Starting phenix.real_space_refine on Sat Feb 17 10:42:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/02_2024/7yla_33904_neut_trim_updated.pdb" } resolution = 2.52 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= 0.005 sd= 0.050 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: 9 Type Number sf(0) Gaussians Zn 1 6.06 5 P 2997 5.49 5 Mg 3 5.21 5 S 88 5.16 5 Na 1 4.78 5 C 47116 2.51 5 N 17459 2.21 5 O 26067 1.98 5 H 32052 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "6 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "M PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z GLU 45": "OE1" <-> "OE2" Residue "b TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "l PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 125784 Number of models: 1 Model: "" Number of chains: 36 Chain: "6" Number of atoms: 6704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 6704 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 403} Chain: "I" Number of atoms: 61752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2876, 61752 Classifications: {'RNA': 2876} Modifications used: {'rna2p': 1, 'rna2p_pur': 278, 'rna2p_pyr': 150, 'rna3p': 5, 'rna3p_pur': 1384, 'rna3p_pyr': 1058} Link IDs: {'rna2p': 429, 'rna3p': 2446} Chain breaks: 4 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 4261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 4236 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Conformer: "B" Number of residues, atoms: 271, 4236 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} bond proxies already assigned to first conformer: 4249 Chain: "L" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3182 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "M" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3171 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2855 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "O" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2694 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "P" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2251 Classifications: {'peptide': 149} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "Q" Number of atoms: 2003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2003 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "R" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "S" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1950 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "T" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2218 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "V" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1960 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "W" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1815 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "X" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1879 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Y" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1967 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Z" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1655 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "a" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1779 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "b" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1546 Classifications: {'peptide': 93} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "c" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1611 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "d" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1533 Classifications: {'peptide': 94} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "e" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1167 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "f" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1277 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "g" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1032 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "h" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 937 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "i" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 902 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "j" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 849 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "k" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 795 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "l" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1077 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "m" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 642 Classifications: {'peptide': 38} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "6" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0JIK SG CYS m 11 100.491 72.227 181.077 1.00 51.71 S ATOM A0JJW SG CYS m 14 100.991 70.613 177.671 1.00 46.63 S ATOM A0JQ6 SG CYS m 27 97.571 70.619 179.458 1.00 46.45 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG K 203 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG K 203 " occ=0.50 Time building chain proxies: 44.24, per 1000 atoms: 0.35 Number of scatterers: 125784 At special positions: 0 Unit cell: (225.128, 218.816, 237.752, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 S 88 16.00 P 2997 15.00 Mg 3 11.99 Na 1 11.00 O 26067 8.00 N 17459 7.00 C 47116 6.00 H 32052 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 68.96 Conformation dependent library (CDL) restraints added in 5.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" ND1 HIS m 33 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 11 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 27 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 14 " Number of angles added : 3 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 107 helices and 48 sheets defined 34.5% alpha, 19.5% beta 935 base pairs and 1458 stacking pairs defined. Time for finding SS restraints: 63.44 Creating SS restraints... Processing helix chain '6' and resid 26 through 38 Processing helix chain '6' and resid 59 through 74 Processing helix chain '6' and resid 85 through 97 removed outlier: 3.796A pdb=" N GLU 6 97 " --> pdb=" O GLU 6 93 " (cutoff:3.500A) Processing helix chain '6' and resid 102 through 115 Processing helix chain '6' and resid 117 through 136 removed outlier: 3.596A pdb=" N ARG 6 135 " --> pdb=" O HIS 6 131 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU 6 136 " --> pdb=" O LEU 6 132 " (cutoff:3.500A) Processing helix chain '6' and resid 158 through 191 Processing helix chain '6' and resid 209 through 219 Processing helix chain '6' and resid 260 through 272 removed outlier: 3.670A pdb=" N LYS 6 268 " --> pdb=" O VAL 6 264 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA 6 269 " --> pdb=" O ALA 6 265 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N THR 6 270 " --> pdb=" O ALA 6 266 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN 6 272 " --> pdb=" O LYS 6 268 " (cutoff:3.500A) Processing helix chain '6' and resid 290 through 306 Processing helix chain '6' and resid 318 through 323 removed outlier: 3.852A pdb=" N LEU 6 322 " --> pdb=" O LYS 6 318 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N GLU 6 323 " --> pdb=" O ILE 6 319 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 318 through 323' Processing helix chain '6' and resid 349 through 362 removed outlier: 3.831A pdb=" N LEU 6 361 " --> pdb=" O LEU 6 357 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER 6 362 " --> pdb=" O THR 6 358 " (cutoff:3.500A) Processing helix chain '6' and resid 376 through 387 Processing helix chain '6' and resid 407 through 418 Processing helix chain 'K' and resid 10 through 16 removed outlier: 7.479A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.876A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 35' Processing helix chain 'K' and resid 131 through 136 Proline residue: K 136 - end of helix Processing helix chain 'K' and resid 207 through 215 removed outlier: 3.711A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 3.920A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 260 through 268 removed outlier: 6.443A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 268' Processing helix chain 'K' and resid 197 through 202 removed outlier: 4.021A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 5.998A pdb=" N THR L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 72 removed outlier: 3.696A pdb=" N ALA L 71 " --> pdb=" O HIS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 103 removed outlier: 4.285A pdb=" N ALA L 102 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ASP L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 98 through 103' Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 39 through 44 Processing helix chain 'M' and resid 24 through 41 removed outlier: 3.706A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 removed outlier: 6.236A pdb=" N THR M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 165 removed outlier: 4.631A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU M 164 " --> pdb=" O ALA M 160 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N HIS M 165 " --> pdb=" O ALA M 161 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 6.339A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'N' and resid 2 through 21 removed outlier: 3.634A pdb=" N ASP N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL N 13 " --> pdb=" O LYS N 9 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS N 14 " --> pdb=" O ASP N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 47 removed outlier: 4.630A pdb=" N ASP N 46 " --> pdb=" O GLU N 42 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 42 through 47' Processing helix chain 'N' and resid 48 through 61 Processing helix chain 'N' and resid 93 through 111 removed outlier: 3.823A pdb=" N ILE N 106 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL N 108 " --> pdb=" O ILE N 104 " (cutoff:3.500A) Proline residue: N 109 - end of helix Processing helix chain 'N' and resid 162 through 174 removed outlier: 3.572A pdb=" N PHE N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 29 Proline residue: N 29 - end of helix Processing helix chain 'N' and resid 134 through 139 Proline residue: N 139 - end of helix Processing helix chain 'O' and resid 2 through 8 Proline residue: O 8 - end of helix Processing helix chain 'O' and resid 60 through 81 removed outlier: 4.100A pdb=" N GLN O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 153 removed outlier: 3.847A pdb=" N TYR O 151 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ARG O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 29 Processing helix chain 'P' and resid 40 through 55 removed outlier: 5.997A pdb=" N ILE P 44 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ALA P 49 " --> pdb=" O GLU P 45 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ALA P 52 " --> pdb=" O GLU P 48 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 62 Processing helix chain 'P' and resid 69 through 75 removed outlier: 4.915A pdb=" N ASN P 73 " --> pdb=" O ALA P 69 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 106 removed outlier: 5.174A pdb=" N ALA P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ALA P 106 " --> pdb=" O ALA P 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 101 through 106' Processing helix chain 'Q' and resid 24 through 29 removed outlier: 4.792A pdb=" N LEU Q 28 " --> pdb=" O VAL Q 24 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY Q 29 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 24 through 29' Processing helix chain 'Q' and resid 34 through 50 removed outlier: 4.004A pdb=" N LYS Q 40 " --> pdb=" O MET Q 36 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN Q 43 " --> pdb=" O CYS Q 39 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER Q 48 " --> pdb=" O ALA Q 44 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE Q 49 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU Q 50 " --> pdb=" O THR Q 46 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 85 removed outlier: 5.508A pdb=" N LEU Q 79 " --> pdb=" O PRO Q 75 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS Q 81 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYS Q 82 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA Q 83 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA Q 84 " --> pdb=" O LEU Q 80 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY Q 85 " --> pdb=" O LYS Q 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 75 through 85' Processing helix chain 'Q' and resid 102 through 115 removed outlier: 3.919A pdb=" N THR Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS Q 113 " --> pdb=" O ILE Q 109 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA Q 115 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 137 removed outlier: 4.919A pdb=" N MET Q 125 " --> pdb=" O ASP Q 121 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N THR Q 126 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG Q 127 " --> pdb=" O GLU Q 123 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER Q 128 " --> pdb=" O ALA Q 124 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Q 133 " --> pdb=" O ILE Q 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 38 Processing helix chain 'R' and resid 88 through 96 Processing helix chain 'R' and resid 97 through 110 removed outlier: 4.612A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) Proline residue: R 110 - end of helix Processing helix chain 'R' and resid 112 through 122 removed outlier: 3.884A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 109 removed outlier: 4.778A pdb=" N ARG S 108 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER S 109 " --> pdb=" O ARG S 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 104 through 109' Processing helix chain 'S' and resid 112 through 119 removed outlier: 3.585A pdb=" N LEU S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 42 removed outlier: 5.614A pdb=" N SER T 42 " --> pdb=" O GLN T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 62 Proline residue: T 62 - end of helix Processing helix chain 'T' and resid 68 through 75 removed outlier: 4.279A pdb=" N ALA T 72 " --> pdb=" O SER T 68 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N ALA T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 85 removed outlier: 3.899A pdb=" N LEU T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA T 83 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 78 through 85' Processing helix chain 'T' and resid 91 through 99 Processing helix chain 'T' and resid 128 through 139 removed outlier: 3.550A pdb=" N ALA T 138 " --> pdb=" O ALA T 134 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY T 139 " --> pdb=" O ILE T 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 58 removed outlier: 4.151A pdb=" N LYS U 58 " --> pdb=" O THR U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 125 removed outlier: 4.092A pdb=" N LYS U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Proline residue: U 125 - end of helix Processing helix chain 'V' and resid 13 through 32 Processing helix chain 'V' and resid 38 through 57 removed outlier: 4.090A pdb=" N ARG V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) Proline residue: V 50 - end of helix removed outlier: 3.564A pdb=" N LYS V 56 " --> pdb=" O ILE V 52 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR V 57 " --> pdb=" O THR V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 71 Processing helix chain 'V' and resid 72 through 88 removed outlier: 4.817A pdb=" N GLY V 84 " --> pdb=" O PHE V 80 " (cutoff:3.500A) Proline residue: V 85 - end of helix Processing helix chain 'W' and resid 2 through 22 removed outlier: 3.869A pdb=" N ARG W 7 " --> pdb=" O LYS W 3 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG W 13 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N ALA W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 86 Processing helix chain 'W' and resid 101 through 114 Processing helix chain 'X' and resid 2 through 13 removed outlier: 3.734A pdb=" N GLN X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 104 removed outlier: 4.691A pdb=" N ARG X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLU X 102 " --> pdb=" O TYR X 98 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N THR X 104 " --> pdb=" O LEU X 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 22 removed outlier: 3.508A pdb=" N LYS Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 Processing helix chain 'Y' and resid 39 through 73 removed outlier: 3.661A pdb=" N ARG Y 51 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS Y 54 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG Y 55 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 87 Processing helix chain 'Y' and resid 91 through 102 Processing helix chain 'Y' and resid 103 through 118 Processing helix chain 'a' and resid 13 through 25 removed outlier: 3.758A pdb=" N LEU a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N VAL a 20 " --> pdb=" O LYS a 16 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE a 24 " --> pdb=" O VAL a 20 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG a 25 " --> pdb=" O ALA a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 40 removed outlier: 3.654A pdb=" N ASP a 34 " --> pdb=" O SER a 30 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR a 39 " --> pdb=" O ILE a 35 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ASN a 40 " --> pdb=" O LEU a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 61 removed outlier: 3.899A pdb=" N VAL a 45 " --> pdb=" O LYS a 41 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS a 49 " --> pdb=" O VAL a 45 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 11 removed outlier: 4.181A pdb=" N LEU b 11 " --> pdb=" O LEU b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 27 Processing helix chain 'b' and resid 39 through 50 Processing helix chain 'c' and resid 66 through 71 removed outlier: 3.900A pdb=" N VAL c 70 " --> pdb=" O GLN c 66 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N ALA c 71 " --> pdb=" O VAL c 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 66 through 71' Processing helix chain 'd' and resid 13 through 24 Processing helix chain 'd' and resid 43 through 53 removed outlier: 4.124A pdb=" N LYS d 53 " --> pdb=" O ASN d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 59 removed outlier: 4.422A pdb=" N SER d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) Processing helix chain 'f' and resid 52 through 63 Processing helix chain 'f' and resid 64 through 75 Processing helix chain 'g' and resid 2 through 10 removed outlier: 4.167A pdb=" N GLU g 8 " --> pdb=" O LYS g 4 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N SER g 10 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 35 removed outlier: 6.282A pdb=" N THR g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 62 removed outlier: 4.774A pdb=" N LYS g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY g 62 " --> pdb=" O ASN g 58 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 28 Processing helix chain 'h' and resid 41 through 52 Processing helix chain 'i' and resid 9 through 19 removed outlier: 4.807A pdb=" N HIS i 19 " --> pdb=" O MET i 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 16 Processing helix chain 'k' and resid 17 through 25 removed outlier: 4.234A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LYS k 25 " --> pdb=" O ARG k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 38 Processing helix chain 'l' and resid 7 through 14 Processing helix chain 'l' and resid 32 through 37 removed outlier: 4.524A pdb=" N LYS l 36 " --> pdb=" O ILE l 32 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA l 37 " --> pdb=" O LEU l 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 32 through 37' Processing helix chain 'l' and resid 38 through 46 Proline residue: l 46 - end of helix Processing helix chain 'l' and resid 51 through 63 removed outlier: 4.279A pdb=" N GLY l 56 " --> pdb=" O LYS l 52 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU l 57 " --> pdb=" O GLY l 53 " (cutoff:3.500A) Proline residue: l 63 - end of helix Processing sheet with id= 1, first strand: chain '6' and resid 39 through 42 removed outlier: 7.257A pdb=" N LEU 6 13 " --> pdb=" O LEU 6 42 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLN 6 43 " --> pdb=" O ALA 6 11 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG 6 49 " --> pdb=" O TYR 6 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '6' and resid 98 through 101 removed outlier: 3.633A pdb=" N ARG 6 99 " --> pdb=" O SER 6 76 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '6' and resid 233 through 241 removed outlier: 7.348A pdb=" N ASP 6 233 " --> pdb=" O VAL 6 253 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N VAL 6 253 " --> pdb=" O ASP 6 233 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR 6 235 " --> pdb=" O ASP 6 251 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR 6 252 " --> pdb=" O LEU 6 202 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLY 6 204 " --> pdb=" O THR 6 252 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG 6 328 " --> pdb=" O TRP 6 341 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '6' and resid 367 through 371 removed outlier: 4.010A pdb=" N SER 6 399 " --> pdb=" O GLU 6 395 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TRP 6 393 " --> pdb=" O SER 6 401 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '6' and resid 10 through 15 Processing sheet with id= 6, first strand: chain 'K' and resid 2 through 5 Processing sheet with id= 7, first strand: chain 'K' and resid 80 through 83 removed outlier: 6.800A pdb=" N LEU K 93 " --> pdb=" O GLU K 79 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'K' and resid 162 through 165 removed outlier: 6.695A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'K' and resid 91 through 96 removed outlier: 4.295A pdb=" N GLU K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'L' and resid 3 through 7 removed outlier: 7.094A pdb=" N ASP L 200 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR L 112 " --> pdb=" O ASP L 200 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'L' and resid 10 through 16 removed outlier: 3.657A pdb=" N GLY L 10 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'L' and resid 79 through 84 removed outlier: 5.835A pdb=" N ARG L 46 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN L 49 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLN L 94 " --> pdb=" O VAL L 34 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'L' and resid 105 through 108 removed outlier: 6.499A pdb=" N LYS L 105 " --> pdb=" O VAL L 177 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'M' and resid 1 through 4 Processing sheet with id= 15, first strand: chain 'M' and resid 117 through 120 Processing sheet with id= 16, first strand: chain 'N' and resid 65 through 69 removed outlier: 3.574A pdb=" N GLY N 86 " --> pdb=" O THR N 68 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N ILE N 85 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS N 33 " --> pdb=" O THR N 157 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY N 39 " --> pdb=" O GLY N 151 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N GLY N 151 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'O' and resid 16 through 19 Processing sheet with id= 18, first strand: chain 'O' and resid 41 through 45 Processing sheet with id= 19, first strand: chain 'O' and resid 94 through 99 removed outlier: 5.241A pdb=" N VAL O 102 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN O 101 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'O' and resid 121 through 125 removed outlier: 5.659A pdb=" N THR O 129 " --> pdb=" O LEU O 89 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'P' and resid 1 through 5 removed outlier: 3.751A pdb=" N LEU P 5 " --> pdb=" O ASP P 17 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASP P 17 " --> pdb=" O LEU P 5 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'R' and resid 52 through 57 removed outlier: 4.774A pdb=" N ASP R 19 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'R' and resid 74 through 78 removed outlier: 7.299A pdb=" N GLY R 83 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'S' and resid 56 through 60 removed outlier: 4.400A pdb=" N ASP S 56 " --> pdb=" O ILE S 43 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LYS S 40 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N THR S 6 " --> pdb=" O CYS S 21 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASN S 82 " --> pdb=" O MET S 7 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'U' and resid 62 through 65 removed outlier: 3.592A pdb=" N TYR U 103 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU U 33 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS U 100 " --> pdb=" O ALA U 35 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'U' and resid 30 through 36 removed outlier: 7.985A pdb=" N SER U 30 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS U 127 " --> pdb=" O VAL U 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'V' and resid 33 through 37 removed outlier: 5.976A pdb=" N ALA V 108 " --> pdb=" O PHE V 102 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE V 102 " --> pdb=" O ALA V 108 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N MET V 110 " --> pdb=" O CYS V 100 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'W' and resid 49 through 53 removed outlier: 3.835A pdb=" N VAL W 49 " --> pdb=" O VAL W 39 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE W 35 " --> pdb=" O THR W 53 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'X' and resid 38 through 45 removed outlier: 6.543A pdb=" N THR X 25 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER X 83 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'X' and resid 49 through 53 removed outlier: 3.756A pdb=" N ALA X 49 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ARG X 53 " --> pdb=" O HIS X 56 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N SER X 57 " --> pdb=" O THR X 76 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Z' and resid 11 through 14 Processing sheet with id= 32, first strand: chain 'Z' and resid 18 through 21 removed outlier: 4.408A pdb=" N GLN Z 18 " --> pdb=" O ILE Z 98 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP Z 95 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LYS Z 60 " --> pdb=" O THR Z 99 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLU Z 31 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Z' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'Z' and resid 65 through 69 removed outlier: 4.864A pdb=" N GLN Z 91 " --> pdb=" O GLY Z 69 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'a' and resid 2 through 8 removed outlier: 4.773A pdb=" N THR a 100 " --> pdb=" O GLY a 79 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'a' and resid 81 through 88 removed outlier: 4.282A pdb=" N ARG a 92 " --> pdb=" O ARG a 88 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'b' and resid 28 through 33 removed outlier: 6.057A pdb=" N ASN b 28 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS b 66 " --> pdb=" O ARG b 77 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ASP b 79 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LYS b 64 " --> pdb=" O ASP b 79 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS b 81 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL b 62 " --> pdb=" O LYS b 81 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA b 83 " --> pdb=" O THR b 60 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR b 60 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N VAL b 85 " --> pdb=" O VAL b 58 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL b 58 " --> pdb=" O VAL b 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'c' and resid 40 through 45 removed outlier: 4.853A pdb=" N ASN c 40 " --> pdb=" O ALA c 63 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'd' and resid 69 through 72 removed outlier: 6.707A pdb=" N ALA d 39 " --> pdb=" O ARG d 9 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE d 89 " --> pdb=" O PRO d 27 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'e' and resid 28 through 32 removed outlier: 4.382A pdb=" N GLU e 29 " --> pdb=" O VAL e 67 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE e 82 " --> pdb=" O GLY e 48 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'e' and resid 51 through 54 removed outlier: 6.507A pdb=" N GLY e 52 " --> pdb=" O LEU e 59 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU e 59 " --> pdb=" O GLY e 52 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLY e 54 " --> pdb=" O HIS e 57 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'f' and resid 12 through 19 removed outlier: 4.374A pdb=" N ASN f 23 " --> pdb=" O SER f 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'f' and resid 35 through 41 Processing sheet with id= 44, first strand: chain 'h' and resid 33 through 39 removed outlier: 4.330A pdb=" N HIS h 34 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N MET h 54 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'i' and resid 28 through 31 removed outlier: 6.417A pdb=" N SER i 29 " --> pdb=" O LYS i 37 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LYS i 37 " --> pdb=" O SER i 29 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP i 31 " --> pdb=" O GLY i 35 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'j' and resid 19 through 26 removed outlier: 6.307A pdb=" N HIS j 19 " --> pdb=" O SER j 13 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE j 48 " --> pdb=" O SER j 14 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU j 34 " --> pdb=" O GLU j 51 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 22 through 25 removed outlier: 5.630A pdb=" N PHE l 22 " --> pdb=" O VAL l 50 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'm' and resid 1 through 5 removed outlier: 3.799A pdb=" N GLY m 38 " --> pdb=" O ARG m 4 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N HIS m 33 " --> pdb=" O CYS m 27 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N CYS m 27 " --> pdb=" O HIS m 33 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ILE m 23 " --> pdb=" O GLN m 37 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N VAL m 22 " --> pdb=" O ARG m 19 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER m 28 " --> pdb=" O ASN m 13 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN m 13 " --> pdb=" O SER m 28 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3345 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2360 hydrogen bonds 3674 hydrogen bond angles 0 basepair planarities 935 basepair parallelities 1458 stacking parallelities Total time for adding SS restraints: 144.67 Time building geometry restraints manager: 73.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 32038 1.03 - 1.23: 806 1.23 - 1.42: 51609 1.42 - 1.62: 49273 1.62 - 1.81: 166 Bond restraints: 133892 Sorted by residual: bond pdb=" C1' GNP 6 501 " pdb=" C2' GNP 6 501 " ideal model delta sigma weight residual 1.273 1.531 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" C3' GNP 6 501 " pdb=" C4' GNP 6 501 " ideal model delta sigma weight residual 1.285 1.524 -0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C ALA K 158 " pdb=" O ALA K 158 " ideal model delta sigma weight residual 1.235 1.112 0.123 1.26e-02 6.30e+03 9.55e+01 bond pdb=" O3' A I 959 " pdb=" P A I 960 " ideal model delta sigma weight residual 1.607 1.481 0.126 1.50e-02 4.44e+03 7.03e+01 bond pdb=" P G I2444 " pdb=" OP2 G I2444 " ideal model delta sigma weight residual 1.485 1.334 0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 133887 not shown) Histogram of bond angle deviations from ideal: 94.31 - 102.34: 3722 102.34 - 110.37: 103822 110.37 - 118.40: 53826 118.40 - 126.43: 54468 126.43 - 134.46: 9393 Bond angle restraints: 225231 Sorted by residual: angle pdb=" O2' U I2884 " pdb=" C2' U I2884 " pdb=" C1' U I2884 " ideal model delta sigma weight residual 111.80 94.31 17.49 1.50e+00 4.44e-01 1.36e+02 angle pdb=" C3' G I2251 " pdb=" C2' G I2251 " pdb=" O2' G I2251 " ideal model delta sigma weight residual 110.70 124.55 -13.85 1.50e+00 4.44e-01 8.52e+01 angle pdb=" C4' G I2445 " pdb=" C3' G I2445 " pdb=" O3' G I2445 " ideal model delta sigma weight residual 113.00 100.44 12.56 1.50e+00 4.44e-01 7.01e+01 angle pdb=" C4' A I2030 " pdb=" C3' A I2030 " pdb=" O3' A I2030 " ideal model delta sigma weight residual 109.40 121.70 -12.30 1.50e+00 4.44e-01 6.72e+01 angle pdb=" O2' A I2600 " pdb=" C2' A I2600 " pdb=" C1' A I2600 " ideal model delta sigma weight residual 108.40 96.91 11.49 1.50e+00 4.44e-01 5.86e+01 ... (remaining 225226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 66788 35.90 - 71.80: 7140 71.80 - 107.70: 789 107.70 - 143.61: 13 143.61 - 179.51: 15 Dihedral angle restraints: 74745 sinusoidal: 62793 harmonic: 11952 Sorted by residual: dihedral pdb=" O4' U I 747 " pdb=" C1' U I 747 " pdb=" N1 U I 747 " pdb=" C2 U I 747 " ideal model delta sinusoidal sigma weight residual -160.00 19.51 -179.51 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U I 545 " pdb=" C1' U I 545 " pdb=" N1 U I 545 " pdb=" C2 U I 545 " ideal model delta sinusoidal sigma weight residual 200.00 35.80 164.20 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' U I2506 " pdb=" C1' U I2506 " pdb=" N1 U I2506 " pdb=" C2 U I2506 " ideal model delta sinusoidal sigma weight residual -160.00 -0.54 -159.46 1 1.50e+01 4.44e-03 8.26e+01 ... (remaining 74742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 19251 0.163 - 0.326: 217 0.326 - 0.489: 8 0.489 - 0.651: 0 0.651 - 0.814: 1 Chirality restraints: 19477 Sorted by residual: chirality pdb=" C3' A I2030 " pdb=" C4' A I2030 " pdb=" O3' A I2030 " pdb=" C2' A I2030 " both_signs ideal model delta sigma weight residual False -2.74 -1.93 -0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" P A I1614 " pdb=" OP1 A I1614 " pdb=" OP2 A I1614 " pdb=" O5' A I1614 " both_signs ideal model delta sigma weight residual True 2.41 -1.97 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" C2' A I1354 " pdb=" C3' A I1354 " pdb=" O2' A I1354 " pdb=" C1' A I1354 " both_signs ideal model delta sigma weight residual False -2.75 -2.33 -0.43 2.00e-01 2.50e+01 4.56e+00 ... (remaining 19474 not shown) Planarity restraints: 11893 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' GNP 6 501 " 0.442 2.00e-02 2.50e+03 6.02e-01 8.16e+03 pdb=" C2' GNP 6 501 " -0.712 2.00e-02 2.50e+03 pdb=" C3' GNP 6 501 " -0.306 2.00e-02 2.50e+03 pdb=" C4' GNP 6 501 " 0.242 2.00e-02 2.50e+03 pdb=" C5' GNP 6 501 " -0.856 2.00e-02 2.50e+03 pdb=" N9 GNP 6 501 " -0.021 2.00e-02 2.50e+03 pdb=" O2' GNP 6 501 " -0.485 2.00e-02 2.50e+03 pdb=" O3' GNP 6 501 " 0.819 2.00e-02 2.50e+03 pdb=" O4' GNP 6 501 " 0.878 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 64 " 0.087 2.00e-02 2.50e+03 4.38e-01 2.87e+03 pdb=" CD GLN O 64 " -0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN O 64 " -0.087 2.00e-02 2.50e+03 pdb=" NE2 GLN O 64 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN O 64 " -0.750 2.00e-02 2.50e+03 pdb="HE22 GLN O 64 " 0.756 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN g 36 " -0.252 2.00e-02 2.50e+03 3.20e-01 1.54e+03 pdb=" CD GLN g 36 " 0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN g 36 " 0.242 2.00e-02 2.50e+03 pdb=" NE2 GLN g 36 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN g 36 " 0.492 2.00e-02 2.50e+03 pdb="HE22 GLN g 36 " -0.501 2.00e-02 2.50e+03 ... (remaining 11890 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 353 1.97 - 2.63: 82694 2.63 - 3.29: 246097 3.29 - 3.94: 426388 3.94 - 4.60: 617199 Nonbonded interactions: 1372731 Sorted by model distance: nonbonded pdb="HD13 LEU 6 386 " pdb=" HB3 ASP 6 410 " model vdw 1.314 2.440 nonbonded pdb="HG22 ILE 6 389 " pdb=" HG3 GLU 6 392 " model vdw 1.393 2.440 nonbonded pdb=" O ASN R 128 " pdb="HD21 ASN R 128 " model vdw 1.539 1.850 nonbonded pdb=" HG3 GLU a 59 " pdb="HD12 ILE a 66 " model vdw 1.611 2.440 nonbonded pdb="HD21 LEU 6 386 " pdb=" HD2 ARG 6 413 " model vdw 1.612 2.440 ... (remaining 1372726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 1.210 Extract box with map and model: 10.400 Check model and map are aligned: 1.330 Set scattering table: 0.840 Process input model: 448.000 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.270 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:9.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 474.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.006 0.258 101840 Z= 0.379 Angle : 0.711 17.487 152367 Z= 0.411 Chirality : 0.045 0.814 19477 Planarity : 0.009 0.602 8177 Dihedral : 22.856 179.507 58254 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.28 % Favored : 95.45 % Rotamer: Outliers : 0.75 % Allowed : 1.14 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.13), residues: 3718 helix: 0.30 (0.16), residues: 1073 sheet: -0.53 (0.19), residues: 694 loop : -1.16 (0.13), residues: 1951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 6 393 HIS 0.013 0.001 HIS l 31 PHE 0.022 0.002 PHE e 69 TYR 0.029 0.002 TYR K 161 ARG 0.018 0.001 ARG l 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 912 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 889 time to evaluate : 4.752 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: 6 29 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6162 (mm-30) REVERT: 6 68 GLU cc_start: 0.6687 (tp30) cc_final: 0.6214 (tp30) REVERT: 6 79 LEU cc_start: 0.7993 (mt) cc_final: 0.7781 (mt) REVERT: 6 81 ASP cc_start: 0.6890 (t0) cc_final: 0.6530 (t0) REVERT: 6 119 GLU cc_start: 0.6378 (tt0) cc_final: 0.5301 (tt0) REVERT: 6 125 GLU cc_start: 0.6593 (pt0) cc_final: 0.6355 (pt0) REVERT: 6 128 GLN cc_start: 0.7447 (mt0) cc_final: 0.7227 (mt0) REVERT: 6 179 GLU cc_start: 0.6591 (mp0) cc_final: 0.5989 (mp0) REVERT: 6 185 ARG cc_start: 0.6899 (mmt-90) cc_final: 0.6219 (mmt-90) REVERT: 6 186 GLU cc_start: 0.7120 (tp30) cc_final: 0.6789 (tp30) REVERT: 6 193 ILE cc_start: 0.6908 (mm) cc_final: 0.6675 (mm) REVERT: 6 200 VAL cc_start: 0.7981 (p) cc_final: 0.7693 (m) REVERT: 6 284 ILE cc_start: 0.7337 (mm) cc_final: 0.7113 (mm) REVERT: 6 345 GLN cc_start: 0.7672 (mp10) cc_final: 0.7435 (mp10) REVERT: 6 352 GLN cc_start: 0.7532 (mp10) cc_final: 0.7151 (mp10) REVERT: K 71 LYS cc_start: 0.7747 (ttmm) cc_final: 0.7394 (ttmt) REVERT: L 14 ILE cc_start: 0.8675 (mm) cc_final: 0.8463 (mp) REVERT: L 139 SER cc_start: 0.8362 (m) cc_final: 0.8148 (m) REVERT: N 15 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8250 (ttpt) REVERT: N 47 LYS cc_start: 0.7974 (tttp) cc_final: 0.7770 (tttp) REVERT: N 72 LYS cc_start: 0.7211 (ptmt) cc_final: 0.6952 (ptmt) REVERT: S 3 GLN cc_start: 0.7136 (mt0) cc_final: 0.6893 (mt0) REVERT: S 70 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.7661 (mmm-85) REVERT: U 3 GLN cc_start: 0.8441 (tt0) cc_final: 0.8233 (tt0) REVERT: W 20 GLU cc_start: 0.6891 (mp0) cc_final: 0.6608 (mp0) REVERT: Z 15 SER cc_start: 0.8332 (p) cc_final: 0.8120 (p) REVERT: Z 68 ARG cc_start: 0.8448 (mtm180) cc_final: 0.8235 (mtm180) REVERT: c 59 VAL cc_start: 0.8337 (m) cc_final: 0.8122 (t) REVERT: d 75 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7901 (mm-40) REVERT: d 76 ASP cc_start: 0.6829 (m-30) cc_final: 0.6624 (m-30) REVERT: h 49 ASN cc_start: 0.8357 (t0) cc_final: 0.7971 (t0) outliers start: 23 outliers final: 13 residues processed: 904 average time/residue: 3.6880 time to fit residues: 4094.9128 Evaluate side-chains 867 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 853 time to evaluate : 4.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 385 GLN Chi-restraints excluded: chain O residue 60 ASP Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 70 ARG Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain T residue 30 THR Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain c residue 99 ASN Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain j residue 48 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 559 optimal weight: 3.9990 chunk 501 optimal weight: 10.0000 chunk 278 optimal weight: 7.9990 chunk 171 optimal weight: 6.9990 chunk 338 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 518 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 chunk 386 optimal weight: 20.0000 chunk 601 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 385 GLN K 128 ASN K 153 GLN M 30 GLN R 128 ASN X 12 GLN Y 56 GLN Z 87 GLN f 36 HIS ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 101840 Z= 0.409 Angle : 0.648 19.896 152367 Z= 0.330 Chirality : 0.041 0.374 19477 Planarity : 0.005 0.120 8177 Dihedral : 23.258 177.743 50923 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.60 % Favored : 95.26 % Rotamer: Outliers : 1.37 % Allowed : 10.07 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.13), residues: 3718 helix: 0.43 (0.16), residues: 1075 sheet: -0.45 (0.18), residues: 739 loop : -1.20 (0.13), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 248 HIS 0.011 0.001 HIS K 200 PHE 0.024 0.002 PHE Y 57 TYR 0.014 0.002 TYR T 58 ARG 0.016 0.001 ARG X 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 882 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 840 time to evaluate : 4.792 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: 6 29 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6188 (mm-30) REVERT: 6 68 GLU cc_start: 0.6682 (tp30) cc_final: 0.6212 (tp30) REVERT: 6 79 LEU cc_start: 0.8030 (mt) cc_final: 0.7791 (mt) REVERT: 6 81 ASP cc_start: 0.6824 (t0) cc_final: 0.6433 (t0) REVERT: 6 119 GLU cc_start: 0.6411 (tt0) cc_final: 0.5862 (tt0) REVERT: 6 128 GLN cc_start: 0.7474 (mt0) cc_final: 0.7263 (mt0) REVERT: 6 185 ARG cc_start: 0.6932 (mmt-90) cc_final: 0.6732 (mmt-90) REVERT: 6 186 GLU cc_start: 0.7137 (tp30) cc_final: 0.6799 (tp30) REVERT: 6 193 ILE cc_start: 0.6989 (mm) cc_final: 0.6763 (mm) REVERT: 6 200 VAL cc_start: 0.8034 (p) cc_final: 0.7765 (m) REVERT: 6 352 GLN cc_start: 0.7515 (mp10) cc_final: 0.7135 (mp10) REVERT: K 71 LYS cc_start: 0.7945 (ttmm) cc_final: 0.7635 (ttmt) REVERT: K 100 GLU cc_start: 0.7359 (tt0) cc_final: 0.7140 (tt0) REVERT: K 184 VAL cc_start: 0.8777 (p) cc_final: 0.8520 (t) REVERT: L 14 ILE cc_start: 0.8731 (mm) cc_final: 0.8520 (mp) REVERT: N 15 LYS cc_start: 0.8492 (ttpt) cc_final: 0.8282 (ttpt) REVERT: N 72 LYS cc_start: 0.7288 (ptmt) cc_final: 0.6960 (ptmt) REVERT: S 3 GLN cc_start: 0.7264 (mt0) cc_final: 0.7046 (mt0) REVERT: U 3 GLN cc_start: 0.8480 (tt0) cc_final: 0.8200 (tt0) REVERT: U 81 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.7065 (mtt180) REVERT: V 65 LEU cc_start: 0.8388 (mt) cc_final: 0.8174 (mm) REVERT: W 20 GLU cc_start: 0.6904 (mp0) cc_final: 0.6521 (mp0) REVERT: Z 15 SER cc_start: 0.8299 (p) cc_final: 0.8099 (p) REVERT: d 75 GLN cc_start: 0.8223 (tp-100) cc_final: 0.7918 (mm-40) REVERT: d 76 ASP cc_start: 0.6797 (m-30) cc_final: 0.6579 (m-30) REVERT: g 44 LYS cc_start: 0.8337 (ttmm) cc_final: 0.8081 (ttmm) REVERT: m 30 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7132 (mm-30) outliers start: 42 outliers final: 24 residues processed: 855 average time/residue: 3.6443 time to fit residues: 3826.0591 Evaluate side-chains 858 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 833 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain P residue 66 ASN Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 18 GLN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain Z residue 51 VAL Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 50 VAL Chi-restraints excluded: chain a residue 68 ASP Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain j residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 334 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 500 optimal weight: 1.9990 chunk 409 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 602 optimal weight: 7.9990 chunk 650 optimal weight: 3.9990 chunk 536 optimal weight: 8.9990 chunk 597 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 483 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 153 GLN R 128 ASN T 54 GLN X 12 GLN Z 87 GLN ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 101840 Z= 0.448 Angle : 0.672 17.323 152367 Z= 0.341 Chirality : 0.043 0.359 19477 Planarity : 0.006 0.099 8177 Dihedral : 23.217 177.515 50911 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 1.43 % Allowed : 11.86 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 3718 helix: 0.36 (0.16), residues: 1084 sheet: -0.51 (0.18), residues: 735 loop : -1.26 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 248 HIS 0.012 0.002 HIS K 200 PHE 0.026 0.002 PHE Y 57 TYR 0.013 0.002 TYR T 58 ARG 0.012 0.001 ARG g 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 881 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 837 time to evaluate : 4.807 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: 6 17 TYR cc_start: 0.7549 (m-10) cc_final: 0.7087 (m-10) REVERT: 6 33 LEU cc_start: 0.7642 (mt) cc_final: 0.7376 (mm) REVERT: 6 68 GLU cc_start: 0.6692 (tp30) cc_final: 0.6230 (tp30) REVERT: 6 79 LEU cc_start: 0.8045 (mt) cc_final: 0.7797 (mt) REVERT: 6 81 ASP cc_start: 0.6852 (t0) cc_final: 0.6452 (t0) REVERT: 6 119 GLU cc_start: 0.6432 (tt0) cc_final: 0.5912 (tt0) REVERT: 6 128 GLN cc_start: 0.7457 (mt0) cc_final: 0.7242 (mt0) REVERT: 6 185 ARG cc_start: 0.6890 (mmt-90) cc_final: 0.6688 (mmt-90) REVERT: 6 186 GLU cc_start: 0.7105 (tp30) cc_final: 0.6761 (tp30) REVERT: 6 193 ILE cc_start: 0.6865 (mm) cc_final: 0.6655 (mm) REVERT: 6 352 GLN cc_start: 0.7497 (mp10) cc_final: 0.7159 (mp10) REVERT: 6 359 GLU cc_start: 0.7824 (tm-30) cc_final: 0.7234 (tm-30) REVERT: K 71 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7701 (tttt) REVERT: K 100 GLU cc_start: 0.7346 (tt0) cc_final: 0.7141 (tt0) REVERT: K 184 VAL cc_start: 0.8728 (p) cc_final: 0.8503 (t) REVERT: L 118 PHE cc_start: 0.8467 (t80) cc_final: 0.8250 (t80) REVERT: N 15 LYS cc_start: 0.8501 (ttpt) cc_final: 0.8285 (ttpt) REVERT: N 72 LYS cc_start: 0.7311 (ptmt) cc_final: 0.6953 (ptmt) REVERT: O 6 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7851 (mppt) REVERT: U 3 GLN cc_start: 0.8491 (tt0) cc_final: 0.8243 (tt0) REVERT: U 81 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7031 (mtt180) REVERT: d 75 GLN cc_start: 0.8251 (tp-100) cc_final: 0.7929 (mm-40) REVERT: d 76 ASP cc_start: 0.6769 (m-30) cc_final: 0.6556 (m-30) outliers start: 44 outliers final: 26 residues processed: 850 average time/residue: 3.8325 time to fit residues: 4017.2987 Evaluate side-chains 857 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 830 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain 6 residue 256 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain V residue 18 GLN Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain m residue 16 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 595 optimal weight: 7.9990 chunk 452 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 604 optimal weight: 0.2980 chunk 639 optimal weight: 2.9990 chunk 315 optimal weight: 4.9990 chunk 572 optimal weight: 1.9990 chunk 172 optimal weight: 5.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 ASN T 54 GLN V 23 ASN X 12 GLN c 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 101840 Z= 0.291 Angle : 0.563 16.247 152367 Z= 0.294 Chirality : 0.037 0.419 19477 Planarity : 0.005 0.099 8177 Dihedral : 23.122 176.764 50906 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 1.47 % Allowed : 13.39 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 3718 helix: 0.68 (0.16), residues: 1080 sheet: -0.48 (0.18), residues: 742 loop : -1.15 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 248 HIS 0.008 0.001 HIS K 200 PHE 0.018 0.001 PHE Y 57 TYR 0.012 0.001 TYR T 58 ARG 0.008 0.000 ARG K 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 877 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 832 time to evaluate : 4.834 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: 6 17 TYR cc_start: 0.7476 (m-10) cc_final: 0.7047 (m-10) REVERT: 6 28 GLN cc_start: 0.7102 (tp40) cc_final: 0.6900 (tp40) REVERT: 6 46 THR cc_start: 0.7586 (t) cc_final: 0.7241 (t) REVERT: 6 68 GLU cc_start: 0.6694 (tp30) cc_final: 0.6230 (tp30) REVERT: 6 79 LEU cc_start: 0.8022 (mt) cc_final: 0.7780 (mt) REVERT: 6 81 ASP cc_start: 0.6825 (t0) cc_final: 0.6435 (t0) REVERT: 6 119 GLU cc_start: 0.6401 (tt0) cc_final: 0.5891 (tt0) REVERT: 6 128 GLN cc_start: 0.7460 (mt0) cc_final: 0.7257 (mt0) REVERT: 6 186 GLU cc_start: 0.7098 (tp30) cc_final: 0.6755 (tp30) REVERT: 6 193 ILE cc_start: 0.6821 (mm) cc_final: 0.6606 (mm) REVERT: 6 352 GLN cc_start: 0.7480 (mp10) cc_final: 0.7094 (mp10) REVERT: 6 359 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7178 (tm-30) REVERT: K 71 LYS cc_start: 0.8141 (ttmm) cc_final: 0.7693 (tttt) REVERT: K 184 VAL cc_start: 0.8710 (p) cc_final: 0.8492 (t) REVERT: N 15 LYS cc_start: 0.8502 (ttpt) cc_final: 0.8276 (ttpt) REVERT: N 72 LYS cc_start: 0.7311 (ptmt) cc_final: 0.6945 (ptmt) REVERT: O 6 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7898 (mppt) REVERT: U 3 GLN cc_start: 0.8471 (tt0) cc_final: 0.8250 (tt0) REVERT: U 81 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.7010 (mtt180) REVERT: d 75 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7897 (mm-40) REVERT: d 76 ASP cc_start: 0.6720 (m-30) cc_final: 0.6508 (m-30) outliers start: 45 outliers final: 27 residues processed: 845 average time/residue: 3.7274 time to fit residues: 3866.4875 Evaluate side-chains 856 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 828 time to evaluate : 4.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 179 GLU Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 81 ARG Chi-restraints excluded: chain V residue 18 GLN Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Y residue 83 LEU Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain m residue 16 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 532 optimal weight: 5.9990 chunk 363 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 476 optimal weight: 5.9990 chunk 264 optimal weight: 7.9990 chunk 546 optimal weight: 5.9990 chunk 442 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 326 optimal weight: 7.9990 chunk 574 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 ASN K 143 ASN R 128 ASN T 54 GLN X 12 GLN ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 101840 Z= 0.485 Angle : 0.694 16.515 152367 Z= 0.349 Chirality : 0.044 0.346 19477 Planarity : 0.006 0.103 8177 Dihedral : 23.142 176.463 50906 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.90 % Favored : 94.97 % Rotamer: Outliers : 1.92 % Allowed : 13.65 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3718 helix: 0.48 (0.16), residues: 1080 sheet: -0.55 (0.18), residues: 762 loop : -1.25 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 248 HIS 0.012 0.002 HIS K 200 PHE 0.027 0.002 PHE Y 57 TYR 0.013 0.002 TYR K 96 ARG 0.009 0.001 ARG V 2 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 882 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 823 time to evaluate : 4.814 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: 6 17 TYR cc_start: 0.7582 (m-10) cc_final: 0.7190 (m-10) REVERT: 6 46 THR cc_start: 0.7635 (t) cc_final: 0.7344 (t) REVERT: 6 68 GLU cc_start: 0.6696 (tp30) cc_final: 0.6264 (tp30) REVERT: 6 79 LEU cc_start: 0.8047 (mt) cc_final: 0.7797 (mt) REVERT: 6 81 ASP cc_start: 0.6858 (t0) cc_final: 0.6464 (t0) REVERT: 6 88 GLN cc_start: 0.8344 (mt0) cc_final: 0.7088 (mt0) REVERT: 6 109 ASP cc_start: 0.6804 (m-30) cc_final: 0.6313 (m-30) REVERT: 6 128 GLN cc_start: 0.7453 (mt0) cc_final: 0.7242 (mt0) REVERT: 6 186 GLU cc_start: 0.7098 (tp30) cc_final: 0.6774 (tp30) REVERT: 6 193 ILE cc_start: 0.6982 (mm) cc_final: 0.6756 (mm) REVERT: 6 352 GLN cc_start: 0.7467 (mp10) cc_final: 0.7096 (mp10) REVERT: 6 359 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7223 (tm-30) REVERT: 6 360 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7795 (mmm-85) REVERT: 6 371 ARG cc_start: 0.6821 (ttp-170) cc_final: 0.6539 (ttp-170) REVERT: K 71 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7703 (tttt) REVERT: K 184 VAL cc_start: 0.8644 (p) cc_final: 0.8427 (t) REVERT: L 118 PHE cc_start: 0.8395 (t80) cc_final: 0.8110 (t80) REVERT: M 69 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7744 (ptt180) REVERT: N 15 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8299 (ttpt) REVERT: N 72 LYS cc_start: 0.7315 (ptmt) cc_final: 0.6920 (ptmt) REVERT: O 6 LYS cc_start: 0.8245 (mmtp) cc_final: 0.7917 (mppt) REVERT: U 3 GLN cc_start: 0.8527 (tt0) cc_final: 0.8235 (tt0) REVERT: U 105 MET cc_start: 0.7430 (ttt) cc_final: 0.7208 (ttt) REVERT: V 65 LEU cc_start: 0.8389 (mt) cc_final: 0.8175 (mm) REVERT: W 20 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6728 (mt-10) REVERT: d 75 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7887 (mm-40) REVERT: d 76 ASP cc_start: 0.6734 (m-30) cc_final: 0.6512 (m-30) outliers start: 59 outliers final: 40 residues processed: 841 average time/residue: 3.7292 time to fit residues: 3847.5842 Evaluate side-chains 860 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 819 time to evaluate : 4.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 93 GLU Chi-restraints excluded: chain 6 residue 179 GLU Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain 6 residue 256 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain R residue 128 ASN Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain V residue 18 GLN Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain m residue 16 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 215 optimal weight: 5.9990 chunk 576 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 375 optimal weight: 8.9990 chunk 157 optimal weight: 30.0000 chunk 640 optimal weight: 0.2980 chunk 531 optimal weight: 0.9980 chunk 296 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 336 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 ASN T 54 GLN X 12 GLN ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 101840 Z= 0.311 Angle : 0.581 16.388 152367 Z= 0.301 Chirality : 0.037 0.404 19477 Planarity : 0.005 0.103 8177 Dihedral : 23.105 176.463 50900 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 1.60 % Allowed : 14.40 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 3718 helix: 0.61 (0.16), residues: 1088 sheet: -0.46 (0.18), residues: 731 loop : -1.19 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 248 HIS 0.009 0.001 HIS K 200 PHE 0.019 0.001 PHE Y 57 TYR 0.012 0.001 TYR T 58 ARG 0.010 0.000 ARG V 2 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 878 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 829 time to evaluate : 4.867 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: 6 17 TYR cc_start: 0.7522 (m-10) cc_final: 0.7137 (m-10) REVERT: 6 46 THR cc_start: 0.7622 (t) cc_final: 0.7339 (t) REVERT: 6 68 GLU cc_start: 0.6693 (tp30) cc_final: 0.6232 (tp30) REVERT: 6 79 LEU cc_start: 0.8028 (mt) cc_final: 0.7779 (mt) REVERT: 6 81 ASP cc_start: 0.6834 (t0) cc_final: 0.6430 (t0) REVERT: 6 109 ASP cc_start: 0.6785 (m-30) cc_final: 0.6292 (m-30) REVERT: 6 128 GLN cc_start: 0.7476 (mt0) cc_final: 0.7262 (mt0) REVERT: 6 186 GLU cc_start: 0.7091 (tp30) cc_final: 0.6755 (tp30) REVERT: 6 193 ILE cc_start: 0.6942 (mm) cc_final: 0.6715 (mm) REVERT: 6 352 GLN cc_start: 0.7458 (mp10) cc_final: 0.7038 (mp10) REVERT: 6 359 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7220 (tm-30) REVERT: 6 371 ARG cc_start: 0.6835 (ttp-170) cc_final: 0.6550 (ttp-170) REVERT: K 71 LYS cc_start: 0.8025 (ttmm) cc_final: 0.7515 (tttt) REVERT: K 184 VAL cc_start: 0.8620 (p) cc_final: 0.8407 (t) REVERT: L 118 PHE cc_start: 0.8354 (t80) cc_final: 0.8092 (t80) REVERT: L 186 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8179 (mp) REVERT: N 15 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8295 (ttpt) REVERT: N 47 LYS cc_start: 0.7969 (tttp) cc_final: 0.7742 (tttp) REVERT: N 72 LYS cc_start: 0.7308 (ptmt) cc_final: 0.6905 (ptmt) REVERT: O 6 LYS cc_start: 0.8240 (mmtp) cc_final: 0.7911 (mppt) REVERT: U 3 GLN cc_start: 0.8475 (tt0) cc_final: 0.8236 (tt0) REVERT: V 65 LEU cc_start: 0.8381 (mt) cc_final: 0.8175 (mm) REVERT: W 20 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6705 (mt-10) REVERT: d 75 GLN cc_start: 0.8243 (tp-100) cc_final: 0.7886 (mm-40) REVERT: d 76 ASP cc_start: 0.6718 (m-30) cc_final: 0.6478 (m-30) outliers start: 49 outliers final: 41 residues processed: 842 average time/residue: 3.7393 time to fit residues: 3859.9055 Evaluate side-chains 870 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 828 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 93 GLU Chi-restraints excluded: chain 6 residue 179 GLU Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain 6 residue 259 LEU Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain V residue 18 GLN Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain l residue 19 LYS Chi-restraints excluded: chain m residue 16 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 617 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 364 optimal weight: 4.9990 chunk 467 optimal weight: 5.9990 chunk 362 optimal weight: 9.9990 chunk 539 optimal weight: 10.0000 chunk 357 optimal weight: 6.9990 chunk 638 optimal weight: 6.9990 chunk 399 optimal weight: 2.9990 chunk 389 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 ASN R 128 ASN T 54 GLN X 12 GLN Y 56 GLN ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 101840 Z= 0.499 Angle : 0.706 16.375 152367 Z= 0.354 Chirality : 0.044 0.341 19477 Planarity : 0.006 0.103 8177 Dihedral : 23.122 176.492 50900 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 1.89 % Allowed : 14.59 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 3718 helix: 0.47 (0.16), residues: 1081 sheet: -0.51 (0.18), residues: 757 loop : -1.26 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 248 HIS 0.012 0.002 HIS K 200 PHE 0.028 0.002 PHE Y 57 TYR 0.013 0.002 TYR K 96 ARG 0.010 0.001 ARG V 2 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 902 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 844 time to evaluate : 4.838 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: 6 28 GLN cc_start: 0.7106 (tp40) cc_final: 0.6896 (tp40) REVERT: 6 68 GLU cc_start: 0.6702 (tp30) cc_final: 0.6273 (tp30) REVERT: 6 79 LEU cc_start: 0.8037 (mt) cc_final: 0.7787 (mt) REVERT: 6 81 ASP cc_start: 0.6858 (t0) cc_final: 0.6459 (t0) REVERT: 6 88 GLN cc_start: 0.8336 (mt0) cc_final: 0.7295 (mt0) REVERT: 6 109 ASP cc_start: 0.6809 (m-30) cc_final: 0.6319 (m-30) REVERT: 6 128 GLN cc_start: 0.7456 (mt0) cc_final: 0.7236 (mt0) REVERT: 6 186 GLU cc_start: 0.7106 (tp30) cc_final: 0.6794 (tp30) REVERT: 6 193 ILE cc_start: 0.6993 (mm) cc_final: 0.6762 (mm) REVERT: 6 352 GLN cc_start: 0.7471 (mp10) cc_final: 0.7079 (mp10) REVERT: 6 359 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7253 (tm-30) REVERT: 6 371 ARG cc_start: 0.6866 (ttp-170) cc_final: 0.6584 (ttp-170) REVERT: K 71 LYS cc_start: 0.8104 (ttmm) cc_final: 0.7676 (tttt) REVERT: K 184 VAL cc_start: 0.8518 (p) cc_final: 0.8296 (t) REVERT: L 52 THR cc_start: 0.8648 (t) cc_final: 0.8442 (p) REVERT: L 118 PHE cc_start: 0.8389 (t80) cc_final: 0.8077 (t80) REVERT: L 186 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8190 (mp) REVERT: M 69 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7754 (ptt180) REVERT: N 15 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8306 (ttpt) REVERT: N 47 LYS cc_start: 0.7966 (tttp) cc_final: 0.7739 (tttp) REVERT: N 72 LYS cc_start: 0.7313 (ptmt) cc_final: 0.6892 (ptmt) REVERT: U 3 GLN cc_start: 0.8542 (tt0) cc_final: 0.8297 (tt0) REVERT: V 65 LEU cc_start: 0.8394 (mt) cc_final: 0.8183 (mm) REVERT: W 20 GLU cc_start: 0.6923 (mt-10) cc_final: 0.6718 (mt-10) REVERT: W 108 ASP cc_start: 0.7182 (m-30) cc_final: 0.6880 (m-30) REVERT: d 75 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7882 (mm-40) REVERT: d 76 ASP cc_start: 0.6728 (m-30) cc_final: 0.6485 (m-30) outliers start: 58 outliers final: 46 residues processed: 858 average time/residue: 3.6668 time to fit residues: 3869.0105 Evaluate side-chains 882 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 834 time to evaluate : 4.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 179 GLU Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain 6 residue 256 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain L residue 184 ARG Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 75 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain V residue 18 GLN Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain l residue 19 LYS Chi-restraints excluded: chain m residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 394 optimal weight: 0.0270 chunk 254 optimal weight: 320.0000 chunk 381 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 405 optimal weight: 8.9990 chunk 434 optimal weight: 8.9990 chunk 315 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 501 optimal weight: 7.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 ASN T 54 GLN X 12 GLN ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 101840 Z= 0.336 Angle : 0.601 16.328 152367 Z= 0.312 Chirality : 0.039 0.395 19477 Planarity : 0.005 0.107 8177 Dihedral : 23.138 177.381 50900 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 1.60 % Allowed : 15.21 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.13), residues: 3718 helix: 0.55 (0.16), residues: 1081 sheet: -0.50 (0.18), residues: 731 loop : -1.21 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 248 HIS 0.010 0.001 HIS K 200 PHE 0.021 0.002 PHE Y 57 TYR 0.013 0.002 TYR K 96 ARG 0.009 0.001 ARG V 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 886 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 837 time to evaluate : 4.775 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: 6 17 TYR cc_start: 0.7582 (m-10) cc_final: 0.7218 (m-10) REVERT: 6 28 GLN cc_start: 0.7102 (tp40) cc_final: 0.6894 (tp40) REVERT: 6 68 GLU cc_start: 0.6730 (tp30) cc_final: 0.6282 (tp30) REVERT: 6 79 LEU cc_start: 0.8028 (mt) cc_final: 0.7783 (mt) REVERT: 6 81 ASP cc_start: 0.6856 (t0) cc_final: 0.6459 (t0) REVERT: 6 109 ASP cc_start: 0.6792 (m-30) cc_final: 0.6299 (m-30) REVERT: 6 128 GLN cc_start: 0.7476 (mt0) cc_final: 0.7261 (mt0) REVERT: 6 186 GLU cc_start: 0.7102 (tp30) cc_final: 0.6787 (tp30) REVERT: 6 193 ILE cc_start: 0.6955 (mm) cc_final: 0.6726 (mm) REVERT: 6 352 GLN cc_start: 0.7457 (mp10) cc_final: 0.7070 (mp10) REVERT: 6 359 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7225 (tm-30) REVERT: 6 371 ARG cc_start: 0.6858 (ttp-170) cc_final: 0.6580 (ttp-170) REVERT: K 71 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7579 (tttt) REVERT: K 184 VAL cc_start: 0.8512 (p) cc_final: 0.8290 (t) REVERT: L 118 PHE cc_start: 0.8351 (t80) cc_final: 0.8084 (t80) REVERT: N 15 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8299 (ttpt) REVERT: N 47 LYS cc_start: 0.7960 (tttp) cc_final: 0.7733 (tttp) REVERT: N 72 LYS cc_start: 0.7318 (ptmt) cc_final: 0.6900 (ptmt) REVERT: R 81 ILE cc_start: 0.8036 (OUTLIER) cc_final: 0.7831 (mt) REVERT: U 3 GLN cc_start: 0.8499 (tt0) cc_final: 0.8258 (tt0) REVERT: V 65 LEU cc_start: 0.8378 (mt) cc_final: 0.8175 (mm) REVERT: W 20 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6702 (mt-10) REVERT: W 108 ASP cc_start: 0.7172 (m-30) cc_final: 0.6858 (m-30) REVERT: d 75 GLN cc_start: 0.8246 (tp-100) cc_final: 0.7887 (mm-40) REVERT: d 76 ASP cc_start: 0.6723 (m-30) cc_final: 0.6486 (m-30) outliers start: 49 outliers final: 44 residues processed: 851 average time/residue: 3.7563 time to fit residues: 3920.9147 Evaluate side-chains 878 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 833 time to evaluate : 4.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 179 GLU Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain 6 residue 256 ILE Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain V residue 18 GLN Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 22 ASP Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain l residue 19 LYS Chi-restraints excluded: chain m residue 16 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 580 optimal weight: 2.9990 chunk 611 optimal weight: 6.9990 chunk 557 optimal weight: 3.9990 chunk 594 optimal weight: 5.9990 chunk 357 optimal weight: 9.9990 chunk 259 optimal weight: 10.0000 chunk 466 optimal weight: 50.0000 chunk 182 optimal weight: 6.9990 chunk 537 optimal weight: 9.9990 chunk 562 optimal weight: 7.9990 chunk 592 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 ASN T 54 GLN X 12 GLN ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 101840 Z= 0.451 Angle : 0.674 16.507 152367 Z= 0.340 Chirality : 0.042 0.401 19477 Planarity : 0.005 0.105 8177 Dihedral : 23.107 179.040 50900 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.01 % Favored : 94.89 % Rotamer: Outliers : 1.66 % Allowed : 15.08 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 3718 helix: 0.49 (0.16), residues: 1082 sheet: -0.48 (0.18), residues: 746 loop : -1.24 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 248 HIS 0.012 0.002 HIS K 200 PHE 0.025 0.002 PHE Y 57 TYR 0.014 0.002 TYR K 96 ARG 0.011 0.001 ARG K 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 883 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 832 time to evaluate : 4.807 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: 6 17 TYR cc_start: 0.7619 (m-10) cc_final: 0.7257 (m-10) REVERT: 6 28 GLN cc_start: 0.7105 (tp40) cc_final: 0.6889 (tp40) REVERT: 6 29 GLU cc_start: 0.6814 (mm-30) cc_final: 0.6595 (mm-30) REVERT: 6 68 GLU cc_start: 0.6735 (tp30) cc_final: 0.6287 (tp30) REVERT: 6 79 LEU cc_start: 0.8028 (mt) cc_final: 0.7782 (mt) REVERT: 6 81 ASP cc_start: 0.6853 (t0) cc_final: 0.6458 (t0) REVERT: 6 88 GLN cc_start: 0.8338 (mt0) cc_final: 0.7122 (mt0) REVERT: 6 109 ASP cc_start: 0.6802 (m-30) cc_final: 0.6309 (m-30) REVERT: 6 128 GLN cc_start: 0.7479 (mt0) cc_final: 0.7259 (mt0) REVERT: 6 186 GLU cc_start: 0.7120 (tp30) cc_final: 0.6806 (tp30) REVERT: 6 193 ILE cc_start: 0.6973 (mm) cc_final: 0.6748 (mm) REVERT: 6 352 GLN cc_start: 0.7469 (mp10) cc_final: 0.7081 (mp10) REVERT: 6 359 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7254 (tm-30) REVERT: 6 371 ARG cc_start: 0.6871 (ttp-170) cc_final: 0.6600 (ttp-170) REVERT: K 71 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7672 (ttmt) REVERT: K 184 VAL cc_start: 0.8501 (p) cc_final: 0.8278 (t) REVERT: L 118 PHE cc_start: 0.8377 (t80) cc_final: 0.8080 (t80) REVERT: M 69 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7759 (ptt180) REVERT: N 15 LYS cc_start: 0.8519 (ttpt) cc_final: 0.8312 (ttpt) REVERT: N 47 LYS cc_start: 0.7971 (tttp) cc_final: 0.7741 (tttp) REVERT: N 72 LYS cc_start: 0.7319 (ptmt) cc_final: 0.6900 (ptmt) REVERT: R 81 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7865 (mt) REVERT: U 3 GLN cc_start: 0.8520 (tt0) cc_final: 0.8274 (tt0) REVERT: V 65 LEU cc_start: 0.8391 (mt) cc_final: 0.8183 (mm) REVERT: W 20 GLU cc_start: 0.6920 (mt-10) cc_final: 0.6704 (mt-10) REVERT: d 75 GLN cc_start: 0.8250 (tp-100) cc_final: 0.7887 (mm-40) REVERT: d 76 ASP cc_start: 0.6725 (m-30) cc_final: 0.6485 (m-30) outliers start: 51 outliers final: 46 residues processed: 844 average time/residue: 3.7832 time to fit residues: 3910.5019 Evaluate side-chains 879 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 831 time to evaluate : 4.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 179 GLU Chi-restraints excluded: chain 6 residue 182 GLU Chi-restraints excluded: chain 6 residue 256 ILE Chi-restraints excluded: chain 6 residue 274 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 128 ARG Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain N residue 38 MET Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 42 THR Chi-restraints excluded: chain V residue 18 GLN Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain V residue 78 LYS Chi-restraints excluded: chain W residue 28 VAL Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain W residue 106 LEU Chi-restraints excluded: chain X residue 57 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain Z residue 29 THR Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain l residue 19 LYS Chi-restraints excluded: chain m residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 390 optimal weight: 1.9990 chunk 628 optimal weight: 0.0770 chunk 383 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 chunk 437 optimal weight: 4.9990 chunk 659 optimal weight: 1.9990 chunk 607 optimal weight: 0.7980 chunk 525 optimal weight: 2.9990 chunk 54 optimal weight: 8.9990 chunk 405 optimal weight: 7.9990 chunk 322 optimal weight: 5.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 ASN R 128 ASN T 54 GLN X 12 GLN c 45 HIS ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 101840 Z= 0.170 Angle : 0.498 16.249 152367 Z= 0.264 Chirality : 0.033 0.470 19477 Planarity : 0.004 0.099 8177 Dihedral : 23.029 178.934 50900 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.21 % Allowed : 15.57 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 3718 helix: 0.86 (0.16), residues: 1081 sheet: -0.45 (0.18), residues: 736 loop : -1.08 (0.14), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 61 HIS 0.006 0.001 HIS W 34 PHE 0.012 0.001 PHE Y 106 TYR 0.010 0.001 TYR Z 2 ARG 0.009 0.000 ARG V 2 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7436 Ramachandran restraints generated. 3718 Oldfield, 0 Emsley, 3718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 141 is missing expected H atoms. Skipping. Residue LYS 35 is missing expected H atoms. Skipping. Evaluate side-chains 871 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 834 time to evaluate : 4.810 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: 6 17 TYR cc_start: 0.7543 (m-10) cc_final: 0.7200 (m-10) REVERT: 6 68 GLU cc_start: 0.6718 (tp30) cc_final: 0.6242 (tp30) REVERT: 6 79 LEU cc_start: 0.7995 (mt) cc_final: 0.7759 (mt) REVERT: 6 81 ASP cc_start: 0.6805 (t0) cc_final: 0.6442 (t0) REVERT: 6 88 GLN cc_start: 0.8315 (mt0) cc_final: 0.7335 (mt0) REVERT: 6 109 ASP cc_start: 0.6727 (m-30) cc_final: 0.6220 (m-30) REVERT: 6 123 GLN cc_start: 0.8020 (mt0) cc_final: 0.7661 (mp10) REVERT: 6 128 GLN cc_start: 0.7474 (mt0) cc_final: 0.7251 (mt0) REVERT: 6 186 GLU cc_start: 0.7028 (tp30) cc_final: 0.6689 (tp30) REVERT: 6 193 ILE cc_start: 0.6890 (mm) cc_final: 0.6652 (mm) REVERT: 6 352 GLN cc_start: 0.7454 (mp10) cc_final: 0.7019 (mp10) REVERT: 6 371 ARG cc_start: 0.6849 (ttp-170) cc_final: 0.6584 (ttp-170) REVERT: K 71 LYS cc_start: 0.7890 (ttmm) cc_final: 0.7601 (ttmt) REVERT: K 184 VAL cc_start: 0.8499 (p) cc_final: 0.8274 (t) REVERT: L 118 PHE cc_start: 0.8300 (t80) cc_final: 0.8058 (t80) REVERT: L 139 SER cc_start: 0.8334 (m) cc_final: 0.8112 (m) REVERT: N 15 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8298 (ttpt) REVERT: N 47 LYS cc_start: 0.7998 (tttp) cc_final: 0.7751 (tttp) REVERT: N 72 LYS cc_start: 0.7363 (ptmt) cc_final: 0.6935 (ptmt) REVERT: S 3 GLN cc_start: 0.7178 (mt0) cc_final: 0.6931 (mt0) REVERT: U 3 GLN cc_start: 0.8448 (tt0) cc_final: 0.8215 (tt0) REVERT: V 65 LEU cc_start: 0.8371 (mt) cc_final: 0.8161 (mm) REVERT: W 20 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6676 (mt-10) outliers start: 37 outliers final: 32 residues processed: 842 average time/residue: 3.7913 time to fit residues: 3907.1941 Evaluate side-chains 865 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 833 time to evaluate : 4.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 167 LEU Chi-restraints excluded: chain 6 residue 179 GLU Chi-restraints excluded: chain K residue 139 SER Chi-restraints excluded: chain K residue 181 MET Chi-restraints excluded: chain K residue 199 GLU Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 93 SER Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 125 SER Chi-restraints excluded: chain N residue 88 LYS Chi-restraints excluded: chain N residue 165 GLU Chi-restraints excluded: chain R residue 5 THR Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 75 SER Chi-restraints excluded: chain S residue 118 LEU Chi-restraints excluded: chain U residue 20 LEU Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain V residue 51 LEU Chi-restraints excluded: chain W residue 67 ASN Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain Z residue 15 SER Chi-restraints excluded: chain a residue 4 ILE Chi-restraints excluded: chain a residue 30 SER Chi-restraints excluded: chain f residue 25 THR Chi-restraints excluded: chain g residue 30 MET Chi-restraints excluded: chain g residue 36 GLN Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain j residue 48 ILE Chi-restraints excluded: chain l residue 19 LYS Chi-restraints excluded: chain m residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 417 optimal weight: 1.9990 chunk 559 optimal weight: 4.9990 chunk 160 optimal weight: 8.9990 chunk 484 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 526 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 540 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 GLN K 134 ASN L 32 ASN R 128 ASN T 54 GLN X 12 GLN ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.092438 restraints weight = 193692.599| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 0.86 r_work: 0.2896 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 101840 Z= 0.483 Angle : 0.682 16.517 152367 Z= 0.342 Chirality : 0.044 0.377 19477 Planarity : 0.006 0.105 8177 Dihedral : 23.059 177.698 50900 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 1.30 % Allowed : 16.09 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.81 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 3718 helix: 0.62 (0.16), residues: 1076 sheet: -0.51 (0.18), residues: 740 loop : -1.17 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 248 HIS 0.010 0.002 HIS K 200 PHE 0.027 0.002 PHE Y 57 TYR 0.015 0.002 TYR Y 47 ARG 0.017 0.001 ARG V 2 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50953.22 seconds wall clock time: 873 minutes 25.92 seconds (52405.92 seconds total)