Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 10:08:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/04_2023/7yla_33904_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/04_2023/7yla_33904.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/04_2023/7yla_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_33904/04_2023/7yla_33904_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/04_2023/7yla_33904_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/04_2023/7yla_33904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/04_2023/7yla_33904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/04_2023/7yla_33904_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yla_33904/04_2023/7yla_33904_neut_trim_updated.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 42.81, per 1000 atoms: 0.34 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: 68.95 Conformation dependent library (CDL) restraints added in 4.2 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 forstructures with more than 99999 atoms! 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: 47.65 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: 134.85 Time building geometry restraints manager: 73.85 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: 57990 35.90 - 71.80: 1783 71.80 - 107.70: 135 107.70 - 143.61: 11 143.61 - 179.51: 13 Dihedral angle restraints: 59932 sinusoidal: 47980 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 59929 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.130 Extract box with map and model: 12.480 Check model and map are aligned: 1.210 Set scattering table: 0.750 Process input model: 411.810 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.300 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:11.390 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 442.470 ------------------------------------------------------------------------------- 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 : 14.581 179.507 47464 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 % 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 *********************** 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 : 4.987 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 outliers start: 23 outliers final: 13 residues processed: 904 average time/residue: 3.6315 time to fit residues: 4045.6397 Evaluate side-chains 867 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 854 time to evaluate : 4.808 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 5 average time/residue: 1.7651 time to fit residues: 18.5118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 h 49 ASN ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.062 101840 Z= 0.413 Angle : 0.651 22.813 152367 Z= 0.333 Chirality : 0.041 0.340 19477 Planarity : 0.005 0.122 8177 Dihedral : 14.136 177.332 40100 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % Rotamer Outliers : 1.47 % 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: -0.90 (0.13), residues: 3718 helix: 0.38 (0.16), residues: 1075 sheet: -0.45 (0.18), residues: 739 loop : -1.20 (0.13), residues: 1904 *********************** 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 889 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 844 time to evaluate : 4.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 24 residues processed: 859 average time/residue: 3.6920 time to fit residues: 3908.6700 Evaluate side-chains 858 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 834 time to evaluate : 4.840 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 11 residues processed: 14 average time/residue: 1.2266 time to fit residues: 34.4158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 500 optimal weight: 5.9990 chunk 409 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 602 optimal weight: 8.9990 chunk 650 optimal weight: 3.9990 chunk 536 optimal weight: 0.7980 chunk 597 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 chunk 483 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 128 ASN T 54 GLN X 12 GLN Z 87 GLN h 49 ASN ** 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: 0.8052 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.082 101840 Z= 0.423 Angle : 0.652 18.092 152367 Z= 0.333 Chirality : 0.042 0.336 19477 Planarity : 0.005 0.101 8177 Dihedral : 14.168 176.604 40100 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer Outliers : 1.66 % 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: 0.41 (0.16), residues: 1077 sheet: -0.49 (0.18), residues: 735 loop : -1.23 (0.13), residues: 1906 *********************** 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 889 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 838 time to evaluate : 4.927 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 outliers start: 51 outliers final: 29 residues processed: 854 average time/residue: 3.7560 time to fit residues: 3943.4024 Evaluate side-chains 860 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 831 time to evaluate : 4.850 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 12 residues processed: 18 average time/residue: 1.2951 time to fit residues: 43.9474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 312 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 604 optimal weight: 2.9990 chunk 639 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 572 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN K 143 ASN M 30 GLN M 92 HIS T 54 GLN V 23 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.051 101840 Z= 0.393 Angle : 0.626 16.572 152367 Z= 0.322 Chirality : 0.040 0.339 19477 Planarity : 0.005 0.100 8177 Dihedral : 14.098 179.413 40100 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.82 % Favored : 95.05 % Rotamer Outliers : 1.56 % 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: -0.89 (0.13), residues: 3718 helix: 0.44 (0.16), residues: 1086 sheet: -0.52 (0.18), residues: 742 loop : -1.21 (0.13), residues: 1890 *********************** 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 892 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 844 time to evaluate : 4.953 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 outliers start: 48 outliers final: 25 residues processed: 861 average time/residue: 3.7847 time to fit residues: 4014.4929 Evaluate side-chains 856 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 831 time to evaluate : 4.871 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 11 residues processed: 14 average time/residue: 1.1547 time to fit residues: 33.7517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 9 optimal weight: 9.9990 chunk 476 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 546 optimal weight: 5.9990 chunk 442 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 574 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.081 101840 Z= 0.555 Angle : 0.749 16.453 152367 Z= 0.373 Chirality : 0.046 0.329 19477 Planarity : 0.006 0.102 8177 Dihedral : 14.237 177.644 40100 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer Outliers : 1.95 % 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: -1.06 (0.13), residues: 3718 helix: 0.28 (0.16), residues: 1080 sheet: -0.58 (0.18), residues: 763 loop : -1.32 (0.13), residues: 1875 *********************** 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 881 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 821 time to evaluate : 4.970 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 outliers start: 60 outliers final: 36 residues processed: 842 average time/residue: 3.8054 time to fit residues: 3956.4890 Evaluate side-chains 854 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 818 time to evaluate : 4.856 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 13 residues processed: 23 average time/residue: 1.5255 time to fit residues: 60.4034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 126 optimal weight: 3.9990 chunk 375 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 640 optimal weight: 0.9990 chunk 531 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 336 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.8023 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 101840 Z= 0.252 Angle : 0.547 16.345 152367 Z= 0.288 Chirality : 0.035 0.378 19477 Planarity : 0.005 0.100 8177 Dihedral : 13.934 178.915 40100 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.52 % Favored : 95.40 % Rotamer Outliers : 1.17 % 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: -0.76 (0.13), residues: 3718 helix: 0.64 (0.16), residues: 1080 sheet: -0.50 (0.18), residues: 752 loop : -1.16 (0.13), residues: 1886 *********************** 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 857 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 821 time to evaluate : 4.969 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 outliers start: 36 outliers final: 22 residues processed: 836 average time/residue: 3.6579 time to fit residues: 3768.6134 Evaluate side-chains 844 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 822 time to evaluate : 4.839 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 11 average time/residue: 1.2716 time to fit residues: 28.8241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 617 optimal weight: 0.2980 chunk 72 optimal weight: 8.9990 chunk 364 optimal weight: 5.9990 chunk 467 optimal weight: 5.9990 chunk 362 optimal weight: 10.0000 chunk 539 optimal weight: 9.9990 chunk 357 optimal weight: 8.9990 chunk 638 optimal weight: 1.9990 chunk 399 optimal weight: 3.9990 chunk 389 optimal weight: 5.9990 chunk 294 optimal weight: 8.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- 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 L 32 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 101840 Z= 0.347 Angle : 0.599 16.396 152367 Z= 0.309 Chirality : 0.038 0.337 19477 Planarity : 0.005 0.101 8177 Dihedral : 13.950 179.264 40100 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer Outliers : 1.34 % 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: -0.80 (0.13), residues: 3718 helix: 0.61 (0.16), residues: 1082 sheet: -0.51 (0.18), residues: 752 loop : -1.20 (0.13), residues: 1884 *********************** 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 879 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 838 time to evaluate : 4.957 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 outliers start: 41 outliers final: 30 residues processed: 853 average time/residue: 3.7495 time to fit residues: 3949.0847 Evaluate side-chains 865 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 835 time to evaluate : 4.859 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 12 residues processed: 18 average time/residue: 1.7798 time to fit residues: 52.8128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 394 optimal weight: 0.9990 chunk 254 optimal weight: 320.0000 chunk 381 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 405 optimal weight: 10.0000 chunk 434 optimal weight: 7.9990 chunk 315 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 501 optimal weight: 9.9990 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.054 101840 Z= 0.447 Angle : 0.664 16.405 152367 Z= 0.337 Chirality : 0.042 0.325 19477 Planarity : 0.005 0.115 8177 Dihedral : 14.036 179.135 40100 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.85 % Favored : 95.05 % Rotamer Outliers : 1.40 % 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: -0.90 (0.13), residues: 3718 helix: 0.46 (0.16), residues: 1081 sheet: -0.52 (0.18), residues: 757 loop : -1.23 (0.13), residues: 1880 *********************** 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 883 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 840 time to evaluate : 4.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 28 residues processed: 856 average time/residue: 3.7650 time to fit residues: 3972.3150 Evaluate side-chains 866 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 838 time to evaluate : 4.872 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 12 residues processed: 16 average time/residue: 1.7387 time to fit residues: 47.0065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 580 optimal weight: 0.9990 chunk 611 optimal weight: 0.7980 chunk 557 optimal weight: 0.9990 chunk 594 optimal weight: 0.8980 chunk 357 optimal weight: 7.9990 chunk 259 optimal weight: 8.9990 chunk 466 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 537 optimal weight: 9.9990 chunk 562 optimal weight: 6.9990 chunk 592 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 101840 Z= 0.140 Angle : 0.480 16.199 152367 Z= 0.257 Chirality : 0.032 0.412 19477 Planarity : 0.004 0.105 8177 Dihedral : 13.708 177.412 40100 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer Outliers : 0.91 % 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: -0.55 (0.14), residues: 3718 helix: 0.86 (0.16), residues: 1080 sheet: -0.42 (0.18), residues: 737 loop : -1.04 (0.14), residues: 1901 *********************** 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 876 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 848 time to evaluate : 5.040 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 outliers start: 28 outliers final: 20 residues processed: 864 average time/residue: 3.7404 time to fit residues: 3985.5178 Evaluate side-chains 849 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 829 time to evaluate : 4.812 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 7 average time/residue: 1.2039 time to fit residues: 19.7179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 390 optimal weight: 4.9990 chunk 628 optimal weight: 0.7980 chunk 383 optimal weight: 6.9990 chunk 298 optimal weight: 8.9990 chunk 437 optimal weight: 7.9990 chunk 659 optimal weight: 6.9990 chunk 607 optimal weight: 0.9980 chunk 525 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 405 optimal weight: 10.0000 chunk 322 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- 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 R 128 ASN T 54 GLN X 12 GLN Y 56 GLN ** c 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 6 ASN ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 101840 Z= 0.354 Angle : 0.593 16.498 152367 Z= 0.305 Chirality : 0.038 0.338 19477 Planarity : 0.005 0.116 8177 Dihedral : 13.799 177.510 40100 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer Outliers : 0.55 % 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: -0.65 (0.13), residues: 3718 helix: 0.74 (0.16), residues: 1078 sheet: -0.41 (0.18), residues: 749 loop : -1.10 (0.14), residues: 1891 ********************** 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 856 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 839 time to evaluate : 4.978 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 outliers start: 17 outliers final: 14 residues processed: 853 average time/residue: 3.7337 time to fit residues: 3930.4983 Evaluate side-chains 858 residues out of total 3067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 844 time to evaluate : 4.824 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 1 average time/residue: 1.0380 time to fit residues: 7.0831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 662 random chunks: chunk 417 optimal weight: 5.9990 chunk 559 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 484 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 526 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 540 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 R 128 ASN T 54 GLN X 12 GLN c 66 GLN ** 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 = 0.3607 r_free = 0.3607 target = 0.132390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.092808 restraints weight = 193560.631| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 0.84 r_work: 0.2899 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 3.09 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 = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.052 101840 Z= 0.430 Angle : 0.651 16.361 152367 Z= 0.331 Chirality : 0.041 0.331 19477 Planarity : 0.005 0.112 8177 Dihedral : 13.910 177.987 40100 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.24 % Rotamer Outliers : 1.01 % 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: -0.79 (0.13), residues: 3718 helix: 0.56 (0.16), residues: 1075 sheet: -0.46 (0.18), residues: 735 loop : -1.17 (0.13), residues: 1908 =============================================================================== Job complete usr+sys time: 50747.92 seconds wall clock time: 871 minutes 24.26 seconds (52284.26 seconds total)