Starting phenix.real_space_refine (version: dev) on Wed Feb 22 20:10:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rja_24482/02_2023/7rja_24482_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rja_24482/02_2023/7rja_24482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rja_24482/02_2023/7rja_24482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rja_24482/02_2023/7rja_24482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rja_24482/02_2023/7rja_24482_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rja_24482/02_2023/7rja_24482_trim_updated.pdb" } resolution = 3.0 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= 0.001 sd= 0.180 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 Process input model Symmetric amino acids flipped Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 282": not complete - not flipped Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 98": "OE1" <-> "OE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 340": "OD1" <-> "OD2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 372": "OD1" <-> "OD2" Residue "J PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 139": "OE1" <-> "OE2" Residue "J ASP 178": "OD1" <-> "OD2" Residue "J GLU 232": "OE1" <-> "OE2" Residue "J TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 252": "OE1" <-> "OE2" Residue "J PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 374": "OE1" <-> "OE2" Residue "J ASP 399": "OD1" <-> "OD2" Residue "T TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 217": "OD1" <-> "OD2" Residue "N ASP 67": "OD1" <-> "OD2" Residue "N ASP 89": "OD1" <-> "OD2" Residue "N GLU 111": "OE1" <-> "OE2" Residue "N ASP 116": "OD1" <-> "OD2" Residue "N ASP 170": "OD1" <-> "OD2" Residue "N ASP 231": "OD1" <-> "OD2" Residue "N GLU 243": "OE1" <-> "OE2" Residue "N ASP 245": "OD1" <-> "OD2" Residue "N ASP 246": "OD1" <-> "OD2" Residue "N ARG 282": not complete - not flipped Residue "Q TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 91": "OE1" <-> "OE2" Residue "Q TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q GLU 109": "OE1" <-> "OE2" Residue "Q PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P GLU 88": "OE1" <-> "OE2" Residue "R TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "L GLU 190": "OE1" <-> "OE2" Residue "L ASP 250": "OD1" <-> "OD2" Residue "L TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 330": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 57452 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6364 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 8, 'TRANS': 407} Chain: "K" Number of atoms: 6146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6146 Classifications: {'peptide': 383} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3736 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "F" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1399 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1148 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 639 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "C" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1740 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 10, 'TRANS': 170} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 209 Chain: "B" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5392 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 345} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 6364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 6364 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 8, 'TRANS': 407} Chain: "T" Number of atoms: 6146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 6146 Classifications: {'peptide': 383} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 23, 'TRANS': 359} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "N" Number of atoms: 3736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3736 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "P" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1399 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "R" Number of atoms: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1148 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 639 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "M" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1740 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 10, 'TRANS': 170} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 489 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 209 Chain: "L" Number of atoms: 5392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 5392 Classifications: {'peptide': 364} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 345} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'HEM': 2, 'U10': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-4': 1, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 137 Unusual residues: {'HEM': 2, 'U10': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-4': 1, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 60 Chain: "N" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.69, per 1000 atoms: 0.38 Number of scatterers: 57452 At special positions: 0 Unit cell: (119.48, 132.87, 158.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 86 16.00 O 5482 8.00 N 4890 7.00 C 18950 6.00 H 28034 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS H 89 " - pdb=" SG CYS H 111 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 111 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 37.07 Conformation dependent library (CDL) restraints added in 3.6 seconds 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7152 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 159 helices and 12 sheets defined 51.6% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 63 through 72 Processing helix chain 'A' and resid 98 through 113 removed outlier: 4.739A pdb=" N THR A 102 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 124 through 138 Processing helix chain 'A' and resid 142 through 154 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 168 through 173 removed outlier: 3.818A pdb=" N GLU A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASN A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 173' Processing helix chain 'A' and resid 176 through 186 Processing helix chain 'A' and resid 189 through 191 No H-bonds generated for 'chain 'A' and resid 189 through 191' Processing helix chain 'A' and resid 202 through 210 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.031A pdb=" N TYR A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 280 removed outlier: 3.912A pdb=" N LYS A 280 " --> pdb=" O THR A 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 324 through 339 removed outlier: 3.537A pdb=" N LEU A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 339 " --> pdb=" O TRP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 Processing helix chain 'A' and resid 365 through 378 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 427 through 434 removed outlier: 3.623A pdb=" N MET A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 6 No H-bonds generated for 'chain 'K' and resid 3 through 6' Processing helix chain 'K' and resid 8 through 17 Processing helix chain 'K' and resid 29 through 51 removed outlier: 3.956A pdb=" N GLY K 33 " --> pdb=" O TRP K 30 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN K 43 " --> pdb=" O LEU K 40 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N SER K 46 " --> pdb=" O GLN K 43 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA K 51 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 70 Processing helix chain 'K' and resid 75 through 102 removed outlier: 3.605A pdb=" N ALA K 86 " --> pdb=" O HIS K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 135 removed outlier: 5.444A pdb=" N MET K 112 " --> pdb=" O PRO K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 153 removed outlier: 4.074A pdb=" N ALA K 153 " --> pdb=" O ASN K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 166 removed outlier: 3.502A pdb=" N ILE K 161 " --> pdb=" O GLY K 158 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL K 162 " --> pdb=" O ASN K 159 " (cutoff:3.500A) Proline residue: K 163 - end of helix removed outlier: 3.512A pdb=" N TRP K 166 " --> pdb=" O PRO K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 204 Proline residue: K 187 - end of helix removed outlier: 4.145A pdb=" N HIS K 204 " --> pdb=" O ALA K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 244 Processing helix chain 'K' and resid 254 through 257 Processing helix chain 'K' and resid 273 through 284 Proline residue: K 277 - end of helix Processing helix chain 'K' and resid 288 through 308 removed outlier: 5.110A pdb=" N LEU K 302 " --> pdb=" O ALA K 298 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU K 303 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Proline residue: K 306 - end of helix Processing helix chain 'K' and resid 320 through 341 removed outlier: 3.761A pdb=" N GLN K 341 " --> pdb=" O GLY K 337 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 382 removed outlier: 4.149A pdb=" N GLN K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR K 363 " --> pdb=" O TYR K 359 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL K 367 " --> pdb=" O TYR K 363 " (cutoff:3.500A) Proline residue: K 368 - end of helix Processing helix chain 'D' and resid 45 through 48 No H-bonds generated for 'chain 'D' and resid 45 through 48' Processing helix chain 'D' and resid 68 through 84 removed outlier: 4.278A pdb=" N ALA D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 103 through 111 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 169 through 176 Processing helix chain 'D' and resid 225 through 240 Processing helix chain 'D' and resid 244 through 277 Proline residue: D 275 - end of helix Processing helix chain 'G' and resid 5 through 16 Processing helix chain 'G' and resid 19 through 35 Proline residue: G 27 - end of helix Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'G' and resid 54 through 62 Processing helix chain 'G' and resid 65 through 84 Processing helix chain 'G' and resid 104 through 121 Processing helix chain 'F' and resid 41 through 81 removed outlier: 3.645A pdb=" N VAL F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LEU F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR F 59 " --> pdb=" O ASN F 55 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 60 " --> pdb=" O GLN F 56 " (cutoff:3.500A) Proline residue: F 63 - end of helix Processing helix chain 'F' and resid 87 through 92 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 77 through 98 Proline residue: H 81 - end of helix Processing helix chain 'H' and resid 102 through 104 No H-bonds generated for 'chain 'H' and resid 102 through 104' Processing helix chain 'H' and resid 112 through 132 removed outlier: 3.890A pdb=" N CYS H 125 " --> pdb=" O CYS H 121 " (cutoff:3.500A) Proline residue: H 128 - end of helix removed outlier: 4.686A pdb=" N PHE H 131 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASN H 132 " --> pdb=" O PRO H 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 41 removed outlier: 3.711A pdb=" N PHE I 24 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N GLU I 39 " --> pdb=" O ASN I 35 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU I 40 " --> pdb=" O LYS I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 54 removed outlier: 5.344A pdb=" N GLY I 52 " --> pdb=" O LYS I 48 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 79 removed outlier: 3.570A pdb=" N ARG C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE C 79 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 140 through 143 No H-bonds generated for 'chain 'C' and resid 140 through 143' Processing helix chain 'B' and resid 47 through 54 Processing helix chain 'B' and resid 64 through 74 removed outlier: 3.741A pdb=" N ARG B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 109 removed outlier: 3.945A pdb=" N LEU B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) Proline residue: B 99 - end of helix removed outlier: 4.283A pdb=" N VAL B 102 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 124 through 135 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 169 through 176 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 205 through 208 Processing helix chain 'B' and resid 248 through 261 removed outlier: 4.462A pdb=" N GLY B 252 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 254 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU B 255 " --> pdb=" O GLY B 252 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 258 " --> pdb=" O GLU B 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 259 " --> pdb=" O VAL B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 275 No H-bonds generated for 'chain 'B' and resid 273 through 275' Processing helix chain 'B' and resid 300 through 314 removed outlier: 3.692A pdb=" N GLN B 305 " --> pdb=" O SER B 301 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 336 removed outlier: 4.667A pdb=" N LYS B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing helix chain 'J' and resid 58 through 60 No H-bonds generated for 'chain 'J' and resid 58 through 60' Processing helix chain 'J' and resid 63 through 72 Processing helix chain 'J' and resid 101 through 113 Processing helix chain 'J' and resid 115 through 120 Processing helix chain 'J' and resid 125 through 138 Processing helix chain 'J' and resid 142 through 154 Processing helix chain 'J' and resid 159 through 161 No H-bonds generated for 'chain 'J' and resid 159 through 161' Processing helix chain 'J' and resid 171 through 173 No H-bonds generated for 'chain 'J' and resid 171 through 173' Processing helix chain 'J' and resid 176 through 186 Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' Processing helix chain 'J' and resid 202 through 210 Processing helix chain 'J' and resid 259 through 267 Processing helix chain 'J' and resid 277 through 280 removed outlier: 4.081A pdb=" N LYS J 280 " --> pdb=" O THR J 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 277 through 280' Processing helix chain 'J' and resid 285 through 290 Processing helix chain 'J' and resid 324 through 339 removed outlier: 4.052A pdb=" N SER J 339 " --> pdb=" O TRP J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 362 Processing helix chain 'J' and resid 365 through 378 Processing helix chain 'J' and resid 385 through 393 Processing helix chain 'J' and resid 397 through 407 Processing helix chain 'J' and resid 421 through 423 No H-bonds generated for 'chain 'J' and resid 421 through 423' Processing helix chain 'J' and resid 427 through 434 removed outlier: 3.624A pdb=" N MET J 434 " --> pdb=" O ASN J 430 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 6 No H-bonds generated for 'chain 'T' and resid 3 through 6' Processing helix chain 'T' and resid 8 through 17 Processing helix chain 'T' and resid 29 through 51 removed outlier: 3.860A pdb=" N GLY T 33 " --> pdb=" O TRP T 30 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN T 43 " --> pdb=" O LEU T 40 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER T 46 " --> pdb=" O GLN T 43 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA T 51 " --> pdb=" O VAL T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 61 through 70 Processing helix chain 'T' and resid 75 through 102 Processing helix chain 'T' and resid 108 through 135 removed outlier: 3.541A pdb=" N VAL T 111 " --> pdb=" O GLN T 108 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N MET T 112 " --> pdb=" O PRO T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 138 through 153 removed outlier: 4.054A pdb=" N ALA T 153 " --> pdb=" O ASN T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 157 through 166 removed outlier: 4.587A pdb=" N VAL T 162 " --> pdb=" O ASN T 159 " (cutoff:3.500A) Proline residue: T 163 - end of helix Processing helix chain 'T' and resid 173 through 202 Proline residue: T 187 - end of helix Processing helix chain 'T' and resid 227 through 245 Processing helix chain 'T' and resid 254 through 257 Processing helix chain 'T' and resid 273 through 284 Proline residue: T 277 - end of helix Processing helix chain 'T' and resid 288 through 308 removed outlier: 3.696A pdb=" N ILE T 299 " --> pdb=" O MET T 295 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU T 302 " --> pdb=" O ALA T 298 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU T 303 " --> pdb=" O ILE T 299 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER T 304 " --> pdb=" O LEU T 300 " (cutoff:3.500A) Proline residue: T 306 - end of helix Processing helix chain 'T' and resid 320 through 341 removed outlier: 3.829A pdb=" N GLN T 341 " --> pdb=" O GLY T 337 " (cutoff:3.500A) Processing helix chain 'T' and resid 346 through 382 removed outlier: 4.061A pdb=" N GLN T 350 " --> pdb=" O VAL T 346 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR T 363 " --> pdb=" O TYR T 359 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL T 367 " --> pdb=" O TYR T 363 " (cutoff:3.500A) Proline residue: T 368 - end of helix Processing helix chain 'N' and resid 45 through 48 No H-bonds generated for 'chain 'N' and resid 45 through 48' Processing helix chain 'N' and resid 68 through 84 removed outlier: 4.373A pdb=" N ALA N 83 " --> pdb=" O ARG N 79 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ALA N 84 " --> pdb=" O GLU N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 103 through 112 removed outlier: 3.543A pdb=" N GLU N 112 " --> pdb=" O ALA N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 143 through 150 Processing helix chain 'N' and resid 169 through 176 Processing helix chain 'N' and resid 225 through 240 Processing helix chain 'N' and resid 244 through 277 Proline residue: N 275 - end of helix Processing helix chain 'Q' and resid 5 through 16 Processing helix chain 'Q' and resid 19 through 35 Proline residue: Q 27 - end of helix Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 45 through 47 No H-bonds generated for 'chain 'Q' and resid 45 through 47' Processing helix chain 'Q' and resid 54 through 62 Processing helix chain 'Q' and resid 65 through 84 Processing helix chain 'Q' and resid 104 through 122 Processing helix chain 'P' and resid 32 through 34 No H-bonds generated for 'chain 'P' and resid 32 through 34' Processing helix chain 'P' and resid 41 through 81 removed outlier: 3.686A pdb=" N VAL P 46 " --> pdb=" O ALA P 42 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR P 49 " --> pdb=" O ALA P 45 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N TYR P 59 " --> pdb=" O ASN P 55 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL P 60 " --> pdb=" O GLN P 56 " (cutoff:3.500A) Proline residue: P 63 - end of helix Processing helix chain 'P' and resid 87 through 92 Processing helix chain 'R' and resid 65 through 74 Processing helix chain 'R' and resid 77 through 98 Proline residue: R 81 - end of helix Processing helix chain 'R' and resid 100 through 104 removed outlier: 4.355A pdb=" N GLU R 103 " --> pdb=" O PRO R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 133 removed outlier: 3.825A pdb=" N CYS R 125 " --> pdb=" O CYS R 121 " (cutoff:3.500A) Proline residue: R 128 - end of helix removed outlier: 4.544A pdb=" N PHE R 131 " --> pdb=" O ALA R 127 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN R 132 " --> pdb=" O PRO R 128 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 41 removed outlier: 3.501A pdb=" N PHE S 24 " --> pdb=" O PHE S 20 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU S 40 " --> pdb=" O LYS S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 54 removed outlier: 5.614A pdb=" N GLY S 52 " --> pdb=" O LYS S 48 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS S 53 " --> pdb=" O ASN S 49 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE S 54 " --> pdb=" O VAL S 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 78 removed outlier: 3.705A pdb=" N SER M 78 " --> pdb=" O ALA M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 88 Processing helix chain 'M' and resid 120 through 126 Processing helix chain 'M' and resid 140 through 143 No H-bonds generated for 'chain 'M' and resid 140 through 143' Processing helix chain 'L' and resid 47 through 54 Processing helix chain 'L' and resid 64 through 74 removed outlier: 3.766A pdb=" N ARG L 69 " --> pdb=" O LEU L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 109 removed outlier: 3.521A pdb=" N LEU L 98 " --> pdb=" O LYS L 95 " (cutoff:3.500A) Proline residue: L 99 - end of helix removed outlier: 4.267A pdb=" N VAL L 102 " --> pdb=" O PRO L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 121 Processing helix chain 'L' and resid 124 through 135 Processing helix chain 'L' and resid 138 through 150 Processing helix chain 'L' and resid 154 through 156 No H-bonds generated for 'chain 'L' and resid 154 through 156' Processing helix chain 'L' and resid 169 through 176 Processing helix chain 'L' and resid 182 through 184 No H-bonds generated for 'chain 'L' and resid 182 through 184' Processing helix chain 'L' and resid 194 through 203 Processing helix chain 'L' and resid 205 through 208 Processing helix chain 'L' and resid 248 through 261 removed outlier: 4.513A pdb=" N GLY L 252 " --> pdb=" O ALA L 249 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR L 254 " --> pdb=" O PHE L 251 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU L 255 " --> pdb=" O GLY L 252 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL L 256 " --> pdb=" O LYS L 253 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER L 258 " --> pdb=" O GLU L 255 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA L 259 " --> pdb=" O VAL L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 272 through 275 Processing helix chain 'L' and resid 300 through 314 removed outlier: 3.682A pdb=" N GLN L 305 " --> pdb=" O SER L 301 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS L 308 " --> pdb=" O ALA L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 319 through 336 removed outlier: 3.652A pdb=" N VAL L 326 " --> pdb=" O LEU L 322 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS L 327 " --> pdb=" O SER L 323 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA L 328 " --> pdb=" O GLU L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 373 No H-bonds generated for 'chain 'L' and resid 371 through 373' Processing sheet with id= A, first strand: chain 'A' and resid 23 through 25 removed outlier: 3.689A pdb=" N GLY A 198 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 45 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 232 through 234 removed outlier: 6.262A pdb=" N ILE A 415 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 114 through 116 Processing sheet with id= D, first strand: chain 'C' and resid 203 through 205 removed outlier: 3.752A pdb=" N GLU C 208 " --> pdb=" O THR C 205 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 18 through 22 removed outlier: 3.735A pdb=" N LYS B 18 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 233 removed outlier: 6.411A pdb=" N TYR B 359 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL B 232 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 361 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 23 through 25 removed outlier: 3.779A pdb=" N GLY J 198 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL J 45 " --> pdb=" O ALA J 94 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 232 through 234 removed outlier: 6.184A pdb=" N ILE J 415 " --> pdb=" O VAL J 233 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 114 through 117 removed outlier: 4.023A pdb=" N ARG N 126 " --> pdb=" O ASP N 117 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 203 through 205 removed outlier: 3.698A pdb=" N GLU M 208 " --> pdb=" O THR M 205 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 18 through 22 removed outlier: 3.740A pdb=" N LYS L 18 " --> pdb=" O ILE L 185 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 229 through 233 removed outlier: 6.439A pdb=" N TYR L 359 " --> pdb=" O ALA L 230 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL L 232 " --> pdb=" O TYR L 359 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA L 361 " --> pdb=" O VAL L 232 " (cutoff:3.500A) 1378 hydrogen bonds defined for protein. 3627 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: 18.26 Time building geometry restraints manager: 38.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.12: 28014 1.12 - 1.41: 12578 1.41 - 1.70: 17424 1.70 - 1.99: 140 1.99 - 2.27: 30 Bond restraints: 58186 Sorted by residual: bond pdb=" CAB HEC N 301 " pdb=" CBB HEC N 301 " ideal model delta sigma weight residual 1.544 1.331 0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CAB HEC D 301 " pdb=" CBB HEC D 301 " ideal model delta sigma weight residual 1.544 1.334 0.210 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C2D HEC D 301 " pdb=" C3D HEC D 301 " ideal model delta sigma weight residual 1.544 1.334 0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C2D HEC N 301 " pdb=" C3D HEC N 301 " ideal model delta sigma weight residual 1.544 1.335 0.209 2.00e-02 2.50e+03 1.10e+02 bond pdb=" CAC HEC D 301 " pdb=" CBC HEC D 301 " ideal model delta sigma weight residual 1.544 1.337 0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 58181 not shown) Histogram of bond angle deviations from ideal: 79.15 - 99.18: 39 99.18 - 119.21: 79428 119.21 - 139.24: 25397 139.24 - 159.27: 0 159.27 - 179.31: 12 Bond angle restraints: 104876 Sorted by residual: angle pdb=" S1 FES C 301 " pdb="FE1 FES C 301 " pdb=" S2 FES C 301 " ideal model delta sigma weight residual 104.33 86.63 17.70 1.20e+00 6.94e-01 2.18e+02 angle pdb=" S1 FES M 301 " pdb="FE1 FES M 301 " pdb=" S2 FES M 301 " ideal model delta sigma weight residual 104.33 86.63 17.70 1.20e+00 6.94e-01 2.17e+02 angle pdb=" S1 FES M 301 " pdb="FE2 FES M 301 " pdb=" S2 FES M 301 " ideal model delta sigma weight residual 104.33 88.17 16.16 1.14e+00 7.69e-01 2.01e+02 angle pdb=" S1 FES C 301 " pdb="FE2 FES C 301 " pdb=" S2 FES C 301 " ideal model delta sigma weight residual 104.33 88.18 16.15 1.14e+00 7.69e-01 2.01e+02 angle pdb="FE1 FES C 301 " pdb=" S2 FES C 301 " pdb="FE2 FES C 301 " ideal model delta sigma weight residual 75.66 89.77 -14.11 1.14e+00 7.69e-01 1.53e+02 ... (remaining 104871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 23080 35.97 - 71.94: 284 71.94 - 107.91: 62 107.91 - 143.89: 1 143.89 - 179.86: 3 Dihedral angle restraints: 23430 sinusoidal: 10174 harmonic: 13256 Sorted by residual: dihedral pdb=" CD ARG N 282 " pdb=" NE ARG N 282 " pdb=" CZ ARG N 282 " pdb=" NH1 ARG N 282 " ideal model delta sinusoidal sigma weight residual 0.00 -179.86 179.86 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" CD ARG D 282 " pdb=" NE ARG D 282 " pdb=" CZ ARG D 282 " pdb=" NH1 ARG D 282 " ideal model delta sinusoidal sigma weight residual 0.00 176.46 -176.46 1 1.00e+01 1.00e-02 1.92e+02 dihedral pdb=" C3M U10 T 403 " pdb=" C3 U10 T 403 " pdb=" O3 U10 T 403 " pdb=" C4 U10 T 403 " ideal model delta sinusoidal sigma weight residual 244.38 82.42 161.95 1 2.00e+01 2.50e-03 4.68e+01 ... (remaining 23427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 3032 0.035 - 0.069: 1145 0.069 - 0.104: 274 0.104 - 0.138: 109 0.138 - 0.173: 14 Chirality restraints: 4574 Sorted by residual: chirality pdb=" CA GLU H 88 " pdb=" N GLU H 88 " pdb=" C GLU H 88 " pdb=" CB GLU H 88 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA ILE B 244 " pdb=" N ILE B 244 " pdb=" C ILE B 244 " pdb=" CB ILE B 244 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" CA ILE B 294 " pdb=" N ILE B 294 " pdb=" C ILE B 294 " pdb=" CB ILE B 294 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 4571 not shown) Planarity restraints: 8846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS K 96 " 0.056 2.00e-02 2.50e+03 4.00e-02 3.59e+01 pdb=" CG HIS K 96 " -0.069 2.00e-02 2.50e+03 pdb=" ND1 HIS K 96 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS K 96 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 HIS K 96 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS K 96 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 HIS K 96 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS K 96 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 HIS K 96 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 184 " -0.014 2.00e-02 2.50e+03 2.57e-02 1.98e+01 pdb=" CG PHE K 184 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE K 184 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE K 184 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE K 184 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 184 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE K 184 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE K 184 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE K 184 " 0.005 2.00e-02 2.50e+03 pdb=" HE1 PHE K 184 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE K 184 " -0.004 2.00e-02 2.50e+03 pdb=" HZ PHE K 184 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE T 184 " 0.021 2.00e-02 2.50e+03 2.49e-02 1.85e+01 pdb=" CG PHE T 184 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE T 184 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE T 184 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE T 184 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE T 184 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE T 184 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE T 184 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE T 184 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE T 184 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE T 184 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE T 184 " -0.004 2.00e-02 2.50e+03 ... (remaining 8843 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 896 2.04 - 2.68: 89176 2.68 - 3.32: 175997 3.32 - 3.96: 223459 3.96 - 4.60: 353503 Nonbonded interactions: 843031 Sorted by model distance: nonbonded pdb=" HG1 THR T 382 " pdb="HD22 ASN Q 101 " model vdw 1.403 2.100 nonbonded pdb="HH21 ARG J 236 " pdb=" OE1 GLN P 22 " model vdw 1.452 1.850 nonbonded pdb="HE21 GLN T 383 " pdb=" OD1 ASN Q 101 " model vdw 1.467 1.850 nonbonded pdb="HH21 ARG D 165 " pdb=" O2A HEC D 301 " model vdw 1.510 1.850 nonbonded pdb=" HE1 TRP D 57 " pdb=" OD1 ASP D 170 " model vdw 1.519 1.850 ... (remaining 843026 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 'A' selection = chain 'J' } ncs_group { reference = chain 'B' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'P' } ncs_group { reference = chain 'G' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = chain 'R' } ncs_group { reference = chain 'I' selection = chain 'S' } ncs_group { reference = chain 'K' selection = chain 'T' } 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: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 S 86 5.16 5 C 18950 2.51 5 N 4890 2.21 5 O 5482 1.98 5 H 28034 0.53 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=1.00 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: 0.930 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: 0.650 Extract box with map and model: 8.610 Check model and map are aligned: 0.650 Process input model: 137.940 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Set scattering table: 0.380 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:9.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.213 30152 Z= 0.395 Angle : 0.655 17.702 41098 Z= 0.376 Chirality : 0.040 0.173 4574 Planarity : 0.004 0.050 5250 Dihedral : 13.443 179.857 10542 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3776 helix: 0.65 (0.12), residues: 1924 sheet: -0.60 (0.29), residues: 328 loop : -0.21 (0.17), residues: 1524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 548 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 546 time to evaluate : 3.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 547 average time/residue: 2.2962 time to fit residues: 1498.1450 Evaluate side-chains 412 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 410 time to evaluate : 3.447 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.6162 time to fit residues: 5.2865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 293 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 339 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN T 31 ASN T 202 HIS ** T 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.076 30152 Z= 0.428 Angle : 0.626 17.713 41098 Z= 0.308 Chirality : 0.042 0.161 4574 Planarity : 0.004 0.054 5250 Dihedral : 8.597 179.508 4168 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3776 helix: 0.70 (0.12), residues: 1932 sheet: -0.61 (0.29), residues: 308 loop : -0.34 (0.16), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 491 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 433 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 34 residues processed: 464 average time/residue: 2.2010 time to fit residues: 1245.5048 Evaluate side-chains 441 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 407 time to evaluate : 3.430 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 21 residues processed: 15 average time/residue: 1.2249 time to fit residues: 29.6808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 1.9990 chunk 105 optimal weight: 0.3980 chunk 282 optimal weight: 4.9990 chunk 231 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 340 optimal weight: 0.7980 chunk 367 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 337 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 381 HIS T 31 ASN T 202 HIS ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 30152 Z= 0.176 Angle : 0.537 13.654 41098 Z= 0.262 Chirality : 0.038 0.153 4574 Planarity : 0.003 0.052 5250 Dihedral : 7.955 179.495 4168 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3776 helix: 0.99 (0.12), residues: 1932 sheet: -0.51 (0.29), residues: 318 loop : -0.08 (0.17), residues: 1526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 485 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 445 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 24 residues processed: 470 average time/residue: 2.1052 time to fit residues: 1201.9077 Evaluate side-chains 433 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 409 time to evaluate : 3.422 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 6 average time/residue: 1.2498 time to fit residues: 14.5509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 30.0000 chunk 255 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 162 optimal weight: 0.9980 chunk 228 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 361 optimal weight: 0.2980 chunk 178 optimal weight: 2.9990 chunk 323 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN J 291 GLN T 31 ASN T 202 HIS T 383 GLN ** Q 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 30152 Z= 0.259 Angle : 0.544 16.216 41098 Z= 0.266 Chirality : 0.039 0.157 4574 Planarity : 0.003 0.052 5250 Dihedral : 7.800 179.795 4168 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.14), residues: 3776 helix: 1.09 (0.12), residues: 1930 sheet: -0.61 (0.29), residues: 324 loop : -0.06 (0.17), residues: 1522 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 484 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 440 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 464 average time/residue: 2.1603 time to fit residues: 1218.6249 Evaluate side-chains 436 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 407 time to evaluate : 3.454 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 12 average time/residue: 1.1481 time to fit residues: 23.5180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 269 optimal weight: 0.0470 chunk 149 optimal weight: 40.0000 chunk 308 optimal weight: 0.0050 chunk 249 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 324 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 34 GLN J 291 GLN T 31 ASN T 202 HIS ** T 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 30152 Z= 0.206 Angle : 0.521 11.075 41098 Z= 0.258 Chirality : 0.039 0.172 4574 Planarity : 0.003 0.049 5250 Dihedral : 7.647 179.690 4168 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.14), residues: 3776 helix: 1.22 (0.12), residues: 1930 sheet: -0.48 (0.29), residues: 318 loop : 0.00 (0.17), residues: 1528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 437 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 25 residues processed: 463 average time/residue: 2.2309 time to fit residues: 1264.3396 Evaluate side-chains 427 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 402 time to evaluate : 3.508 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 8 average time/residue: 1.1582 time to fit residues: 18.3690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 2.9990 chunk 325 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 361 optimal weight: 0.1980 chunk 300 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN C 34 GLN J 291 GLN T 202 HIS ** T 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 383 GLN Q 13 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 30152 Z= 0.293 Angle : 0.556 17.082 41098 Z= 0.269 Chirality : 0.039 0.155 4574 Planarity : 0.004 0.070 5250 Dihedral : 7.634 179.872 4168 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.14), residues: 3776 helix: 1.24 (0.12), residues: 1932 sheet: -0.60 (0.29), residues: 324 loop : -0.04 (0.17), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 480 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 429 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 30 residues processed: 454 average time/residue: 2.1275 time to fit residues: 1171.7311 Evaluate side-chains 443 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 413 time to evaluate : 3.448 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 20 residues processed: 14 average time/residue: 0.9767 time to fit residues: 24.0642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 264 optimal weight: 0.9980 chunk 204 optimal weight: 0.8980 chunk 304 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 360 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN C 34 GLN T 202 HIS ** T 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 47 GLN L 174 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 30152 Z= 0.260 Angle : 0.548 15.589 41098 Z= 0.268 Chirality : 0.039 0.153 4574 Planarity : 0.004 0.064 5250 Dihedral : 7.576 179.694 4168 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.14), residues: 3776 helix: 1.28 (0.12), residues: 1932 sheet: -0.55 (0.29), residues: 324 loop : 0.00 (0.17), residues: 1520 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 469 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 430 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 28 residues processed: 454 average time/residue: 2.1631 time to fit residues: 1200.6952 Evaluate side-chains 443 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 415 time to evaluate : 3.448 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 9 average time/residue: 0.8690 time to fit residues: 16.2994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 4.9990 chunk 143 optimal weight: 40.0000 chunk 215 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 229 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN C 34 GLN ** J 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 HIS ** T 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 30152 Z= 0.284 Angle : 0.557 13.324 41098 Z= 0.272 Chirality : 0.039 0.154 4574 Planarity : 0.004 0.058 5250 Dihedral : 7.488 178.180 4168 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.14), residues: 3776 helix: 1.28 (0.12), residues: 1936 sheet: -0.57 (0.29), residues: 324 loop : -0.03 (0.17), residues: 1516 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 464 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 420 time to evaluate : 3.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 448 average time/residue: 2.1802 time to fit residues: 1213.0286 Evaluate side-chains 437 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 408 time to evaluate : 4.050 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 10 average time/residue: 1.2930 time to fit residues: 22.5239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 10.0000 chunk 345 optimal weight: 1.9990 chunk 315 optimal weight: 3.9990 chunk 335 optimal weight: 50.0000 chunk 202 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 chunk 263 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 303 optimal weight: 0.0170 chunk 317 optimal weight: 0.9990 chunk 334 optimal weight: 8.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 GLN ** J 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 HIS ** T 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 383 GLN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 84 HIS L 174 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 30152 Z= 0.313 Angle : 0.573 15.674 41098 Z= 0.279 Chirality : 0.040 0.170 4574 Planarity : 0.004 0.056 5250 Dihedral : 7.459 177.944 4168 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.14), residues: 3776 helix: 1.26 (0.12), residues: 1934 sheet: -0.59 (0.29), residues: 324 loop : -0.07 (0.17), residues: 1518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 426 time to evaluate : 3.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 24 residues processed: 448 average time/residue: 2.1743 time to fit residues: 1182.5941 Evaluate side-chains 439 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 415 time to evaluate : 3.430 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 6 average time/residue: 0.6277 time to fit residues: 10.7384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 1.9990 chunk 355 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 246 optimal weight: 1.9990 chunk 372 optimal weight: 2.9990 chunk 342 optimal weight: 3.9990 chunk 296 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN C 34 GLN ** J 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 HIS ** T 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 30152 Z= 0.309 Angle : 0.573 16.797 41098 Z= 0.280 Chirality : 0.040 0.199 4574 Planarity : 0.004 0.125 5250 Dihedral : 7.430 178.323 4168 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3776 helix: 1.24 (0.12), residues: 1934 sheet: -0.60 (0.29), residues: 324 loop : -0.09 (0.17), residues: 1518 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Residue ALA 112 is missing expected H atoms. Skipping. Residue LYS 124 is missing expected H atoms. Skipping. Residue LYS 36 is missing expected H atoms. Skipping. Residue TYR 43 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue TYR 32 is missing expected H atoms. Skipping. Residue MET 88 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue VAL 91 is missing expected H atoms. Skipping. Residue VAL 93 is missing expected H atoms. Skipping. Residue LYS 94 is missing expected H atoms. Skipping. Residue LEU 95 is missing expected H atoms. Skipping. Residue ILE 98 is missing expected H atoms. Skipping. Residue LYS 102 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue ILE 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue LYS 107 is missing expected H atoms. Skipping. Residue LYS 111 is missing expected H atoms. Skipping. Residue VAL 113 is missing expected H atoms. Skipping. Residue ILE 115 is missing expected H atoms. Skipping. Residue THR 119 is missing expected H atoms. Skipping. Residue ILE 123 is missing expected H atoms. Skipping. Residue VAL 129 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue THR 133 is missing expected H atoms. Skipping. Residue LEU 134 is missing expected H atoms. Skipping. Residue VAL 144 is missing expected H atoms. Skipping. Residue LYS 145 is missing expected H atoms. Skipping. Residue LYS 146 is missing expected H atoms. Skipping. Residue MET 152 is missing expected H atoms. Skipping. Residue LEU 153 is missing expected H atoms. Skipping. Residue ILE 155 is missing expected H atoms. Skipping. Residue THR 157 is missing expected H atoms. Skipping. Residue LEU 159 is missing expected H atoms. Skipping. Residue VAL 162 is missing expected H atoms. Skipping. Residue ILE 164 is missing expected H atoms. Skipping. Residue SER 180 is missing expected H atoms. Skipping. Residue TYR 182 is missing expected H atoms. Skipping. Residue ILE 184 is missing expected H atoms. Skipping. Residue SER 185 is missing expected H atoms. Skipping. Residue ILE 188 is missing expected H atoms. Skipping. Residue LYS 190 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue LEU 197 is missing expected H atoms. Skipping. Residue ILE 199 is missing expected H atoms. Skipping. Residue TYR 202 is missing expected H atoms. Skipping. Residue THR 205 is missing expected H atoms. Skipping. Residue THR 209 is missing expected H atoms. Skipping. Residue SER 214 is missing expected H atoms. Skipping. Residue LYS 218 is missing expected H atoms. Skipping. Residue LEU 220 is missing expected H atoms. Skipping. Evaluate side-chains 453 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 426 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 24 residues processed: 445 average time/residue: 2.2438 time to fit residues: 1215.8619 Evaluate side-chains 430 residues out of total 3212 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 406 time to evaluate : 3.489 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 6 average time/residue: 0.6605 time to fit residues: 11.0230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 273 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 305 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN I 49 ASN C 34 GLN J 134 GLN J 156 GLN ** J 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 202 HIS ** T 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 383 GLN Q 13 ASN Q 30 GLN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 174 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096947 restraints weight = 120339.538| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.42 r_work: 0.3003 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 30152 Z= 0.180 Angle : 0.535 14.308 41098 Z= 0.262 Chirality : 0.039 0.172 4574 Planarity : 0.004 0.079 5250 Dihedral : 7.303 178.802 4168 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.14), residues: 3776 helix: 1.39 (0.12), residues: 1932 sheet: -0.43 (0.29), residues: 318 loop : 0.05 (0.17), residues: 1526 =============================================================================== Job complete usr+sys time: 17577.48 seconds wall clock time: 302 minutes 54.11 seconds (18174.11 seconds total)