Starting phenix.real_space_refine (version: dev) on Tue Dec 20 12:19:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cte_26988/12_2022/8cte_26988_updated.pdb" } resolution = 2.9 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= 0.007 sd= 0.083 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "W TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 33": "OE1" <-> "OE2" Residue "T PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 38844 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3431 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 432} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 233 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 29} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "X" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5167 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 2943 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 380, 2919 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 365} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 2962 Chain: "L" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2938 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Q" Number of atoms: 2954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 2954 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 6339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6339 Classifications: {'peptide': 804} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 755} Chain breaks: 3 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "T" Number of atoms: 6406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 814, 6406 Classifications: {'peptide': 814} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 768} Chain breaks: 4 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "S" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "O" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "R" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "M" Number of atoms: 1838 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Conformer: "B" Number of residues, atoms: 247, 1827 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 240} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'P1L:plan-1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 bond proxies already assigned to first conformer: 1850 Chain: "L" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'AJP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 43 Chain: "P" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ATYR K 34 " occ=0.55 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.45 residue: pdb=" N ATYR K 242 " occ=0.53 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.47 residue: pdb=" N AARG S 234 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG S 234 " occ=0.52 residue: pdb=" N AARG O 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG O 234 " occ=0.50 residue: pdb=" N AARG R 234 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG R 234 " occ=0.50 residue: pdb=" N AARG M 234 " occ=0.51 ... (20 atoms not shown) pdb=" NH2BARG M 234 " occ=0.49 Time building chain proxies: 25.80, per 1000 atoms: 0.66 Number of scatterers: 38844 At special positions: 0 Unit cell: (137.78, 182.6, 201.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 174 16.00 P 6 15.00 O 6837 8.00 N 6491 7.00 C 25336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG P1002 " - " ASN P 642 " " NAG T1002 " - " ASN T 642 " Time building additional restraints: 17.09 Conformation dependent library (CDL) restraints added in 7.1 seconds 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 200 helices and 19 sheets defined 56.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 58 through 66 Processing helix chain 'A' and resid 81 through 88 Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 114 through 120 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 166 Processing helix chain 'A' and resid 176 through 182 Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 209 through 216 Processing helix chain 'A' and resid 219 through 228 Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 252 through 261 Processing helix chain 'A' and resid 275 through 282 removed outlier: 3.526A pdb=" N ASN A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 308 through 314 Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 351 through 360 Processing helix chain 'A' and resid 374 through 380 Processing helix chain 'A' and resid 384 through 392 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 417 through 425 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'W' and resid 5 through 7 No H-bonds generated for 'chain 'W' and resid 5 through 7' Processing helix chain 'W' and resid 9 through 16 Processing helix chain 'W' and resid 18 through 21 Processing helix chain 'X' and resid 14 through 20 Processing helix chain 'X' and resid 52 through 57 Processing helix chain 'X' and resid 152 through 159 Processing helix chain 'X' and resid 188 through 198 removed outlier: 3.882A pdb=" N LYS X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 206 removed outlier: 4.167A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 208 through 226 Processing helix chain 'X' and resid 248 through 256 Processing helix chain 'X' and resid 265 through 282 removed outlier: 5.594A pdb=" N TRP X 269 " --> pdb=" O GLY X 266 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU X 271 " --> pdb=" O ALA X 268 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 373 Processing helix chain 'X' and resid 382 through 388 Processing helix chain 'X' and resid 432 through 435 No H-bonds generated for 'chain 'X' and resid 432 through 435' Processing helix chain 'X' and resid 442 through 458 Processing helix chain 'K' and resid 13 through 31 Processing helix chain 'K' and resid 44 through 64 removed outlier: 3.886A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 98 removed outlier: 3.651A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU K 93 " --> pdb=" O GLN K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.536A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA K 129 " --> pdb=" O ILE K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 161 Processing helix chain 'K' and resid 166 through 186 removed outlier: 3.745A pdb=" N LEU K 169 " --> pdb=" O HIS K 166 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS K 171 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR K 173 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE K 175 " --> pdb=" O PHE K 172 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR K 178 " --> pdb=" O PHE K 175 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 224 Proline residue: K 221 - end of helix Processing helix chain 'K' and resid 231 through 255 Processing helix chain 'K' and resid 267 through 280 removed outlier: 3.511A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU K 275 " --> pdb=" O HIS K 271 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ALA K 276 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLY K 277 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLY K 278 " --> pdb=" O VAL K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 311 Processing helix chain 'K' and resid 327 through 349 removed outlier: 3.660A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU K 349 " --> pdb=" O VAL K 345 " (cutoff:3.500A) Processing helix chain 'K' and resid 361 through 388 Processing helix chain 'K' and resid 391 through 393 No H-bonds generated for 'chain 'K' and resid 391 through 393' Processing helix chain 'K' and resid 398 through 400 No H-bonds generated for 'chain 'K' and resid 398 through 400' Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'L' and resid 4 through 23 Processing helix chain 'L' and resid 51 through 68 removed outlier: 4.153A pdb=" N PHE L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY L 66 " --> pdb=" O PHE L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 103 removed outlier: 3.795A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 131 removed outlier: 3.772A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 161 removed outlier: 3.640A pdb=" N VAL L 150 " --> pdb=" O ILE L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 205 through 227 Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 234 through 261 removed outlier: 3.678A pdb=" N LEU L 252 " --> pdb=" O ALA L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 265 No H-bonds generated for 'chain 'L' and resid 263 through 265' Processing helix chain 'L' and resid 269 through 282 removed outlier: 4.289A pdb=" N THR L 276 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU L 277 " --> pdb=" O GLN L 273 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 320 removed outlier: 4.813A pdb=" N THR L 315 " --> pdb=" O TYR L 311 " (cutoff:3.500A) Proline residue: L 316 - end of helix Processing helix chain 'L' and resid 330 through 350 removed outlier: 5.334A pdb=" N LEU L 336 " --> pdb=" O ASN L 332 " (cutoff:3.500A) Proline residue: L 337 - end of helix Processing helix chain 'L' and resid 358 through 383 Processing helix chain 'L' and resid 399 through 401 No H-bonds generated for 'chain 'L' and resid 399 through 401' Processing helix chain 'Q' and resid 4 through 23 Processing helix chain 'Q' and resid 47 through 68 Proline residue: Q 52 - end of helix removed outlier: 4.153A pdb=" N PHE Q 65 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 103 removed outlier: 3.795A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 131 removed outlier: 3.772A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 161 removed outlier: 3.639A pdb=" N VAL Q 150 " --> pdb=" O ILE Q 146 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 188 Processing helix chain 'Q' and resid 192 through 194 No H-bonds generated for 'chain 'Q' and resid 192 through 194' Processing helix chain 'Q' and resid 205 through 227 Proline residue: Q 223 - end of helix Processing helix chain 'Q' and resid 234 through 261 removed outlier: 3.679A pdb=" N LEU Q 252 " --> pdb=" O ALA Q 248 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 265 No H-bonds generated for 'chain 'Q' and resid 263 through 265' Processing helix chain 'Q' and resid 269 through 282 removed outlier: 4.288A pdb=" N THR Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LEU Q 277 " --> pdb=" O GLN Q 273 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA Q 278 " --> pdb=" O ASN Q 274 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLY Q 279 " --> pdb=" O ALA Q 275 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N GLY Q 280 " --> pdb=" O THR Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 320 removed outlier: 4.813A pdb=" N THR Q 315 " --> pdb=" O TYR Q 311 " (cutoff:3.500A) Proline residue: Q 316 - end of helix Processing helix chain 'Q' and resid 330 through 350 removed outlier: 5.333A pdb=" N LEU Q 336 " --> pdb=" O ASN Q 332 " (cutoff:3.500A) Proline residue: Q 337 - end of helix Processing helix chain 'Q' and resid 358 through 383 Processing helix chain 'Q' and resid 399 through 401 No H-bonds generated for 'chain 'Q' and resid 399 through 401' Processing helix chain 'N' and resid 89 through 113 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'P' and resid 104 through 115 Processing helix chain 'P' and resid 128 through 141 Processing helix chain 'P' and resid 147 through 157 removed outlier: 4.495A pdb=" N GLU P 151 " --> pdb=" O GLN P 148 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU P 157 " --> pdb=" O LEU P 154 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 166 No H-bonds generated for 'chain 'P' and resid 164 through 166' Processing helix chain 'P' and resid 195 through 200 Processing helix chain 'P' and resid 278 through 290 Processing helix chain 'P' and resid 292 through 299 Processing helix chain 'P' and resid 304 through 316 Processing helix chain 'P' and resid 329 through 348 removed outlier: 4.125A pdb=" N LEU P 335 " --> pdb=" O ALA P 331 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N VAL P 336 " --> pdb=" O LEU P 332 " (cutoff:3.500A) Proline residue: P 337 - end of helix Processing helix chain 'P' and resid 380 through 393 Proline residue: P 391 - end of helix Processing helix chain 'P' and resid 395 through 400 removed outlier: 5.040A pdb=" N ALA P 400 " --> pdb=" O ASP P 396 " (cutoff:3.500A) Processing helix chain 'P' and resid 403 through 430 removed outlier: 3.560A pdb=" N PHE P 414 " --> pdb=" O ILE P 410 " (cutoff:3.500A) Proline residue: P 419 - end of helix Processing helix chain 'P' and resid 437 through 454 Processing helix chain 'P' and resid 466 through 482 Processing helix chain 'P' and resid 486 through 506 Processing helix chain 'P' and resid 509 through 515 removed outlier: 3.746A pdb=" N LEU P 512 " --> pdb=" O GLY P 509 " (cutoff:3.500A) Processing helix chain 'P' and resid 518 through 546 removed outlier: 3.501A pdb=" N LEU P 540 " --> pdb=" O THR P 536 " (cutoff:3.500A) Processing helix chain 'P' and resid 570 through 593 removed outlier: 3.557A pdb=" N ASN P 593 " --> pdb=" O ARG P 589 " (cutoff:3.500A) Processing helix chain 'P' and resid 599 through 607 Processing helix chain 'P' and resid 609 through 623 Processing helix chain 'P' and resid 661 through 689 removed outlier: 3.799A pdb=" N PHE P 665 " --> pdb=" O ILE P 661 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA P 668 " --> pdb=" O MET P 664 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU P 669 " --> pdb=" O PHE P 665 " (cutoff:3.500A) Proline residue: P 670 - end of helix Processing helix chain 'P' and resid 692 through 694 No H-bonds generated for 'chain 'P' and resid 692 through 694' Processing helix chain 'P' and resid 702 through 718 removed outlier: 3.509A pdb=" N LEU P 718 " --> pdb=" O GLY P 714 " (cutoff:3.500A) Processing helix chain 'P' and resid 728 through 737 Processing helix chain 'P' and resid 761 through 773 Processing helix chain 'P' and resid 777 through 782 removed outlier: 4.009A pdb=" N ARG P 782 " --> pdb=" O PRO P 778 " (cutoff:3.500A) Processing helix chain 'P' and resid 785 through 798 Processing helix chain 'P' and resid 804 through 813 removed outlier: 4.002A pdb=" N PHE P 813 " --> pdb=" O ILE P 809 " (cutoff:3.500A) Processing helix chain 'P' and resid 816 through 818 No H-bonds generated for 'chain 'P' and resid 816 through 818' Processing helix chain 'P' and resid 823 through 826 No H-bonds generated for 'chain 'P' and resid 823 through 826' Processing helix chain 'P' and resid 830 through 851 Processing helix chain 'P' and resid 856 through 877 Proline residue: P 860 - end of helix Proline residue: P 868 - end of helix removed outlier: 4.843A pdb=" N LEU P 873 " --> pdb=" O ARG P 870 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU P 874 " --> pdb=" O ARG P 871 " (cutoff:3.500A) Proline residue: P 875 - end of helix Processing helix chain 'P' and resid 880 through 886 Processing helix chain 'T' and resid 43 through 46 Processing helix chain 'T' and resid 104 through 115 Processing helix chain 'T' and resid 128 through 141 Processing helix chain 'T' and resid 147 through 157 removed outlier: 4.494A pdb=" N GLU T 151 " --> pdb=" O GLN T 148 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU T 157 " --> pdb=" O LEU T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 166 No H-bonds generated for 'chain 'T' and resid 164 through 166' Processing helix chain 'T' and resid 195 through 200 Processing helix chain 'T' and resid 278 through 290 Processing helix chain 'T' and resid 292 through 299 Processing helix chain 'T' and resid 304 through 316 Processing helix chain 'T' and resid 329 through 346 removed outlier: 4.125A pdb=" N LEU T 335 " --> pdb=" O ALA T 331 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL T 336 " --> pdb=" O LEU T 332 " (cutoff:3.500A) Proline residue: T 337 - end of helix Processing helix chain 'T' and resid 380 through 393 Proline residue: T 391 - end of helix Processing helix chain 'T' and resid 395 through 400 removed outlier: 5.039A pdb=" N ALA T 400 " --> pdb=" O ASP T 396 " (cutoff:3.500A) Processing helix chain 'T' and resid 403 through 430 removed outlier: 3.559A pdb=" N PHE T 414 " --> pdb=" O ILE T 410 " (cutoff:3.500A) Proline residue: T 419 - end of helix Processing helix chain 'T' and resid 437 through 454 Processing helix chain 'T' and resid 466 through 482 Processing helix chain 'T' and resid 486 through 506 Processing helix chain 'T' and resid 509 through 515 removed outlier: 3.747A pdb=" N LEU T 512 " --> pdb=" O GLY T 509 " (cutoff:3.500A) Processing helix chain 'T' and resid 518 through 546 removed outlier: 3.501A pdb=" N LEU T 540 " --> pdb=" O THR T 536 " (cutoff:3.500A) Processing helix chain 'T' and resid 570 through 593 removed outlier: 3.556A pdb=" N ASN T 593 " --> pdb=" O ARG T 589 " (cutoff:3.500A) Processing helix chain 'T' and resid 599 through 607 Processing helix chain 'T' and resid 609 through 623 Processing helix chain 'T' and resid 661 through 689 removed outlier: 3.799A pdb=" N PHE T 665 " --> pdb=" O ILE T 661 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ALA T 668 " --> pdb=" O MET T 664 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LEU T 669 " --> pdb=" O PHE T 665 " (cutoff:3.500A) Proline residue: T 670 - end of helix Processing helix chain 'T' and resid 692 through 694 No H-bonds generated for 'chain 'T' and resid 692 through 694' Processing helix chain 'T' and resid 702 through 718 removed outlier: 3.508A pdb=" N LEU T 718 " --> pdb=" O GLY T 714 " (cutoff:3.500A) Processing helix chain 'T' and resid 728 through 737 Processing helix chain 'T' and resid 761 through 773 Processing helix chain 'T' and resid 777 through 782 removed outlier: 4.009A pdb=" N ARG T 782 " --> pdb=" O PRO T 778 " (cutoff:3.500A) Processing helix chain 'T' and resid 785 through 798 Processing helix chain 'T' and resid 804 through 813 removed outlier: 4.002A pdb=" N PHE T 813 " --> pdb=" O ILE T 809 " (cutoff:3.500A) Processing helix chain 'T' and resid 816 through 818 No H-bonds generated for 'chain 'T' and resid 816 through 818' Processing helix chain 'T' and resid 823 through 826 No H-bonds generated for 'chain 'T' and resid 823 through 826' Processing helix chain 'T' and resid 830 through 851 Processing helix chain 'T' and resid 856 through 877 Proline residue: T 860 - end of helix Proline residue: T 868 - end of helix removed outlier: 4.843A pdb=" N LEU T 873 " --> pdb=" O ARG T 870 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU T 874 " --> pdb=" O ARG T 871 " (cutoff:3.500A) Proline residue: T 875 - end of helix Processing helix chain 'T' and resid 880 through 886 Processing helix chain 'S' and resid 4 through 6 No H-bonds generated for 'chain 'S' and resid 4 through 6' Processing helix chain 'S' and resid 8 through 32 Processing helix chain 'S' and resid 34 through 36 No H-bonds generated for 'chain 'S' and resid 34 through 36' Processing helix chain 'S' and resid 49 through 71 removed outlier: 5.789A pdb=" N HIS S 69 " --> pdb=" O GLN S 65 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE S 70 " --> pdb=" O SER S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 85 Processing helix chain 'S' and resid 91 through 115 Processing helix chain 'S' and resid 135 through 156 Processing helix chain 'S' and resid 168 through 187 removed outlier: 5.508A pdb=" N ASP S 185 " --> pdb=" O LEU S 181 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N TYR S 186 " --> pdb=" O LEU S 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 203 removed outlier: 3.532A pdb=" N SER S 199 " --> pdb=" O ARG S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 211 through 229 Proline residue: S 216 - end of helix Processing helix chain 'S' and resid 238 through 247 removed outlier: 3.511A pdb=" N VAL S 244 " --> pdb=" O ASP S 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP S 245 " --> pdb=" O ARG S 241 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR S 246 " --> pdb=" O VAL S 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 6 No H-bonds generated for 'chain 'O' and resid 4 through 6' Processing helix chain 'O' and resid 8 through 32 Processing helix chain 'O' and resid 34 through 36 No H-bonds generated for 'chain 'O' and resid 34 through 36' Processing helix chain 'O' and resid 49 through 71 removed outlier: 5.788A pdb=" N HIS O 69 " --> pdb=" O GLN O 65 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE O 70 " --> pdb=" O SER O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 85 Processing helix chain 'O' and resid 91 through 115 Processing helix chain 'O' and resid 135 through 156 Processing helix chain 'O' and resid 168 through 187 removed outlier: 5.508A pdb=" N ASP O 185 " --> pdb=" O LEU O 181 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR O 186 " --> pdb=" O LEU O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 193 through 203 removed outlier: 3.532A pdb=" N SER O 199 " --> pdb=" O ARG O 195 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 229 Proline residue: O 216 - end of helix Processing helix chain 'O' and resid 238 through 247 removed outlier: 3.511A pdb=" N VAL O 244 " --> pdb=" O ASP O 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP O 245 " --> pdb=" O ARG O 241 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 6 No H-bonds generated for 'chain 'R' and resid 4 through 6' Processing helix chain 'R' and resid 8 through 32 Processing helix chain 'R' and resid 34 through 36 No H-bonds generated for 'chain 'R' and resid 34 through 36' Processing helix chain 'R' and resid 49 through 71 removed outlier: 5.788A pdb=" N HIS R 69 " --> pdb=" O GLN R 65 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE R 70 " --> pdb=" O SER R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 85 Processing helix chain 'R' and resid 91 through 115 Processing helix chain 'R' and resid 135 through 156 Processing helix chain 'R' and resid 168 through 187 removed outlier: 5.508A pdb=" N ASP R 185 " --> pdb=" O LEU R 181 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR R 186 " --> pdb=" O LEU R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 203 removed outlier: 3.532A pdb=" N SER R 199 " --> pdb=" O ARG R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 229 Proline residue: R 216 - end of helix Processing helix chain 'R' and resid 238 through 247 removed outlier: 3.511A pdb=" N VAL R 244 " --> pdb=" O ASP R 240 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP R 245 " --> pdb=" O ARG R 241 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR R 246 " --> pdb=" O VAL R 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 6 No H-bonds generated for 'chain 'M' and resid 4 through 6' Processing helix chain 'M' and resid 8 through 32 Processing helix chain 'M' and resid 34 through 36 No H-bonds generated for 'chain 'M' and resid 34 through 36' Processing helix chain 'M' and resid 49 through 71 removed outlier: 5.788A pdb=" N HIS M 69 " --> pdb=" O GLN M 65 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE M 70 " --> pdb=" O SER M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 85 Processing helix chain 'M' and resid 91 through 115 Processing helix chain 'M' and resid 135 through 156 Processing helix chain 'M' and resid 168 through 187 removed outlier: 5.508A pdb=" N ASP M 185 " --> pdb=" O LEU M 181 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR M 186 " --> pdb=" O LEU M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 203 removed outlier: 3.533A pdb=" N SER M 199 " --> pdb=" O ARG M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 211 through 229 Proline residue: M 216 - end of helix Processing helix chain 'M' and resid 238 through 247 removed outlier: 3.511A pdb=" N VAL M 244 " --> pdb=" O ASP M 240 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TRP M 245 " --> pdb=" O ARG M 241 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR M 246 " --> pdb=" O VAL M 242 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.584A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU X 119 " --> pdb=" O LEU X 131 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN X 133 " --> pdb=" O TYR X 117 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR X 117 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THR X 135 " --> pdb=" O GLY X 115 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLY X 115 " --> pdb=" O THR X 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'X' and resid 7 through 11 removed outlier: 6.839A pdb=" N TYR X 44 " --> pdb=" O LYS X 8 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS X 10 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE X 42 " --> pdb=" O CYS X 10 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'X' and resid 163 through 169 Processing sheet with id= D, first strand: chain 'X' and resid 286 through 288 removed outlier: 4.479A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'X' and resid 294 through 296 Processing sheet with id= F, first strand: chain 'X' and resid 303 through 308 removed outlier: 6.496A pdb=" N SER X 392 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N GLU X 306 " --> pdb=" O SER X 392 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL X 394 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N TYR X 308 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP X 396 " --> pdb=" O TYR X 308 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'X' and resid 419 through 421 Processing sheet with id= H, first strand: chain 'X' and resid 475 through 480 Processing sheet with id= I, first strand: chain 'X' and resid 484 through 486 removed outlier: 6.396A pdb=" N ALA X 584 " --> pdb=" O LEU X 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'X' and resid 576 through 583 removed outlier: 6.233A pdb=" N ALA X 515 " --> pdb=" O LYS X 525 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N LYS X 525 " --> pdb=" O ALA X 515 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'X' and resid 590 through 594 Processing sheet with id= L, first strand: chain 'X' and resid 597 through 599 removed outlier: 8.189A pdb=" N ALA X 598 " --> pdb=" O SER X 681 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N THR X 683 " --> pdb=" O ALA X 598 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY X 627 " --> pdb=" O ARG X 633 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG X 633 " --> pdb=" O GLY X 627 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'K' and resid 32 through 34 removed outlier: 6.021A pdb=" N VAL K 106 " --> pdb=" O HIS K 33 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'P' and resid 85 through 87 removed outlier: 6.851A pdb=" N LEU P 61 " --> pdb=" O ALA P 78 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG P 80 " --> pdb=" O VAL P 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL P 59 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG P 233 " --> pdb=" O LEU P 64 " (cutoff:3.500A) removed outlier: 9.906A pdb=" N MET P 66 " --> pdb=" O ARG P 233 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU P 228 " --> pdb=" O PRO P 261 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N ARG P 263 " --> pdb=" O LEU P 228 " (cutoff:3.500A) removed outlier: 12.096A pdb=" N LEU P 230 " --> pdb=" O ARG P 263 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N LEU P 265 " --> pdb=" O LEU P 230 " (cutoff:3.500A) removed outlier: 12.289A pdb=" N GLY P 232 " --> pdb=" O LEU P 265 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N VAL P 267 " --> pdb=" O GLY P 232 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR P 118 " --> pdb=" O PHE P 244 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ARG P 246 " --> pdb=" O THR P 118 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU P 120 " --> pdb=" O ARG P 246 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'P' and resid 65 through 67 Processing sheet with id= P, first strand: chain 'P' and resid 739 through 742 removed outlier: 5.453A pdb=" N GLY P 742 " --> pdb=" O ILE P 753 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE P 753 " --> pdb=" O GLY P 742 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'T' and resid 85 through 87 removed outlier: 6.851A pdb=" N LEU T 61 " --> pdb=" O ALA T 78 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG T 80 " --> pdb=" O VAL T 59 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL T 59 " --> pdb=" O ARG T 80 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ARG T 233 " --> pdb=" O LEU T 64 " (cutoff:3.500A) removed outlier: 9.905A pdb=" N MET T 66 " --> pdb=" O ARG T 233 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU T 228 " --> pdb=" O PRO T 261 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ARG T 263 " --> pdb=" O LEU T 228 " (cutoff:3.500A) removed outlier: 12.095A pdb=" N LEU T 230 " --> pdb=" O ARG T 263 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N LEU T 265 " --> pdb=" O LEU T 230 " (cutoff:3.500A) removed outlier: 12.288A pdb=" N GLY T 232 " --> pdb=" O LEU T 265 " (cutoff:3.500A) removed outlier: 9.585A pdb=" N VAL T 267 " --> pdb=" O GLY T 232 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR T 118 " --> pdb=" O PHE T 244 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ARG T 246 " --> pdb=" O THR T 118 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU T 120 " --> pdb=" O ARG T 246 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'T' and resid 65 through 67 Processing sheet with id= S, first strand: chain 'T' and resid 739 through 742 removed outlier: 5.453A pdb=" N GLY T 742 " --> pdb=" O ILE T 753 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE T 753 " --> pdb=" O GLY T 742 " (cutoff:3.500A) 2039 hydrogen bonds defined for protein. 5890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.65 Time building geometry restraints manager: 18.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6074 1.31 - 1.43: 10428 1.43 - 1.56: 22922 1.56 - 1.69: 8 1.69 - 1.81: 291 Bond restraints: 39723 Sorted by residual: bond pdb=" C PRO Q 293 " pdb=" O PRO Q 293 " ideal model delta sigma weight residual 1.237 1.194 0.043 1.26e-02 6.30e+03 1.18e+01 bond pdb=" N VAL Q 373 " pdb=" CA VAL Q 373 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.38e+00 bond pdb=" N GLU X 405 " pdb=" CA GLU X 405 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.21e-02 6.83e+03 8.59e+00 bond pdb=" N ILE Q 188 " pdb=" CA ILE Q 188 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.10e+00 bond pdb=" N VAL Q 185 " pdb=" CA VAL Q 185 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.92e+00 ... (remaining 39718 not shown) Histogram of bond angle deviations from ideal: 99.12 - 106.13: 1078 106.13 - 113.14: 22264 113.14 - 120.15: 13472 120.15 - 127.17: 16776 127.17 - 134.18: 469 Bond angle restraints: 54059 Sorted by residual: angle pdb=" N LEU Q 189 " pdb=" CA LEU Q 189 " pdb=" C LEU Q 189 " ideal model delta sigma weight residual 113.02 107.15 5.87 1.20e+00 6.94e-01 2.40e+01 angle pdb=" C TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta sigma weight residual 110.79 118.53 -7.74 1.66e+00 3.63e-01 2.17e+01 angle pdb=" N ASP X 408 " pdb=" CA ASP X 408 " pdb=" C ASP X 408 " ideal model delta sigma weight residual 109.96 103.41 6.55 1.50e+00 4.44e-01 1.91e+01 angle pdb=" CA VAL Q 374 " pdb=" C VAL Q 374 " pdb=" O VAL Q 374 " ideal model delta sigma weight residual 120.85 116.30 4.55 1.06e+00 8.90e-01 1.84e+01 angle pdb=" CA MET Q 378 " pdb=" C MET Q 378 " pdb=" O MET Q 378 " ideal model delta sigma weight residual 120.42 116.19 4.23 1.06e+00 8.90e-01 1.59e+01 ... (remaining 54054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 22533 23.90 - 47.81: 569 47.81 - 71.71: 117 71.71 - 95.61: 24 95.61 - 119.52: 1 Dihedral angle restraints: 23244 sinusoidal: 8983 harmonic: 14261 Sorted by residual: dihedral pdb=" C TYR Q 180 " pdb=" N TYR Q 180 " pdb=" CA TYR Q 180 " pdb=" CB TYR Q 180 " ideal model delta harmonic sigma weight residual -122.60 -134.40 11.80 0 2.50e+00 1.60e-01 2.23e+01 dihedral pdb=" CA LEU O 182 " pdb=" C LEU O 182 " pdb=" N ALA O 183 " pdb=" CA ALA O 183 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA LEU S 182 " pdb=" C LEU S 182 " pdb=" N ALA S 183 " pdb=" CA ALA S 183 " ideal model delta harmonic sigma weight residual 180.00 -159.84 -20.16 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 23241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 5826 0.066 - 0.132: 552 0.132 - 0.199: 24 0.199 - 0.265: 2 0.265 - 0.331: 4 Chirality restraints: 6408 Sorted by residual: chirality pdb=" CA TYR Q 180 " pdb=" N TYR Q 180 " pdb=" C TYR Q 180 " pdb=" CB TYR Q 180 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C11 AJP Q 501 " pdb=" C10 AJP Q 501 " pdb=" C12 AJP Q 501 " pdb=" C16 AJP Q 501 " both_signs ideal model delta sigma weight residual False 2.20 2.49 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C11 AJP Q 502 " pdb=" C10 AJP Q 502 " pdb=" C12 AJP Q 502 " pdb=" C16 AJP Q 502 " both_signs ideal model delta sigma weight residual False 2.20 2.47 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 6405 not shown) Planarity restraints: 6700 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER X 576 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C SER X 576 " -0.053 2.00e-02 2.50e+03 pdb=" O SER X 576 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS X 577 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 403 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" C THR X 403 " 0.045 2.00e-02 2.50e+03 pdb=" O THR X 403 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU X 404 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 407 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C THR X 407 " -0.040 2.00e-02 2.50e+03 pdb=" O THR X 407 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP X 408 " 0.014 2.00e-02 2.50e+03 ... (remaining 6697 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 4195 2.75 - 3.29: 39027 3.29 - 3.83: 70039 3.83 - 4.36: 81152 4.36 - 4.90: 139514 Nonbonded interactions: 333927 Sorted by model distance: nonbonded pdb=" O PHE K 28 " pdb=" OG1 THR K 32 " model vdw 2.214 2.440 nonbonded pdb=" OE2 GLU X 331 " pdb=" OH TYR X 435 " model vdw 2.239 2.440 nonbonded pdb=" OG SER X 91 " pdb=" OG1 THR X 107 " model vdw 2.240 2.440 nonbonded pdb=" OE2 GLU X 634 " pdb=" OG1 THR T 42 " model vdw 2.275 2.440 nonbonded pdb=" O ARG X 194 " pdb=" OG SER X 197 " model vdw 2.289 2.440 ... (remaining 333922 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'N' } ncs_group { reference = (chain 'L' and resid 1 through 409) selection = (chain 'Q' and (resid 1 through 26 or resid 48 through 409)) } ncs_group { reference = (chain 'M' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'O' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'R' and (resid 3 through 233 or resid 235 through 249)) selection = (chain 'S' and (resid 3 through 233 or resid 235 through 249)) } ncs_group { reference = (chain 'P' and ((resid 56 and (name N or name CA or name C or name O or name CB \ )) or resid 57 through 181 or resid 192 through 348 or resid 371 through 894 or \ resid 1001 through 1004)) selection = (chain 'T' and (resid 56 through 203 or resid 217 through 894 or resid 1001 thro \ ugh 1004)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 174 5.16 5 C 25336 2.51 5 N 6491 2.21 5 O 6837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 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: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 24.440 Check model and map are aligned: 0.600 Convert atoms to be neutral: 0.330 Process input model: 105.300 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.002 0.050 39723 Z= 0.162 Angle : 0.525 7.738 54059 Z= 0.310 Chirality : 0.040 0.331 6408 Planarity : 0.004 0.055 6698 Dihedral : 11.293 119.518 14064 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.61 % Favored : 98.27 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.96 % 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: 2.02 (0.12), residues: 4925 helix: 2.01 (0.09), residues: 2841 sheet: 1.44 (0.29), residues: 345 loop : 0.28 (0.15), residues: 1739 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 846 time to evaluate : 4.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 16 residues processed: 908 average time/residue: 1.3697 time to fit residues: 1537.5178 Evaluate side-chains 645 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 629 time to evaluate : 4.535 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.3598 time to fit residues: 7.4766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 0.3980 chunk 373 optimal weight: 1.9990 chunk 207 optimal weight: 0.2980 chunk 127 optimal weight: 4.9990 chunk 252 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 386 optimal weight: 0.2980 chunk 149 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 287 optimal weight: 0.0570 chunk 447 optimal weight: 3.9990 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 136 ASN A 137 GLN A 138 ASN A 165 ASN A 183 ASN A 215 HIS A 237 GLN A 350 HIS W 18 GLN X 133 GLN X 433 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 559 ASN X 632 HIS X 646 ASN K 33 HIS K 41 GLN K 49 GLN K 52 GLN K 236 ASN K 260 HIS L 98 GLN L 104 GLN L 117 ASN L 292 HIS L 395 ASN Q 55 GLN Q 98 GLN Q 102 GLN Q 104 GLN P 198 GLN P 330 GLN P 377 GLN P 457 GLN P 630 GLN P 683 GLN P 819 HIS T 37 HIS T 330 GLN T 377 GLN T 457 GLN T 545 GLN T 630 GLN T 683 GLN T 819 HIS S 122 ASN R 101 GLN R 122 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 39723 Z= 0.157 Angle : 0.487 9.065 54059 Z= 0.245 Chirality : 0.038 0.245 6408 Planarity : 0.004 0.048 6698 Dihedral : 5.303 107.339 5510 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.41 % Favored : 98.47 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 2.22 (0.12), residues: 4925 helix: 2.19 (0.10), residues: 2843 sheet: 1.32 (0.28), residues: 360 loop : 0.38 (0.15), residues: 1722 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 654 time to evaluate : 4.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 33 residues processed: 699 average time/residue: 1.4783 time to fit residues: 1276.4032 Evaluate side-chains 647 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 614 time to evaluate : 4.459 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 18 residues processed: 16 average time/residue: 0.5201 time to fit residues: 19.8383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 372 optimal weight: 0.0170 chunk 304 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 448 optimal weight: 0.8980 chunk 484 optimal weight: 0.5980 chunk 399 optimal weight: 0.9990 chunk 444 optimal weight: 5.9990 chunk 152 optimal weight: 0.5980 chunk 359 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 136 ASN A 165 ASN W 18 GLN X 133 GLN X 559 ASN X 570 HIS K 49 GLN L 117 ASN L 292 HIS L 395 ASN Q 55 GLN Q 98 GLN Q 104 GLN D 82 GLN T 275 HIS T 554 ASN T 736 ASN S 122 ASN M 74 HIS M 88 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 39723 Z= 0.182 Angle : 0.501 8.229 54059 Z= 0.254 Chirality : 0.039 0.167 6408 Planarity : 0.004 0.048 6698 Dihedral : 5.411 108.134 5510 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.55 % Favored : 98.33 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % 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: 2.16 (0.12), residues: 4925 helix: 2.10 (0.10), residues: 2863 sheet: 1.24 (0.27), residues: 357 loop : 0.40 (0.15), residues: 1705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 623 time to evaluate : 4.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 41 residues processed: 671 average time/residue: 1.4230 time to fit residues: 1183.3460 Evaluate side-chains 624 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 583 time to evaluate : 4.485 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 26 residues processed: 15 average time/residue: 0.5546 time to fit residues: 19.5121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 443 optimal weight: 3.9990 chunk 337 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 214 optimal weight: 2.9990 chunk 301 optimal weight: 0.8980 chunk 450 optimal weight: 2.9990 chunk 476 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 426 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 136 ASN A 138 ASN A 165 ASN X 517 HIS K 49 GLN L 98 GLN L 117 ASN L 292 HIS Q 98 GLN P 651 HIS T 275 HIS T 554 ASN S 122 ASN M 88 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 39723 Z= 0.318 Angle : 0.611 8.408 54059 Z= 0.311 Chirality : 0.043 0.219 6408 Planarity : 0.005 0.051 6698 Dihedral : 5.917 107.633 5510 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.00 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.12), residues: 4925 helix: 1.66 (0.10), residues: 2852 sheet: 0.86 (0.27), residues: 345 loop : 0.21 (0.15), residues: 1728 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 631 time to evaluate : 4.487 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 59 residues processed: 697 average time/residue: 1.4306 time to fit residues: 1235.5769 Evaluate side-chains 668 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 609 time to evaluate : 4.721 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 36 residues processed: 24 average time/residue: 0.8430 time to fit residues: 35.1662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 396 optimal weight: 1.9990 chunk 270 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 406 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 243 optimal weight: 0.6980 chunk 427 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 123 HIS A 165 ASN A 251 ASN W 18 GLN X 133 GLN X 151 ASN X 154 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN K 52 GLN L 117 ASN L 292 HIS P 133 ASN P 339 GLN T 198 GLN T 275 HIS T 545 GLN S 122 ASN M 88 GLN M 122 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 39723 Z= 0.276 Angle : 0.568 8.750 54059 Z= 0.289 Chirality : 0.041 0.232 6408 Planarity : 0.005 0.048 6698 Dihedral : 5.831 106.571 5510 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.81 % Favored : 98.08 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.12), residues: 4925 helix: 1.62 (0.10), residues: 2866 sheet: 0.72 (0.27), residues: 350 loop : 0.17 (0.15), residues: 1709 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 629 time to evaluate : 4.537 Fit side-chains revert: symmetry clash outliers start: 110 outliers final: 56 residues processed: 690 average time/residue: 1.4627 time to fit residues: 1268.8199 Evaluate side-chains 662 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 606 time to evaluate : 4.390 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 38 residues processed: 19 average time/residue: 0.6043 time to fit residues: 24.4526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 0.9980 chunk 429 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 279 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 476 optimal weight: 0.8980 chunk 395 optimal weight: 2.9990 chunk 220 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 165 ASN X 133 GLN X 646 ASN K 52 GLN K 362 GLN L 292 HIS P 339 GLN ** P 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 HIS T 198 GLN T 545 GLN S 122 ASN M 88 GLN M 122 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 39723 Z= 0.238 Angle : 0.547 8.374 54059 Z= 0.278 Chirality : 0.040 0.209 6408 Planarity : 0.004 0.048 6698 Dihedral : 5.758 106.207 5510 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.92 % Favored : 97.98 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.12), residues: 4925 helix: 1.68 (0.10), residues: 2866 sheet: 0.70 (0.27), residues: 351 loop : 0.17 (0.15), residues: 1708 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 621 time to evaluate : 4.709 Fit side-chains revert: symmetry clash outliers start: 97 outliers final: 55 residues processed: 678 average time/residue: 1.4528 time to fit residues: 1215.8060 Evaluate side-chains 667 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 612 time to evaluate : 4.396 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 38 residues processed: 17 average time/residue: 0.6346 time to fit residues: 22.2162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 459 optimal weight: 0.9980 chunk 53 optimal weight: 0.0070 chunk 271 optimal weight: 5.9990 chunk 348 optimal weight: 9.9990 chunk 269 optimal weight: 0.7980 chunk 401 optimal weight: 0.9990 chunk 266 optimal weight: 9.9990 chunk 475 optimal weight: 2.9990 chunk 297 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 219 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 165 ASN A 198 ASN W 18 GLN X 133 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN L 117 ASN L 292 HIS P 192 HIS P 547 HIS T 545 GLN S 122 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 39723 Z= 0.213 Angle : 0.535 8.791 54059 Z= 0.271 Chirality : 0.039 0.195 6408 Planarity : 0.004 0.045 6698 Dihedral : 5.693 105.865 5510 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.00 % Rotamer Outliers : 2.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.12), residues: 4925 helix: 1.73 (0.10), residues: 2865 sheet: 0.72 (0.27), residues: 351 loop : 0.17 (0.15), residues: 1709 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 628 time to evaluate : 4.463 Fit side-chains revert: symmetry clash outliers start: 90 outliers final: 60 residues processed: 682 average time/residue: 1.4847 time to fit residues: 1257.5086 Evaluate side-chains 675 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 615 time to evaluate : 4.502 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 42 residues processed: 18 average time/residue: 0.6639 time to fit residues: 24.5735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 293 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 283 optimal weight: 0.1980 chunk 143 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 302 optimal weight: 4.9990 chunk 323 optimal weight: 0.7980 chunk 234 optimal weight: 0.9980 chunk 44 optimal weight: 0.0970 chunk 373 optimal weight: 0.4980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 165 ASN A 198 ASN X 133 GLN X 551 ASN X 559 ASN K 49 GLN L 117 ASN L 292 HIS T 545 GLN S 122 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 39723 Z= 0.170 Angle : 0.512 9.267 54059 Z= 0.259 Chirality : 0.038 0.175 6408 Planarity : 0.004 0.045 6698 Dihedral : 5.549 105.330 5510 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.81 % Favored : 98.08 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.12), residues: 4925 helix: 1.84 (0.10), residues: 2860 sheet: 0.76 (0.27), residues: 351 loop : 0.22 (0.15), residues: 1714 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 618 time to evaluate : 4.558 Fit side-chains revert: symmetry clash outliers start: 68 outliers final: 51 residues processed: 663 average time/residue: 1.5051 time to fit residues: 1233.3327 Evaluate side-chains 668 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 617 time to evaluate : 4.438 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 43 residues processed: 9 average time/residue: 0.6283 time to fit residues: 14.6668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 2.9990 chunk 455 optimal weight: 0.6980 chunk 415 optimal weight: 0.4980 chunk 442 optimal weight: 0.0470 chunk 266 optimal weight: 6.9990 chunk 192 optimal weight: 0.7980 chunk 347 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 400 optimal weight: 0.7980 chunk 418 optimal weight: 0.6980 chunk 441 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 136 ASN A 165 ASN X 133 GLN X 551 ASN K 49 GLN L 117 ASN L 292 HIS N 82 GLN T 545 GLN S 122 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 39723 Z= 0.184 Angle : 0.518 9.967 54059 Z= 0.262 Chirality : 0.038 0.184 6408 Planarity : 0.004 0.049 6698 Dihedral : 5.529 105.435 5510 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.00 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.12), residues: 4925 helix: 1.84 (0.10), residues: 2864 sheet: 0.81 (0.27), residues: 347 loop : 0.24 (0.15), residues: 1714 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 613 time to evaluate : 4.306 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 48 residues processed: 663 average time/residue: 1.4807 time to fit residues: 1228.9275 Evaluate side-chains 653 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 605 time to evaluate : 4.590 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 42 residues processed: 7 average time/residue: 0.7630 time to fit residues: 14.2287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 0.0870 chunk 468 optimal weight: 0.0020 chunk 285 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 491 optimal weight: 0.7980 chunk 452 optimal weight: 0.6980 chunk 391 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 302 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 136 ASN A 138 ASN A 165 ASN X 133 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 ASN X 602 GLN K 49 GLN L 117 ASN L 292 HIS Q 331 HIS T 545 GLN S 122 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 39723 Z= 0.173 Angle : 0.519 10.342 54059 Z= 0.261 Chirality : 0.038 0.188 6408 Planarity : 0.004 0.065 6698 Dihedral : 5.479 105.108 5510 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.94 % Favored : 97.98 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.12), residues: 4925 helix: 1.88 (0.10), residues: 2865 sheet: 0.79 (0.27), residues: 347 loop : 0.26 (0.15), residues: 1713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9850 Ramachandran restraints generated. 4925 Oldfield, 0 Emsley, 4925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 608 time to evaluate : 4.684 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 44 residues processed: 654 average time/residue: 1.4541 time to fit residues: 1180.2819 Evaluate side-chains 650 residues out of total 4133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 606 time to evaluate : 4.367 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 38 residues processed: 6 average time/residue: 0.6871 time to fit residues: 12.0656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 310 optimal weight: 5.9990 chunk 416 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 360 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 391 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 402 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 136 ASN A 165 ASN W 18 GLN X 133 GLN ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 551 ASN X 559 ASN K 49 GLN L 117 ASN L 292 HIS P 434 GLN T 545 GLN S 122 ASN ** R 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.118898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.098001 restraints weight = 114936.712| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.24 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 39723 Z= 0.250 Angle : 0.564 14.972 54059 Z= 0.285 Chirality : 0.040 0.187 6408 Planarity : 0.004 0.059 6698 Dihedral : 5.662 105.826 5510 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.84 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.12), residues: 4925 helix: 1.75 (0.10), residues: 2854 sheet: 0.70 (0.27), residues: 347 loop : 0.19 (0.15), residues: 1724 =============================================================================== Job complete usr+sys time: 16651.87 seconds wall clock time: 294 minutes 52.02 seconds (17692.02 seconds total)