8383 (mmtt) REVERT: S 1 MET cc_start: 0.8340 (mpp) cc_final: 0.8027 (mpp) REVERT: S 62 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8251 (p0) REVERT: S 63 LEU cc_start: 0.8880 (tt) cc_final: 0.8618 (pp) REVERT: S 90 ILE cc_start: 0.8585 (pt) cc_final: 0.8237 (tp) REVERT: T 20 PHE cc_start: 0.8786 (p90) cc_final: 0.8565 (p90) REVERT: T 22 PRO cc_start: 0.8209 (Cg_exo) cc_final: 0.7856 (Cg_endo) REVERT: T 57 GLU cc_start: 0.8163 (tp30) cc_final: 0.7795 (mp0) REVERT: T 60 THR cc_start: 0.9055 (m) cc_final: 0.8545 (p) REVERT: T 103 LEU cc_start: 0.8922 (tp) cc_final: 0.8683 (tp) REVERT: T 110 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6547 (mp) REVERT: U 52 GLN cc_start: 0.9311 (tp40) cc_final: 0.9036 (mm-40) REVERT: U 80 MET cc_start: 0.7959 (mtt) cc_final: 0.7431 (mtp) REVERT: U 94 MET cc_start: 0.9269 (mmm) cc_final: 0.8700 (mmm) REVERT: V 2 TYR cc_start: 0.7116 (p90) cc_final: 0.6820 (p90) REVERT: V 35 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8083 (m-80) REVERT: V 40 PHE cc_start: 0.8934 (t80) cc_final: 0.8666 (t80) REVERT: V 86 GLN cc_start: 0.8991 (tt0) cc_final: 0.8742 (mt0) REVERT: V 97 ILE cc_start: 0.9036 (mp) cc_final: 0.8635 (tp) REVERT: W 52 LYS cc_start: 0.9633 (mttm) cc_final: 0.9180 (mttp) REVERT: X 16 ARG cc_start: 0.8996 (mmm-85) cc_final: 0.8655 (mmm-85) REVERT: X 57 MET cc_start: 0.6178 (mtp) cc_final: 0.5462 (mtp) REVERT: X 59 TYR cc_start: 0.7438 (OUTLIER) cc_final: 0.5468 (m-10) REVERT: X 76 ARG cc_start: 0.8976 (ttm110) cc_final: 0.8755 (mtm180) REVERT: Y 27 PHE cc_start: 0.9229 (m-80) cc_final: 0.8968 (m-80) REVERT: Y 30 LYS cc_start: 0.9488 (mttt) cc_final: 0.9104 (mtmm) REVERT: Y 42 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8913 (ptpp) REVERT: Y 69 MET cc_start: 0.7686 (mtp) cc_final: 0.7248 (mtp) REVERT: a 76 LYS cc_start: 0.9154 (mppt) cc_final: 0.8542 (mppt) REVERT: a 80 PHE cc_start: 0.8686 (m-80) cc_final: 0.8124 (m-10) REVERT: a 86 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8696 (tttm) REVERT: b 22 MET cc_start: 0.7091 (mtt) cc_final: 0.6867 (mtt) REVERT: c 30 PHE cc_start: 0.8809 (m-10) cc_final: 0.8434 (m-80) REVERT: c 38 GLU cc_start: 0.8084 (mp0) cc_final: 0.7705 (mp0) REVERT: c 42 ARG cc_start: 0.9092 (ptp90) cc_final: 0.8785 (ptp90) REVERT: d 19 GLN cc_start: 0.9318 (mp10) cc_final: 0.9096 (mp10) REVERT: d 24 ARG cc_start: 0.8767 (tpt170) cc_final: 0.8413 (tpt90) REVERT: d 46 MET cc_start: 0.9004 (ptp) cc_final: 0.8699 (ptp) REVERT: d 49 LYS cc_start: 0.8925 (tttt) cc_final: 0.8486 (tppt) REVERT: f 7 ARG cc_start: 0.8700 (ppp80) cc_final: 0.7395 (ptp90) REVERT: f 10 LYS cc_start: 0.8013 (ttmt) cc_final: 0.7449 (tttt) REVERT: f 14 ARG cc_start: 0.9169 (mpt-90) cc_final: 0.8823 (mpt-90) REVERT: f 22 LEU cc_start: 0.9107 (tp) cc_final: 0.8829 (pt) REVERT: f 27 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8120 (ttt) REVERT: f 37 LYS cc_start: 0.8075 (ttpt) cc_final: 0.7705 (tppt) REVERT: f 42 VAL cc_start: 0.8580 (t) cc_final: 0.8202 (t) REVERT: g 24 ARG cc_start: 0.9106 (mmp80) cc_final: 0.8701 (mmp80) REVERT: g 25 ASN cc_start: 0.9243 (m-40) cc_final: 0.8182 (t0) REVERT: g 26 ASN cc_start: 0.8632 (m110) cc_final: 0.8190 (m110) REVERT: g 28 ASP cc_start: 0.9502 (p0) cc_final: 0.9254 (p0) REVERT: g 38 ARG cc_start: 0.8646 (mtp180) cc_final: 0.8173 (mtp180) REVERT: h 8 ASN cc_start: 0.8791 (t0) cc_final: 0.8427 (t0) REVERT: h 9 ASN cc_start: 0.8644 (m-40) cc_final: 0.8337 (m110) REVERT: h 13 SER cc_start: 0.9525 (m) cc_final: 0.8968 (t) REVERT: h 14 LYS cc_start: 0.9393 (ttmm) cc_final: 0.9069 (mmtm) REVERT: h 22 MET cc_start: 0.9372 (mmm) cc_final: 0.8672 (mmm) REVERT: h 25 LYS cc_start: 0.9442 (tppt) cc_final: 0.9142 (tppp) REVERT: i 32 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (mt) REVERT: j 33 LYS cc_start: 0.8555 (ttmt) cc_final: 0.8200 (ttpt) outliers start: 173 outliers final: 141 residues processed: 824 average time/residue: 0.9083 time to fit residues: 1265.5603 Evaluate side-chains 867 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 707 time to evaluate : 4.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 LYS Chi-restraints excluded: chain 0 residue 60 HIS Chi-restraints excluded: chain 0 residue 76 CYS Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 238 ARG Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 361 ILE Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 180 GLU Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 49 HIS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 19 VAL Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain N residue 129 SER Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 103 LYS Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 37 ASN Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 17 LEU Chi-restraints excluded: chain T residue 24 ASP Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 74 PHE Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 35 PHE Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 31 GLU Chi-restraints excluded: chain W residue 38 LEU Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 64 MET Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 97 ASN Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 59 TYR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 40 MET Chi-restraints excluded: chain Y residue 42 LYS Chi-restraints excluded: chain Y residue 49 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 48 GLN Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 36 GLN Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 21 LYS Chi-restraints excluded: chain f residue 27 MET Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 61 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 388 optimal weight: 2.9990 chunk 624 optimal weight: 10.0000 chunk 381 optimal weight: 6.9990 chunk 296 optimal weight: 20.0000 chunk 434 optimal weight: 8.9990 chunk 655 optimal weight: 4.9990 chunk 603 optimal weight: 20.0000 chunk 522 optimal weight: 30.0000 chunk 54 optimal weight: 40.0000 chunk 403 optimal weight: 30.0000 chunk 320 optimal weight: 20.0000 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 ASN ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 101236 Z= 0.264 Angle : 0.739 14.516 151523 Z= 0.377 Chirality : 0.039 0.425 19389 Planarity : 0.005 0.062 8035 Dihedral : 25.312 179.943 50770 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 31.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.44 % Favored : 88.51 % Rotamer: Outliers : 5.57 % Allowed : 28.02 % Favored : 66.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.68 (0.13), residues: 3646 helix: -0.66 (0.15), residues: 1061 sheet: -2.01 (0.19), residues: 623 loop : -2.38 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Q 65 HIS 0.008 0.002 HIS Q 13 PHE 0.058 0.003 PHE S 34 TYR 0.019 0.002 TYR V 76 ARG 0.013 0.001 ARG X 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 722 time to evaluate : 4.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 20 MET cc_start: 0.7657 (mmm) cc_final: 0.7378 (mmm) REVERT: 0 53 HIS cc_start: 0.9018 (t-90) cc_final: 0.8747 (t70) REVERT: 0 55 SER cc_start: 0.7625 (t) cc_final: 0.7183 (t) REVERT: 0 76 CYS cc_start: 0.5543 (OUTLIER) cc_final: 0.4991 (m) REVERT: 0 100 MET cc_start: 0.9059 (mpp) cc_final: 0.8772 (mmp) REVERT: 0 102 PHE cc_start: 0.9590 (m-80) cc_final: 0.9152 (m-10) REVERT: 0 118 LEU cc_start: 0.9622 (tp) cc_final: 0.9352 (mm) REVERT: 0 123 MET cc_start: 0.3470 (mmt) cc_final: 0.2743 (mmt) REVERT: 0 238 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7734 (ppt170) REVERT: 0 327 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8730 (pt) REVERT: E 123 ASP cc_start: 0.8536 (t0) cc_final: 0.8052 (p0) REVERT: E 143 ASN cc_start: 0.8303 (t0) cc_final: 0.8096 (t0) REVERT: E 183 MET cc_start: 0.8727 (mpp) cc_final: 0.7776 (mpp) REVERT: E 216 ILE cc_start: 0.8943 (mt) cc_final: 0.8589 (tp) REVERT: E 225 MET cc_start: 0.8453 (mtt) cc_final: 0.7928 (mmm) REVERT: F 16 PHE cc_start: 0.8163 (m-80) cc_final: 0.7496 (m-80) REVERT: F 134 SER cc_start: 0.8211 (p) cc_final: 0.7827 (m) REVERT: F 152 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8482 (t0) REVERT: G 40 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8682 (tp40) REVERT: G 83 TRP cc_start: 0.8950 (m100) cc_final: 0.8469 (m100) REVERT: H 152 MET cc_start: 0.7721 (mpp) cc_final: 0.7283 (mpp) REVERT: H 161 ASN cc_start: 0.9291 (m110) cc_final: 0.8474 (m110) REVERT: H 172 GLN cc_start: 0.9223 (tt0) cc_final: 0.8951 (tt0) REVERT: I 41 ASP cc_start: 0.9180 (m-30) cc_final: 0.8941 (t70) REVERT: I 42 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.5253 (mmt) REVERT: I 76 MET cc_start: 0.7742 (ptt) cc_final: 0.7475 (ptt) REVERT: K 54 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9150 (mt) REVERT: K 61 TYR cc_start: 0.9074 (t80) cc_final: 0.8708 (t80) REVERT: K 125 MET cc_start: 0.8535 (mmp) cc_final: 0.8317 (mmp) REVERT: K 127 MET cc_start: 0.7921 (mmm) cc_final: 0.7547 (mmm) REVERT: K 135 MET cc_start: 0.8610 (mmp) cc_final: 0.8348 (mmt) REVERT: N 26 LEU cc_start: 0.9234 (pt) cc_final: 0.8869 (pp) REVERT: N 45 TYR cc_start: 0.8748 (t80) cc_final: 0.8114 (t80) REVERT: N 81 HIS cc_start: 0.7772 (m90) cc_final: 0.7530 (m170) REVERT: N 93 MET cc_start: 0.9394 (mmm) cc_final: 0.8463 (tpp) REVERT: N 100 LYS cc_start: 0.9202 (mttt) cc_final: 0.8572 (tmmt) REVERT: N 109 MET cc_start: 0.8325 (mmm) cc_final: 0.7505 (mmp) REVERT: O 1 MET cc_start: 0.5637 (tpt) cc_final: 0.5391 (tpt) REVERT: O 5 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8956 (mm-30) REVERT: O 9 LYS cc_start: 0.9409 (ptpp) cc_final: 0.9208 (pptt) REVERT: O 25 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8235 (tp) REVERT: O 34 ASN cc_start: 0.8866 (p0) cc_final: 0.8657 (p0) REVERT: O 53 LYS cc_start: 0.9415 (mppt) cc_final: 0.8760 (mmtm) REVERT: O 56 GLU cc_start: 0.8327 (mp0) cc_final: 0.7960 (mp0) REVERT: O 91 LYS cc_start: 0.8682 (tptt) cc_final: 0.8388 (tptt) REVERT: O 110 ASN cc_start: 0.9472 (t0) cc_final: 0.8654 (t0) REVERT: O 120 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: P 33 LYS cc_start: 0.9211 (mmmt) cc_final: 0.8952 (mmmt) REVERT: P 59 GLN cc_start: 0.9107 (pt0) cc_final: 0.8265 (tm-30) REVERT: P 60 ARG cc_start: 0.8336 (ptp-170) cc_final: 0.7991 (ptp-170) REVERT: P 85 PHE cc_start: 0.8278 (m-80) cc_final: 0.7943 (m-80) REVERT: P 111 ILE cc_start: 0.7830 (mm) cc_final: 0.7247 (tp) REVERT: Q 1 MET cc_start: 0.7413 (tpp) cc_final: 0.6989 (tpp) REVERT: Q 17 MET cc_start: 0.8144 (tpp) cc_final: 0.7720 (ptt) REVERT: Q 57 TYR cc_start: 0.9063 (t80) cc_final: 0.8651 (t80) REVERT: Q 83 MET cc_start: 0.8857 (mmt) cc_final: 0.8148 (tpp) REVERT: R 8 ARG cc_start: 0.8162 (mmt180) cc_final: 0.7704 (mtt180) REVERT: R 10 SER cc_start: 0.8872 (p) cc_final: 0.8458 (m) REVERT: R 46 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8764 (mmtt) REVERT: R 52 LYS cc_start: 0.8834 (mttt) cc_final: 0.8413 (mmtt) REVERT: S 1 MET cc_start: 0.8236 (mpp) cc_final: 0.7888 (mmm) REVERT: S 63 LEU cc_start: 0.8935 (tt) cc_final: 0.8664 (pp) REVERT: T 20 PHE cc_start: 0.8869 (p90) cc_final: 0.8641 (p90) REVERT: T 22 PRO cc_start: 0.8268 (Cg_exo) cc_final: 0.7922 (Cg_endo) REVERT: T 57 GLU cc_start: 0.8103 (tp30) cc_final: 0.7707 (mp0) REVERT: T 103 LEU cc_start: 0.8944 (tp) cc_final: 0.8627 (tp) REVERT: T 110 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6495 (mp) REVERT: U 37 GLN cc_start: 0.9244 (pt0) cc_final: 0.9016 (pt0) REVERT: U 52 GLN cc_start: 0.9293 (tp40) cc_final: 0.9008 (mm-40) REVERT: U 80 MET cc_start: 0.7995 (mtt) cc_final: 0.7471 (mtp) REVERT: U 94 MET cc_start: 0.9282 (mmm) cc_final: 0.8720 (mmm) REVERT: V 2 TYR cc_start: 0.7205 (p90) cc_final: 0.6925 (p90) REVERT: V 35 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: V 40 PHE cc_start: 0.8944 (t80) cc_final: 0.8650 (t80) REVERT: V 86 GLN cc_start: 0.8988 (tt0) cc_final: 0.8735 (mt0) REVERT: V 97 ILE cc_start: 0.9061 (mp) cc_final: 0.8665 (tp) REVERT: W 52 LYS cc_start: 0.9637 (mttm) cc_final: 0.9191 (mttp) REVERT: X 57 MET cc_start: 0.6211 (mtp) cc_final: 0.5488 (mtp) REVERT: X 59 TYR cc_start: 0.7422 (OUTLIER) cc_final: 0.5540 (m-10) REVERT: X 76 ARG cc_start: 0.9005 (ttm110) cc_final: 0.8785 (mtp180) REVERT: Y 27 PHE cc_start: 0.9242 (m-80) cc_final: 0.8993 (m-80) REVERT: Y 30 LYS cc_start: 0.9493 (mttt) cc_final: 0.9084 (mtmm) REVERT: Y 42 LYS cc_start: 0.9317 (OUTLIER) cc_final: 0.8917 (ptpp) REVERT: Y 69 MET cc_start: 0.7662 (mtp) cc_final: 0.7371 (mtp) REVERT: a 76 LYS cc_start: 0.9169 (mppt) cc_final: 0.8603 (mppt) REVERT: a 80 PHE cc_start: 0.8750 (m-80) cc_final: 0.8484 (m-10) REVERT: b 22 MET cc_start: 0.7140 (mtt) cc_final: 0.6893 (mtt) REVERT: c 1 MET cc_start: 0.9430 (tpp) cc_final: 0.9200 (tpp) REVERT: c 17 LYS cc_start: 0.9598 (mttt) cc_final: 0.9314 (mttt) REVERT: c 30 PHE cc_start: 0.8846 (m-10) cc_final: 0.8437 (m-80) REVERT: c 37 LEU cc_start: 0.8206 (pt) cc_final: 0.7248 (tp) REVERT: c 38 GLU cc_start: 0.7938 (mp0) cc_final: 0.7651 (mp0) REVERT: c 47 ARG cc_start: 0.8246 (mtp180) cc_final: 0.7807 (mtp180) REVERT: d 19 GLN cc_start: 0.9323 (mp10) cc_final: 0.9107 (mp10) REVERT: d 24 ARG cc_start: 0.8710 (tpt170) cc_final: 0.8063 (tpt90) REVERT: d 29 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8339 (mmtp) REVERT: d 46 MET cc_start: 0.9000 (ptp) cc_final: 0.8698 (ptp) REVERT: d 49 LYS cc_start: 0.8945 (tttt) cc_final: 0.8539 (tppt) REVERT: f 7 ARG cc_start: 0.8736 (ppp80) cc_final: 0.7420 (ptp90) REVERT: f 10 LYS cc_start: 0.7949 (ttmt) cc_final: 0.7650 (tttt) REVERT: f 16 ARG cc_start: 0.8592 (ttp-170) cc_final: 0.8131 (ttp-170) REVERT: f 22 LEU cc_start: 0.9086 (tp) cc_final: 0.8826 (pt) REVERT: f 37 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7872 (tppt) REVERT: f 42 VAL cc_start: 0.8611 (t) cc_final: 0.8250 (t) REVERT: g 25 ASN cc_start: 0.9243 (m-40) cc_final: 0.8168 (t0) REVERT: g 26 ASN cc_start: 0.8636 (m110) cc_final: 0.8085 (m110) REVERT: g 28 ASP cc_start: 0.9515 (p0) cc_final: 0.9243 (p0) REVERT: g 38 ARG cc_start: 0.8663 (mtp180) cc_final: 0.8186 (mtp180) REVERT: h 8 ASN cc_start: 0.8810 (t0) cc_final: 0.8473 (t0) REVERT: h 9 ASN cc_start: 0.8618 (m-40) cc_final: 0.8392 (m110) REVERT: h 13 SER cc_start: 0.9536 (m) cc_final: 0.8496 (t) REVERT: h 14 LYS cc_start: 0.9394 (ttmm) cc_final: 0.9139 (mmtt) REVERT: h 25 LYS cc_start: 0.9460 (tppt) cc_final: 0.9172 (tppp) REVERT: i 4 MET cc_start: 0.8260 (mmt) cc_final: 0.7548 (mmm) REVERT: i 32 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8621 (mt) REVERT: j 33 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8258 (ttpt) outliers start: 168 outliers final: 142 residues processed: 814 average time/residue: 0.9033 time to fit residues: 1244.3843 Evaluate side-chains 860 residues out of total 3121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 703 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 42 LYS Chi-restraints excluded: chain 0 residue 76 CYS Chi-restraints excluded: chain 0 residue 156 VAL Chi-restraints excluded: chain 0 residue 238 ARG Chi-restraints excluded: chain 0 residue 327 LEU Chi-restraints excluded: chain 0 residue 361 ILE Chi-restraints excluded: chain 0 residue 368 THR Chi-restraints excluded: chain 0 residue 419 ILE Chi-restraints excluded: chain E residue 38 HIS Chi-restraints excluded: chain E residue 45 ASN Chi-restraints excluded: chain E residue 46 GLN Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 125 LYS Chi-restraints excluded: chain E residue 134 ASN Chi-restraints excluded: chain E residue 140 VAL Chi-restraints excluded: chain E residue 198 GLU Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain F residue 91 TYR Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 133 MET Chi-restraints excluded: chain F residue 140 HIS Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 153 ARG Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 40 GLN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 49 HIS Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 93 THR Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 185 ASP Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 193 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 42 MET Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 169 VAL Chi-restraints excluded: chain K residue 52 LEU Chi-restraints excluded: chain K residue 54 ILE Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain L residue 75 PHE Chi-restraints excluded: chain L residue 108 ILE Chi-restraints excluded: chain N residue 8 ASN Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 62 LYS Chi-restraints excluded: chain N residue 97 TYR Chi-restraints excluded: chain N residue 102 LEU Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 12 ASP Chi-restraints excluded: chain O residue 20 LEU Chi-restraints excluded: chain O residue 25 LEU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 78 SER Chi-restraints excluded: chain O residue 99 PHE Chi-restraints excluded: chain O residue 102 VAL Chi-restraints excluded: chain O residue 120 GLU Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 23 ILE Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 3 LEU Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 44 ASN Chi-restraints excluded: chain R residue 9 THR Chi-restraints excluded: chain R residue 16 MET Chi-restraints excluded: chain R residue 33 THR Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 74 GLU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 103 LYS Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 5 THR Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 37 ASN Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 49 ASN Chi-restraints excluded: chain S residue 53 LEU Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 109 LEU Chi-restraints excluded: chain S residue 119 LYS Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 24 ASP Chi-restraints excluded: chain T residue 27 ARG Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 74 PHE Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 91 LYS Chi-restraints excluded: chain T residue 109 ARG Chi-restraints excluded: chain T residue 110 ILE Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 39 VAL Chi-restraints excluded: chain V residue 25 LEU Chi-restraints excluded: chain V residue 35 PHE Chi-restraints excluded: chain V residue 39 LEU Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 73 VAL Chi-restraints excluded: chain V residue 76 TYR Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 55 ILE Chi-restraints excluded: chain W residue 64 MET Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 97 ASN Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 58 ASN Chi-restraints excluded: chain X residue 59 TYR Chi-restraints excluded: chain X residue 63 SER Chi-restraints excluded: chain X residue 84 THR Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 39 ASN Chi-restraints excluded: chain Y residue 42 LYS Chi-restraints excluded: chain Y residue 49 GLN Chi-restraints excluded: chain Y residue 85 VAL Chi-restraints excluded: chain Y residue 89 LYS Chi-restraints excluded: chain Y residue 92 ARG Chi-restraints excluded: chain a residue 40 THR Chi-restraints excluded: chain a residue 48 GLN Chi-restraints excluded: chain a residue 58 ASN Chi-restraints excluded: chain a residue 86 LYS Chi-restraints excluded: chain b residue 23 ASN Chi-restraints excluded: chain b residue 46 LYS Chi-restraints excluded: chain c residue 11 THR Chi-restraints excluded: chain c residue 45 GLU Chi-restraints excluded: chain d residue 13 ILE Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 26 LEU Chi-restraints excluded: chain d residue 29 LYS Chi-restraints excluded: chain d residue 31 THR Chi-restraints excluded: chain d residue 55 SER Chi-restraints excluded: chain f residue 3 VAL Chi-restraints excluded: chain f residue 15 LEU Chi-restraints excluded: chain f residue 21 LYS Chi-restraints excluded: chain h residue 4 THR Chi-restraints excluded: chain h residue 31 LEU Chi-restraints excluded: chain h residue 40 LYS Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain i residue 32 LEU Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 658 random chunks: chunk 414 optimal weight: 1.9990 chunk 556 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 481 optimal weight: 5.9990 chunk 77 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 522 optimal weight: 8.9990 chunk 218 optimal weight: 20.0000 chunk 536 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 300 ASN ** 0 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.042042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.034218 restraints weight = 814639.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.035410 restraints weight = 280107.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.036124 restraints weight = 142331.545| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 101236 Z= 0.247 Angle : 0.727 14.847 151523 Z= 0.370 Chirality : 0.038 0.428 19389 Planarity : 0.005 0.074 8035 Dihedral : 25.299 179.967 50770 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 30.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.33 % Favored : 88.62 % Rotamer: Outliers : 5.50 % Allowed : 28.48 % Favored : 66.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.68 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -2.62 (0.13), residues: 3646 helix: -0.66 (0.15), residues: 1064 sheet: -1.88 (0.20), residues: 609 loop : -2.36 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Q 65 HIS 0.012 0.002 HIS N 133 PHE 0.051 0.002 PHE S 34 TYR 0.019 0.002 TYR V 76 ARG 0.012 0.001 ARG g 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20965.05 seconds wall clock time: 372 minutes 55.87 seconds (22375.87 seconds total)