Starting phenix.real_space_refine (version: dev) on Fri Dec 16 19:42:57 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v0k_26943/12_2022/7v0k_26943_updated.pdb" } resolution = 2.4 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= 0.006 sd= 0.085 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 "K ASP 53": "OD1" <-> "OD2" Residue "K PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 340": "OE1" <-> "OE2" Residue "K ASP 403": "OD1" <-> "OD2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 161": "OE1" <-> "OE2" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 393": "OD1" <-> "OD2" Residue "Q GLU 25": "OE1" <-> "OE2" Residue "Q TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 201": "OE1" <-> "OE2" Residue "Q GLU 231": "OE1" <-> "OE2" Residue "Q ASP 234": "OD1" <-> "OD2" Residue "Q GLU 262": "OE1" <-> "OE2" Residue "Q PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 11": "OD1" <-> "OD2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H GLU 142": "OE1" <-> "OE2" Residue "H ASP 143": "OD1" <-> "OD2" Residue "H ASP 185": "OD1" <-> "OD2" Residue "H ASP 260": "OD1" <-> "OD2" Residue "H TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 328": "OD1" <-> "OD2" Residue "H ASP 337": "OD1" <-> "OD2" Residue "H GLU 388": "OE1" <-> "OE2" Residue "H GLU 402": "OE1" <-> "OE2" Residue "H GLU 438": "OE1" <-> "OE2" Residue "H GLU 451": "OE1" <-> "OE2" Residue "W ASP 7": "OD1" <-> "OD2" Residue "W GLU 17": "OE1" <-> "OE2" Residue "W GLU 22": "OE1" <-> "OE2" Residue "X GLU 19": "OE1" <-> "OE2" Residue "X GLU 20": "OE1" <-> "OE2" Residue "X GLU 96": "OE1" <-> "OE2" Residue "X ASP 172": "OD1" <-> "OD2" Residue "X GLU 177": "OE1" <-> "OE2" Residue "X GLU 311": "OE1" <-> "OE2" Residue "X GLU 400": "OE1" <-> "OE2" Residue "X GLU 446": "OE1" <-> "OE2" Residue "X GLU 449": "OE1" <-> "OE2" Residue "X GLU 452": "OE1" <-> "OE2" Residue "X ASP 490": "OD1" <-> "OD2" Residue "X GLU 502": "OE1" <-> "OE2" Residue "X PHE 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 553": "OE1" <-> "OE2" Residue "X GLU 572": "OE1" <-> "OE2" Residue "X GLU 596": "OE1" <-> "OE2" Residue "X GLU 599": "OE1" <-> "OE2" Residue "X GLU 619": "OE1" <-> "OE2" Residue "X ASP 620": "OD1" <-> "OD2" Residue "X GLU 645": "OE1" <-> "OE2" Residue "X PHE 654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "O TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 109": "OE1" <-> "OE2" Residue "O ASP 122": "OD1" <-> "OD2" Residue "O ASP 137": "OD1" <-> "OD2" Residue "O GLU 152": "OE1" <-> "OE2" Residue "O ASP 183": "OD1" <-> "OD2" Residue "O ASP 223": "OD1" <-> "OD2" Residue "O GLU 252": "OE1" <-> "OE2" Residue "O GLU 257": "OE1" <-> "OE2" Residue "O GLU 291": "OE1" <-> "OE2" Residue "O GLU 306": "OE1" <-> "OE2" Residue "O GLU 341": "OE1" <-> "OE2" Residue "O TYR 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 480": "OE1" <-> "OE2" Residue "O GLU 485": "OE1" <-> "OE2" Residue "O PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 522": "OE1" <-> "OE2" Residue "O GLU 535": "OE1" <-> "OE2" Residue "O TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 597": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 755": "OE1" <-> "OE2" Residue "O ASP 807": "OD1" <-> "OD2" Residue "O TYR 818": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 63": "OE1" <-> "OE2" Residue "P PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 151": "OE1" <-> "OE2" Residue "P GLU 166": "OE1" <-> "OE2" Residue "P PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 329": "OE1" <-> "OE2" Residue "P GLU 341": "OE1" <-> "OE2" Residue "P TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 399": "OD1" <-> "OD2" Residue "P PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 429": "OE1" <-> "OE2" Residue "P PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 480": "OE1" <-> "OE2" Residue "P GLU 522": "OE1" <-> "OE2" Residue "P ASP 621": "OD1" <-> "OD2" Residue "P ASP 626": "OD1" <-> "OD2" Residue "P TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 705": "OD1" <-> "OD2" Residue "P GLU 755": "OE1" <-> "OE2" Residue "P GLU 777": "OE1" <-> "OE2" Residue "P TYR 818": "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: 32037 Number of models: 1 Model: "" Number of chains: 22 Chain: "K" Number of atoms: 2954 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: 2949 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: "H" 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: 5174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5174 Classifications: {'peptide': 658} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 627} Chain breaks: 3 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: "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: "O" 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: "P" 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: "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: "O" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PLC': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 206 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 2, 'PLC': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "L" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 89 Classifications: {'water': 89} Link IDs: {None: 88} Chain: "Q" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 80 Classifications: {'water': 80} Link IDs: {None: 79} Chain: "H" Number of atoms: 77 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Conformer: "B" Number of residues, atoms: 76, 76 Classifications: {'water': 76} Link IDs: {None: 75} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "X" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 190 Classifications: {'water': 190} Link IDs: {None: 189} Chain: "O" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 53 Classifications: {'water': 53} Link IDs: {None: 52} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ATYR K 34 " occ=0.52 ... (22 atoms not shown) pdb=" OH BTYR K 34 " occ=0.48 residue: pdb=" N APHE K 239 " occ=0.53 ... (20 atoms not shown) pdb=" CZ BPHE K 239 " occ=0.47 residue: pdb=" N ATYR K 242 " occ=0.62 ... (22 atoms not shown) pdb=" OH BTYR K 242 " occ=0.38 residue: pdb=" O AHOH H1961 " occ=0.57 pdb=" O BHOH H1961 " occ=0.43 Time building chain proxies: 19.27, per 1000 atoms: 0.60 Number of scatterers: 32037 At special positions: 0 Unit cell: (141.515, 178.035, 191.73, 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 154 16.00 P 8 15.00 O 6115 8.00 N 5231 7.00 C 20529 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 O1002 " - " ASN O 642 " " NAG P1002 " - " ASN P 642 " Time building additional restraints: 13.55 Conformation dependent library (CDL) restraints added in 4.7 seconds 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 156 helices and 17 sheets defined 53.8% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.19 Creating SS restraints... Processing helix chain 'K' and resid 12 through 31 Processing helix chain 'K' and resid 44 through 65 removed outlier: 3.791A pdb=" N VAL K 50 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU K 62 " --> pdb=" O ALA K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 97 removed outlier: 3.749A pdb=" N GLN K 89 " --> pdb=" O ALA K 85 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 129 removed outlier: 3.549A pdb=" N VAL K 123 " --> pdb=" O SER K 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.434A 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 167 through 186 removed outlier: 3.559A pdb=" N ARG K 170 " --> pdb=" O MET K 167 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYR K 173 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE K 175 " --> pdb=" O PHE K 172 " (cutoff:3.500A) removed outlier: 3.513A 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: 3.825A pdb=" N SER K 272 " --> pdb=" O THR K 268 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU K 275 " --> pdb=" O HIS K 271 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA K 276 " --> pdb=" O SER K 272 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLY K 277 " --> pdb=" O ALA K 273 " (cutoff:3.500A) removed outlier: 5.371A 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: 3.669A pdb=" N VAL K 348 " --> pdb=" O ILE K 344 " (cutoff:3.500A) removed outlier: 4.058A 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: 4.041A pdb=" N PHE L 65 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY L 66 " --> pdb=" O PHE L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 103 removed outlier: 3.692A pdb=" N GLN L 92 " --> pdb=" O ALA L 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 131 removed outlier: 3.764A pdb=" N ALA L 131 " --> pdb=" O ILE L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 161 Processing helix chain 'L' and resid 175 through 188 Processing helix chain 'L' and resid 192 through 194 No H-bonds generated for 'chain 'L' and resid 192 through 194' Processing helix chain 'L' and resid 205 through 227 removed outlier: 3.659A pdb=" N ILE L 213 " --> pdb=" O LEU L 209 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY L 214 " --> pdb=" O PHE L 210 " (cutoff:3.500A) Proline residue: L 223 - end of helix Processing helix chain 'L' and resid 234 through 261 removed outlier: 3.675A 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: 4.292A pdb=" N THR L 276 " --> pdb=" O ILE L 272 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU L 277 " --> pdb=" O GLN L 273 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ALA L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLY L 279 " --> pdb=" O ALA L 275 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY L 280 " --> pdb=" O THR L 276 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL L 281 " --> pdb=" O LEU L 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 292 through 320 removed outlier: 4.601A 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: 5.315A 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 71 Proline residue: Q 52 - end of helix removed outlier: 4.313A pdb=" N PHE Q 65 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY Q 66 " --> pdb=" O PHE Q 62 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR Q 70 " --> pdb=" O GLY Q 66 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE Q 71 " --> pdb=" O PHE Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 76 through 103 removed outlier: 3.819A pdb=" N GLN Q 92 " --> pdb=" O ALA Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 131 removed outlier: 3.757A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 138 through 161 removed outlier: 3.597A 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: 3.619A 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: 4.302A pdb=" N THR Q 276 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N LEU Q 277 " --> pdb=" O GLN Q 273 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA Q 278 " --> pdb=" O ASN Q 274 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY Q 279 " --> pdb=" O ALA Q 275 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLY Q 280 " --> pdb=" O THR Q 276 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 320 removed outlier: 4.572A 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 351 removed outlier: 5.270A 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 384 Processing helix chain 'Q' and resid 399 through 401 No H-bonds generated for 'chain 'Q' and resid 399 through 401' Processing helix chain 'H' and resid 12 through 22 Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 48 through 55 Processing helix chain 'H' and resid 58 through 66 Processing helix chain 'H' and resid 81 through 88 Processing helix chain 'H' and resid 91 through 99 Processing helix chain 'H' and resid 114 through 120 Processing helix chain 'H' and resid 124 through 132 Processing helix chain 'H' and resid 147 through 153 Processing helix chain 'H' and resid 157 through 166 Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 186 through 195 Processing helix chain 'H' and resid 209 through 216 Processing helix chain 'H' and resid 219 through 227 Processing helix chain 'H' and resid 242 through 248 Processing helix chain 'H' and resid 252 through 260 Processing helix chain 'H' and resid 275 through 281 Processing helix chain 'H' and resid 285 through 293 Processing helix chain 'H' and resid 308 through 314 Processing helix chain 'H' and resid 318 through 326 Processing helix chain 'H' and resid 341 through 348 Processing helix chain 'H' and resid 351 through 359 Processing helix chain 'H' and resid 374 through 380 Processing helix chain 'H' and resid 384 through 393 Processing helix chain 'H' and resid 407 through 414 Processing helix chain 'H' and resid 417 through 425 Processing helix chain 'H' and resid 440 through 447 Processing helix chain 'H' and resid 450 through 458 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: 3.800A pdb=" N LYS X 198 " --> pdb=" O ARG X 194 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 206 removed outlier: 3.960A 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 257 Processing helix chain 'X' and resid 265 through 282 removed outlier: 5.606A pdb=" N TRP X 269 " --> pdb=" O GLY X 266 " (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 'X' and resid 549 through 551 No H-bonds generated for 'chain 'X' and resid 549 through 551' Processing helix chain 'N' and resid 89 through 113 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'O' and resid 104 through 115 Processing helix chain 'O' and resid 128 through 141 Processing helix chain 'O' and resid 147 through 157 removed outlier: 4.206A pdb=" N GLU O 151 " --> pdb=" O GLN O 148 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU O 152 " --> pdb=" O ASP O 149 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU O 153 " --> pdb=" O ARG O 150 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU O 154 " --> pdb=" O GLU O 151 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 166 No H-bonds generated for 'chain 'O' and resid 164 through 166' Processing helix chain 'O' and resid 195 through 200 Processing helix chain 'O' and resid 278 through 290 Processing helix chain 'O' and resid 292 through 300 Processing helix chain 'O' and resid 304 through 316 Processing helix chain 'O' and resid 329 through 348 removed outlier: 4.162A pdb=" N LEU O 335 " --> pdb=" O ALA O 331 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL O 336 " --> pdb=" O LEU O 332 " (cutoff:3.500A) Proline residue: O 337 - end of helix Processing helix chain 'O' and resid 380 through 393 Proline residue: O 391 - end of helix Processing helix chain 'O' and resid 395 through 400 removed outlier: 5.190A pdb=" N ALA O 400 " --> pdb=" O ASP O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 430 removed outlier: 3.698A pdb=" N PHE O 414 " --> pdb=" O ILE O 410 " (cutoff:3.500A) Proline residue: O 419 - end of helix Processing helix chain 'O' and resid 437 through 454 Processing helix chain 'O' and resid 466 through 481 Processing helix chain 'O' and resid 486 through 506 removed outlier: 3.505A pdb=" N LEU O 499 " --> pdb=" O PHE O 495 " (cutoff:3.500A) Processing helix chain 'O' and resid 509 through 515 Processing helix chain 'O' and resid 518 through 546 Processing helix chain 'O' and resid 570 through 593 removed outlier: 3.567A pdb=" N ASN O 593 " --> pdb=" O ARG O 589 " (cutoff:3.500A) Processing helix chain 'O' and resid 599 through 607 Processing helix chain 'O' and resid 609 through 623 Processing helix chain 'O' and resid 661 through 689 removed outlier: 3.678A pdb=" N PHE O 665 " --> pdb=" O ILE O 661 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ALA O 668 " --> pdb=" O MET O 664 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N LEU O 669 " --> pdb=" O PHE O 665 " (cutoff:3.500A) Proline residue: O 670 - end of helix Processing helix chain 'O' and resid 692 through 694 No H-bonds generated for 'chain 'O' and resid 692 through 694' Processing helix chain 'O' and resid 704 through 719 removed outlier: 3.677A pdb=" N LEU O 718 " --> pdb=" O GLY O 714 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE O 719 " --> pdb=" O VAL O 715 " (cutoff:3.500A) Processing helix chain 'O' and resid 728 through 737 Processing helix chain 'O' and resid 761 through 774 removed outlier: 4.802A pdb=" N ILE O 774 " --> pdb=" O VAL O 770 " (cutoff:3.500A) Processing helix chain 'O' and resid 777 through 782 removed outlier: 4.533A pdb=" N ARG O 782 " --> pdb=" O PRO O 778 " (cutoff:3.500A) Processing helix chain 'O' and resid 785 through 798 Processing helix chain 'O' and resid 804 through 812 Processing helix chain 'O' and resid 823 through 826 No H-bonds generated for 'chain 'O' and resid 823 through 826' Processing helix chain 'O' and resid 830 through 852 Processing helix chain 'O' and resid 856 through 872 Proline residue: O 860 - end of helix Proline residue: O 868 - end of helix Processing helix chain 'O' and resid 874 through 876 No H-bonds generated for 'chain 'O' and resid 874 through 876' Processing helix chain 'O' and resid 880 through 886 Processing helix chain 'P' and resid 43 through 46 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: 3.614A pdb=" N ARG P 150 " --> pdb=" O PRO P 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLU P 151 " --> pdb=" O GLN P 148 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU P 157 " --> pdb=" O LEU P 154 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 169 removed outlier: 3.982A pdb=" N GLU P 168 " --> pdb=" O GLY P 165 " (cutoff:3.500A) 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 300 Processing helix chain 'P' and resid 304 through 316 Processing helix chain 'P' and resid 328 through 342 removed outlier: 4.108A pdb=" N LEU P 335 " --> pdb=" O ALA P 331 " (cutoff:3.500A) removed outlier: 4.229A 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 400 Proline residue: P 391 - end of helix removed outlier: 5.425A pdb=" N LEU P 394 " --> pdb=" O TYR P 390 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER P 395 " --> pdb=" O PRO P 391 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA P 400 " --> pdb=" O ASP P 396 " (cutoff:3.500A) Processing helix chain 'P' and resid 403 through 431 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 removed outlier: 3.509A pdb=" N LEU P 499 " --> pdb=" O PHE P 495 " (cutoff:3.500A) Processing helix chain 'P' and resid 509 through 515 removed outlier: 3.642A pdb=" N LEU P 512 " --> pdb=" O GLY P 509 " (cutoff:3.500A) Processing helix chain 'P' and resid 518 through 546 removed outlier: 3.640A pdb=" N LEU P 540 " --> pdb=" O THR P 536 " (cutoff:3.500A) Processing helix chain 'P' and resid 570 through 593 removed outlier: 3.550A 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: 3.633A pdb=" N PHE P 665 " --> pdb=" O ILE P 661 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA P 668 " --> pdb=" O MET P 664 " (cutoff:3.500A) removed outlier: 5.148A 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 704 through 718 removed outlier: 3.718A 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 774 removed outlier: 4.825A pdb=" N ILE P 774 " --> pdb=" O VAL P 770 " (cutoff:3.500A) Processing helix chain 'P' and resid 777 through 782 removed outlier: 4.032A pdb=" N ARG P 782 " --> pdb=" O PRO P 778 " (cutoff:3.500A) Processing helix chain 'P' and resid 785 through 800 removed outlier: 4.078A pdb=" N LEU P 800 " --> pdb=" O GLY P 796 " (cutoff:3.500A) Processing helix chain 'P' and resid 804 through 813 removed outlier: 3.945A pdb=" N PHE P 813 " --> pdb=" O ILE P 809 " (cutoff:3.500A) 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: 5.054A pdb=" N LEU P 873 " --> pdb=" O ARG P 870 " (cutoff:3.500A) removed outlier: 5.956A 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 sheet with id= A, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.719A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU X 119 " --> pdb=" O LEU X 131 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLN X 133 " --> pdb=" O TYR X 117 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TYR X 117 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR X 135 " --> pdb=" O GLY X 115 " (cutoff:3.500A) removed outlier: 6.468A 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: 6.764A pdb=" N TYR X 44 " --> pdb=" O LYS X 8 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS X 10 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE X 42 " --> pdb=" O CYS X 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU X 96 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.784A 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 292 removed outlier: 11.812A pdb=" N THR X 328 " --> pdb=" O PRO X 351 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 3.995A 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 309 removed outlier: 6.553A pdb=" N SER X 392 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N GLU X 306 " --> pdb=" O SER X 392 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL X 394 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N TYR X 308 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 6.302A 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: 6.382A 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: 6.314A pdb=" N ALA X 515 " --> pdb=" O LYS X 525 " (cutoff:3.500A) removed outlier: 5.571A 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: 8.213A pdb=" N ALA X 598 " --> pdb=" O SER X 681 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N THR X 683 " --> pdb=" O ALA X 598 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 84 through 87 removed outlier: 6.961A pdb=" N LEU O 61 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG O 80 " --> pdb=" O VAL O 59 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL O 59 " --> pdb=" O ARG O 80 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N ARG O 233 " --> pdb=" O LEU O 64 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N MET O 66 " --> pdb=" O ARG O 233 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU O 228 " --> pdb=" O ARG O 263 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU O 265 " --> pdb=" O LEU O 228 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LEU O 230 " --> pdb=" O LEU O 265 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL O 267 " --> pdb=" O LEU O 230 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY O 232 " --> pdb=" O VAL O 267 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LEU O 269 " --> pdb=" O GLY O 232 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ARG O 263 " --> pdb=" O LEU O 247 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N THR O 118 " --> pdb=" O PHE O 244 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ARG O 246 " --> pdb=" O THR O 118 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU O 120 " --> pdb=" O ARG O 246 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 65 through 67 Processing sheet with id= O, first strand: chain 'O' and resid 739 through 741 Processing sheet with id= P, first strand: chain 'P' and resid 85 through 87 removed outlier: 6.652A pdb=" N LEU P 61 " --> pdb=" O ALA P 78 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ARG P 80 " --> pdb=" O VAL P 59 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL P 59 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ARG P 233 " --> pdb=" O LEU P 64 " (cutoff:3.500A) removed outlier: 10.451A pdb=" N MET P 66 " --> pdb=" O ARG P 233 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU P 228 " --> pdb=" O ARG P 263 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU P 265 " --> pdb=" O LEU P 228 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU P 230 " --> pdb=" O LEU P 265 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL P 267 " --> pdb=" O LEU P 230 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY P 232 " --> pdb=" O VAL P 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU P 269 " --> pdb=" O GLY P 232 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG P 263 " --> pdb=" O LEU P 247 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR P 118 " --> pdb=" O PHE P 244 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ARG P 246 " --> pdb=" O THR P 118 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU P 120 " --> pdb=" O ARG P 246 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'P' and resid 739 through 741 1582 hydrogen bonds defined for protein. 4518 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: 12.02 Time building geometry restraints manager: 14.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5607 1.33 - 1.45: 7934 1.45 - 1.58: 18390 1.58 - 1.70: 12 1.70 - 1.83: 263 Bond restraints: 32206 Sorted by residual: bond pdb=" C1B PIO P1006 " pdb=" O3C PIO P1006 " ideal model delta sigma weight residual 1.398 1.328 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1B PIO P1005 " pdb=" O3C PIO P1005 " ideal model delta sigma weight residual 1.398 1.329 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C PRO O 815 " pdb=" O PRO O 815 " ideal model delta sigma weight residual 1.246 1.217 0.028 8.50e-03 1.38e+04 1.11e+01 bond pdb=" CA PRO O 815 " pdb=" C PRO O 815 " ideal model delta sigma weight residual 1.514 1.532 -0.018 5.50e-03 3.31e+04 1.03e+01 bond pdb=" C PRO P 815 " pdb=" O PRO P 815 " ideal model delta sigma weight residual 1.243 1.217 0.026 8.50e-03 1.38e+04 9.20e+00 ... (remaining 32201 not shown) Histogram of bond angle deviations from ideal: 93.77 - 101.87: 115 101.87 - 109.97: 4576 109.97 - 118.08: 20458 118.08 - 126.18: 18147 126.18 - 134.28: 501 Bond angle restraints: 43797 Sorted by residual: angle pdb=" N PRO O 598 " pdb=" CA PRO O 598 " pdb=" C PRO O 598 " ideal model delta sigma weight residual 111.14 103.88 7.26 1.56e+00 4.11e-01 2.17e+01 angle pdb=" CB MET W 11 " pdb=" CG MET W 11 " pdb=" SD MET W 11 " ideal model delta sigma weight residual 112.70 126.64 -13.94 3.00e+00 1.11e-01 2.16e+01 angle pdb=" C LYS O 814 " pdb=" N PRO O 815 " pdb=" CA PRO O 815 " ideal model delta sigma weight residual 119.66 122.72 -3.06 7.30e-01 1.88e+00 1.75e+01 angle pdb=" N LYS O 817 " pdb=" CA LYS O 817 " pdb=" C LYS O 817 " ideal model delta sigma weight residual 111.28 106.96 4.32 1.09e+00 8.42e-01 1.57e+01 angle pdb=" C LYS P 814 " pdb=" N PRO P 815 " pdb=" CA PRO P 815 " ideal model delta sigma weight residual 119.66 122.50 -2.84 7.20e-01 1.93e+00 1.56e+01 ... (remaining 43792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 17295 24.62 - 49.24: 1349 49.24 - 73.86: 239 73.86 - 98.48: 57 98.48 - 123.10: 1 Dihedral angle restraints: 18941 sinusoidal: 7448 harmonic: 11493 Sorted by residual: dihedral pdb=" CA TRP O 81 " pdb=" C TRP O 81 " pdb=" N VAL O 82 " pdb=" CA VAL O 82 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLU Q 201 " pdb=" C GLU Q 201 " pdb=" N GLU Q 202 " pdb=" CA GLU Q 202 " ideal model delta harmonic sigma weight residual -180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA VAL H 435 " pdb=" C VAL H 435 " pdb=" N LYS H 436 " pdb=" CA LYS H 436 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 18938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4425 0.063 - 0.127: 652 0.127 - 0.190: 55 0.190 - 0.253: 8 0.253 - 0.316: 5 Chirality restraints: 5145 Sorted by residual: chirality pdb=" C1 NAG O1002 " pdb=" ND2 ASN O 642 " pdb=" C2 NAG O1002 " pdb=" O5 NAG O1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C08 AJP Q 502 " pdb=" C07 AJP Q 502 " pdb=" C10 AJP Q 502 " pdb=" O09 AJP Q 502 " both_signs ideal model delta sigma weight residual False 2.56 2.84 -0.28 2.00e-01 2.50e+01 1.92e+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 1.83e+00 ... (remaining 5142 not shown) Planarity restraints: 5437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL P 822 " -0.080 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO P 823 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO P 823 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO P 823 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 225 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO K 226 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO K 226 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO K 226 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU P 874 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.71e+00 pdb=" N PRO P 875 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO P 875 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO P 875 " -0.036 5.00e-02 4.00e+02 ... (remaining 5434 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3052 2.74 - 3.28: 32769 3.28 - 3.82: 60489 3.82 - 4.36: 71671 4.36 - 4.90: 117683 Nonbonded interactions: 285664 Sorted by model distance: nonbonded pdb=" OE2 GLU X 331 " pdb=" OH TYR X 435 " model vdw 2.205 2.440 nonbonded pdb=" OE1 GLU P 472 " pdb=" OH TYR P 486 " model vdw 2.210 2.440 nonbonded pdb=" OE1 GLU O 472 " pdb=" OH TYR O 486 " model vdw 2.231 2.440 nonbonded pdb=" O LEU P 427 " pdb=" OG1 THR P 431 " model vdw 2.245 2.440 nonbonded pdb=" OG1 THR X 496 " pdb=" O HOH X 701 " model vdw 2.250 2.440 ... (remaining 285659 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 'O' 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 'P' 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 8 5.49 5 S 154 5.16 5 C 20529 2.51 5 N 5231 2.21 5 O 6115 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=0.38 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: 108.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 151.520 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.590 Process input model: 85.140 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 361.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 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 : 0.004 0.070 32206 Z= 0.282 Angle : 0.712 13.939 43797 Z= 0.396 Chirality : 0.046 0.316 5145 Planarity : 0.006 0.120 5435 Dihedral : 17.857 123.102 11525 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.80 % Favored : 98.07 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.27 (0.13), residues: 3951 helix: 1.34 (0.11), residues: 2226 sheet: 1.29 (0.28), residues: 339 loop : 0.04 (0.16), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 615 time to evaluate : 3.732 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 34 residues processed: 668 average time/residue: 1.4491 time to fit residues: 1155.9255 Evaluate side-chains 602 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 568 time to evaluate : 3.686 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 32 residues processed: 4 average time/residue: 0.7010 time to fit residues: 8.7707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 335 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 166 optimal weight: 0.1980 chunk 102 optimal weight: 4.9990 chunk 202 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 311 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 189 optimal weight: 0.6980 chunk 231 optimal weight: 0.0030 chunk 360 optimal weight: 2.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 GLN W 15 ASN X 68 GLN X 128 GLN X 175 GLN ** X 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 611 GLN X 646 ASN O 133 ASN O 404 GLN O 564 GLN P 37 HIS P 625 GLN P 683 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.0804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 32206 Z= 0.170 Angle : 0.521 8.673 43797 Z= 0.266 Chirality : 0.039 0.146 5145 Planarity : 0.005 0.076 5435 Dihedral : 6.582 89.375 4412 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.60 % Favored : 98.28 % Rotamer Outliers : 3.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.67 (0.13), residues: 3951 helix: 1.67 (0.11), residues: 2227 sheet: 1.43 (0.27), residues: 340 loop : 0.21 (0.16), residues: 1384 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 582 time to evaluate : 3.831 Fit side-chains outliers start: 126 outliers final: 53 residues processed: 652 average time/residue: 1.4536 time to fit residues: 1122.5514 Evaluate side-chains 615 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 562 time to evaluate : 4.005 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 33 residues processed: 22 average time/residue: 0.3856 time to fit residues: 19.1715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 300 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 361 optimal weight: 1.9990 chunk 390 optimal weight: 3.9990 chunk 321 optimal weight: 0.4980 chunk 358 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 289 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 GLN X 68 GLN X 128 GLN X 175 GLN X 499 ASN X 646 ASN O 133 ASN O 404 GLN O 564 GLN O 569 ASN O 884 GLN P 37 HIS P 339 GLN P 625 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 32206 Z= 0.245 Angle : 0.572 10.112 43797 Z= 0.294 Chirality : 0.042 0.148 5145 Planarity : 0.005 0.064 5435 Dihedral : 6.511 88.967 4412 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.88 % Favored : 98.05 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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 (0.13), residues: 3951 helix: 1.63 (0.11), residues: 2227 sheet: 1.21 (0.27), residues: 341 loop : 0.22 (0.16), residues: 1383 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 582 time to evaluate : 3.385 Fit side-chains outliers start: 119 outliers final: 55 residues processed: 652 average time/residue: 1.4746 time to fit residues: 1141.2260 Evaluate side-chains 623 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 568 time to evaluate : 3.951 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 33 residues processed: 23 average time/residue: 0.5088 time to fit residues: 23.3331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 356 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 242 optimal weight: 0.4980 chunk 362 optimal weight: 2.9990 chunk 383 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 343 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 394 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 GLN X 128 GLN X 175 GLN X 350 HIS ** X 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN O 133 ASN O 564 GLN P 37 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 32206 Z= 0.304 Angle : 0.611 10.653 43797 Z= 0.314 Chirality : 0.044 0.171 5145 Planarity : 0.005 0.061 5435 Dihedral : 6.501 87.479 4412 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.98 % Favored : 97.97 % Rotamer Outliers : 3.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.47 (0.13), residues: 3951 helix: 1.55 (0.11), residues: 2215 sheet: 1.01 (0.27), residues: 349 loop : 0.16 (0.16), residues: 1387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 577 time to evaluate : 3.538 Fit side-chains outliers start: 119 outliers final: 60 residues processed: 653 average time/residue: 1.5524 time to fit residues: 1202.8573 Evaluate side-chains 619 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 559 time to evaluate : 4.352 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 39 residues processed: 22 average time/residue: 0.4738 time to fit residues: 21.9964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 319 optimal weight: 1.9990 chunk 217 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 285 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 327 optimal weight: 0.0470 chunk 265 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 344 optimal weight: 0.0370 chunk 96 optimal weight: 1.9990 overall best weight: 0.5556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 ASN ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 GLN ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 GLN X 128 GLN X 175 GLN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN O 133 ASN O 404 GLN O 564 GLN O 880 ASN P 37 HIS P 83 GLN P 124 GLN P 569 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 32206 Z= 0.179 Angle : 0.525 9.281 43797 Z= 0.268 Chirality : 0.040 0.136 5145 Planarity : 0.005 0.058 5435 Dihedral : 6.152 86.544 4412 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.78 % Favored : 98.17 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.71 (0.13), residues: 3951 helix: 1.72 (0.11), residues: 2218 sheet: 1.07 (0.27), residues: 347 loop : 0.31 (0.16), residues: 1386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 588 time to evaluate : 4.062 Fit side-chains outliers start: 99 outliers final: 53 residues processed: 650 average time/residue: 1.5496 time to fit residues: 1191.1268 Evaluate side-chains 628 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 575 time to evaluate : 3.680 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 38 residues processed: 17 average time/residue: 0.6216 time to fit residues: 20.4455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 129 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 384 optimal weight: 3.9990 chunk 318 optimal weight: 3.9990 chunk 177 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 127 optimal weight: 0.3980 chunk 201 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 236 ASN ** K 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 58 HIS ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 422 ASN W 18 GLN X 68 GLN X 128 GLN X 175 GLN X 225 GLN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 611 GLN X 646 ASN O 404 GLN P 37 HIS P 83 GLN P 569 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 32206 Z= 0.203 Angle : 0.543 10.418 43797 Z= 0.277 Chirality : 0.040 0.139 5145 Planarity : 0.005 0.056 5435 Dihedral : 6.102 86.819 4412 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.85 % Favored : 98.12 % Rotamer Outliers : 2.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.72 (0.13), residues: 3951 helix: 1.73 (0.11), residues: 2215 sheet: 1.09 (0.27), residues: 347 loop : 0.32 (0.16), residues: 1389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 576 time to evaluate : 3.607 Fit side-chains outliers start: 95 outliers final: 57 residues processed: 632 average time/residue: 1.5734 time to fit residues: 1182.3035 Evaluate side-chains 625 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 568 time to evaluate : 4.108 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 40 residues processed: 19 average time/residue: 0.8077 time to fit residues: 26.2824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 370 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 218 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 323 optimal weight: 1.9990 chunk 214 optimal weight: 0.8980 chunk 382 optimal weight: 5.9990 chunk 239 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 58 HIS L 394 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 GLN X 128 GLN X 175 GLN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN O 203 GLN O 564 GLN P 37 HIS P 83 GLN P 124 GLN P 569 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 32206 Z= 0.229 Angle : 0.564 11.425 43797 Z= 0.287 Chirality : 0.041 0.150 5145 Planarity : 0.005 0.056 5435 Dihedral : 6.090 86.166 4412 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.10 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.68 (0.13), residues: 3951 helix: 1.70 (0.11), residues: 2215 sheet: 1.08 (0.27), residues: 347 loop : 0.29 (0.16), residues: 1389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 573 time to evaluate : 4.042 Fit side-chains outliers start: 96 outliers final: 60 residues processed: 633 average time/residue: 1.5791 time to fit residues: 1194.2272 Evaluate side-chains 631 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 571 time to evaluate : 3.820 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 41 residues processed: 21 average time/residue: 0.7312 time to fit residues: 26.5407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 236 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 243 optimal weight: 0.8980 chunk 260 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 300 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 233 GLN K 389 ASN L 58 HIS L 394 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN X 68 GLN X 128 GLN X 175 GLN X 225 GLN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN O 564 GLN P 37 HIS P 83 GLN P 124 GLN P 569 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 32206 Z= 0.216 Angle : 0.556 11.636 43797 Z= 0.283 Chirality : 0.041 0.143 5145 Planarity : 0.005 0.055 5435 Dihedral : 5.986 85.287 4412 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.88 % Favored : 98.10 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.71 (0.13), residues: 3951 helix: 1.72 (0.11), residues: 2216 sheet: 1.09 (0.27), residues: 347 loop : 0.32 (0.16), residues: 1388 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 575 time to evaluate : 3.750 Fit side-chains outliers start: 93 outliers final: 57 residues processed: 633 average time/residue: 1.5122 time to fit residues: 1132.6344 Evaluate side-chains 627 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 570 time to evaluate : 3.923 Switching outliers to nearest non-outliers outliers start: 57 outliers final: 43 residues processed: 16 average time/residue: 0.5684 time to fit residues: 18.3171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 348 optimal weight: 0.0030 chunk 366 optimal weight: 3.9990 chunk 334 optimal weight: 0.9990 chunk 356 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 155 optimal weight: 0.4980 chunk 279 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 322 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 chunk 355 optimal weight: 0.8980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 58 HIS ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN X 68 GLN X 128 GLN X 175 GLN X 225 GLN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN O 564 GLN P 37 HIS P 83 GLN P 124 GLN P 569 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 32206 Z= 0.199 Angle : 0.548 12.839 43797 Z= 0.278 Chirality : 0.040 0.141 5145 Planarity : 0.005 0.055 5435 Dihedral : 5.896 86.354 4412 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.80 % Favored : 98.17 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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 (0.13), residues: 3951 helix: 1.77 (0.11), residues: 2204 sheet: 1.13 (0.27), residues: 343 loop : 0.34 (0.16), residues: 1404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 574 time to evaluate : 4.035 Fit side-chains outliers start: 62 outliers final: 49 residues processed: 621 average time/residue: 1.6568 time to fit residues: 1229.3141 Evaluate side-chains 620 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 571 time to evaluate : 3.661 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 40 residues processed: 11 average time/residue: 0.7443 time to fit residues: 15.6988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 234 optimal weight: 7.9990 chunk 377 optimal weight: 0.7980 chunk 230 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 262 optimal weight: 0.9980 chunk 395 optimal weight: 0.1980 chunk 364 optimal weight: 4.9990 chunk 314 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 58 HIS L 394 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 68 GLN X 128 GLN X 175 GLN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 611 GLN X 646 ASN O 404 GLN P 37 HIS P 83 GLN P 124 GLN P 569 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 32206 Z= 0.213 Angle : 0.565 13.186 43797 Z= 0.286 Chirality : 0.041 0.143 5145 Planarity : 0.005 0.080 5435 Dihedral : 5.900 85.004 4412 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.15 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.74 (0.13), residues: 3951 helix: 1.75 (0.11), residues: 2204 sheet: 1.12 (0.27), residues: 343 loop : 0.35 (0.16), residues: 1404 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7902 Ramachandran restraints generated. 3951 Oldfield, 0 Emsley, 3951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 571 time to evaluate : 3.699 Fit side-chains outliers start: 59 outliers final: 48 residues processed: 617 average time/residue: 1.6036 time to fit residues: 1188.5552 Evaluate side-chains 615 residues out of total 3365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 567 time to evaluate : 3.783 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 40 residues processed: 10 average time/residue: 0.6169 time to fit residues: 14.4589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 250 optimal weight: 3.9990 chunk 335 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 290 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 315 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 323 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 389 ASN L 58 HIS L 394 GLN ** H 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 18 GLN X 68 GLN X 128 GLN X 175 GLN ** X 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 646 ASN O 404 GLN P 37 HIS P 83 GLN P 124 GLN P 569 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.082934 restraints weight = 82209.608| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.52 r_work: 0.2708 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3390 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3390 r_free = 0.3390 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3390 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 32206 Z= 0.241 Angle : 0.588 13.845 43797 Z= 0.297 Chirality : 0.041 0.146 5145 Planarity : 0.005 0.076 5435 Dihedral : 5.941 84.196 4412 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.90 % Favored : 98.07 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.12 % 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: 1.69 (0.13), residues: 3951 helix: 1.72 (0.11), residues: 2198 sheet: 1.16 (0.27), residues: 335 loop : 0.28 (0.16), residues: 1418 =============================================================================== Job complete usr+sys time: 18477.86 seconds wall clock time: 331 minutes 11.54 seconds (19871.54 seconds total)