Starting phenix.real_space_refine on Mon Mar 25 20:37:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywc_6852/03_2024/5ywc_6852_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywc_6852/03_2024/5ywc_6852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywc_6852/03_2024/5ywc_6852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywc_6852/03_2024/5ywc_6852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywc_6852/03_2024/5ywc_6852_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ywc_6852/03_2024/5ywc_6852_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 272 5.16 5 C 33148 2.51 5 N 8672 2.21 5 O 8984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "B ARG 486": "NH1" <-> "NH2" Residue "B ARG 504": "NH1" <-> "NH2" Residue "B ARG 521": "NH1" <-> "NH2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 534": "NH1" <-> "NH2" Residue "B ARG 598": "NH1" <-> "NH2" Residue "B ARG 620": "NH1" <-> "NH2" Residue "B ARG 702": "NH1" <-> "NH2" Residue "B ARG 705": "NH1" <-> "NH2" Residue "B ARG 826": "NH1" <-> "NH2" Residue "B ARG 835": "NH1" <-> "NH2" Residue "B ARG 878": "NH1" <-> "NH2" Residue "B ARG 882": "NH1" <-> "NH2" Residue "B ARG 919": "NH1" <-> "NH2" Residue "B ARG 1099": "NH1" <-> "NH2" Residue "B ARG 1111": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "B ARG 1183": "NH1" <-> "NH2" Residue "B ARG 1218": "NH1" <-> "NH2" Residue "B ARG 1274": "NH1" <-> "NH2" Residue "B ARG 1300": "NH1" <-> "NH2" Residue "B ARG 1353": "NH1" <-> "NH2" Residue "B ARG 1394": "NH1" <-> "NH2" Residue "B ARG 1402": "NH1" <-> "NH2" Residue "B ARG 1421": "NH1" <-> "NH2" Residue "B ARG 1487": "NH1" <-> "NH2" Residue "B ARG 1498": "NH1" <-> "NH2" Residue "B ARG 1531": "NH1" <-> "NH2" Residue "B ARG 1539": "NH1" <-> "NH2" Residue "B ARG 1554": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 258": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "D ARG 486": "NH1" <-> "NH2" Residue "D ARG 504": "NH1" <-> "NH2" Residue "D ARG 521": "NH1" <-> "NH2" Residue "D ARG 527": "NH1" <-> "NH2" Residue "D ARG 534": "NH1" <-> "NH2" Residue "D ARG 598": "NH1" <-> "NH2" Residue "D ARG 620": "NH1" <-> "NH2" Residue "D ARG 702": "NH1" <-> "NH2" Residue "D ARG 705": "NH1" <-> "NH2" Residue "D ARG 826": "NH1" <-> "NH2" Residue "D ARG 835": "NH1" <-> "NH2" Residue "D ARG 878": "NH1" <-> "NH2" Residue "D ARG 882": "NH1" <-> "NH2" Residue "D ARG 919": "NH1" <-> "NH2" Residue "D ARG 1099": "NH1" <-> "NH2" Residue "D ARG 1111": "NH1" <-> "NH2" Residue "D ARG 1145": "NH1" <-> "NH2" Residue "D ARG 1183": "NH1" <-> "NH2" Residue "D ARG 1218": "NH1" <-> "NH2" Residue "D ARG 1274": "NH1" <-> "NH2" Residue "D ARG 1300": "NH1" <-> "NH2" Residue "D ARG 1353": "NH1" <-> "NH2" Residue "D ARG 1394": "NH1" <-> "NH2" Residue "D ARG 1402": "NH1" <-> "NH2" Residue "D ARG 1421": "NH1" <-> "NH2" Residue "D ARG 1487": "NH1" <-> "NH2" Residue "D ARG 1498": "NH1" <-> "NH2" Residue "D ARG 1531": "NH1" <-> "NH2" Residue "D ARG 1539": "NH1" <-> "NH2" Residue "D ARG 1554": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 248": "NH1" <-> "NH2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "F ARG 486": "NH1" <-> "NH2" Residue "F ARG 504": "NH1" <-> "NH2" Residue "F ARG 521": "NH1" <-> "NH2" Residue "F ARG 527": "NH1" <-> "NH2" Residue "F ARG 534": "NH1" <-> "NH2" Residue "F ARG 598": "NH1" <-> "NH2" Residue "F ARG 620": "NH1" <-> "NH2" Residue "F ARG 702": "NH1" <-> "NH2" Residue "F ARG 705": "NH1" <-> "NH2" Residue "F ARG 826": "NH1" <-> "NH2" Residue "F ARG 835": "NH1" <-> "NH2" Residue "F ARG 878": "NH1" <-> "NH2" Residue "F ARG 882": "NH1" <-> "NH2" Residue "F ARG 919": "NH1" <-> "NH2" Residue "F ARG 1099": "NH1" <-> "NH2" Residue "F ARG 1111": "NH1" <-> "NH2" Residue "F ARG 1145": "NH1" <-> "NH2" Residue "F ARG 1183": "NH1" <-> "NH2" Residue "F ARG 1218": "NH1" <-> "NH2" Residue "F ARG 1274": "NH1" <-> "NH2" Residue "F ARG 1300": "NH1" <-> "NH2" Residue "F ARG 1353": "NH1" <-> "NH2" Residue "F ARG 1394": "NH1" <-> "NH2" Residue "F ARG 1402": "NH1" <-> "NH2" Residue "F ARG 1421": "NH1" <-> "NH2" Residue "F ARG 1487": "NH1" <-> "NH2" Residue "F ARG 1498": "NH1" <-> "NH2" Residue "F ARG 1531": "NH1" <-> "NH2" Residue "F ARG 1539": "NH1" <-> "NH2" Residue "F ARG 1554": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 248": "NH1" <-> "NH2" Residue "H ARG 258": "NH1" <-> "NH2" Residue "H ARG 265": "NH1" <-> "NH2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "H ARG 370": "NH1" <-> "NH2" Residue "H ARG 486": "NH1" <-> "NH2" Residue "H ARG 504": "NH1" <-> "NH2" Residue "H ARG 521": "NH1" <-> "NH2" Residue "H ARG 527": "NH1" <-> "NH2" Residue "H ARG 534": "NH1" <-> "NH2" Residue "H ARG 598": "NH1" <-> "NH2" Residue "H ARG 620": "NH1" <-> "NH2" Residue "H ARG 702": "NH1" <-> "NH2" Residue "H ARG 705": "NH1" <-> "NH2" Residue "H ARG 826": "NH1" <-> "NH2" Residue "H ARG 835": "NH1" <-> "NH2" Residue "H ARG 878": "NH1" <-> "NH2" Residue "H ARG 882": "NH1" <-> "NH2" Residue "H ARG 919": "NH1" <-> "NH2" Residue "H ARG 1099": "NH1" <-> "NH2" Residue "H ARG 1111": "NH1" <-> "NH2" Residue "H ARG 1145": "NH1" <-> "NH2" Residue "H ARG 1183": "NH1" <-> "NH2" Residue "H ARG 1218": "NH1" <-> "NH2" Residue "H ARG 1274": "NH1" <-> "NH2" Residue "H ARG 1300": "NH1" <-> "NH2" Residue "H ARG 1353": "NH1" <-> "NH2" Residue "H ARG 1394": "NH1" <-> "NH2" Residue "H ARG 1402": "NH1" <-> "NH2" Residue "H ARG 1421": "NH1" <-> "NH2" Residue "H ARG 1487": "NH1" <-> "NH2" Residue "H ARG 1498": "NH1" <-> "NH2" Residue "H ARG 1531": "NH1" <-> "NH2" Residue "H ARG 1539": "NH1" <-> "NH2" Residue "H ARG 1554": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 51108 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2463 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 10231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 10231 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 44, 'TRANS': 1277} Chain breaks: 10 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 151 Chain: "C" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2463 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 10231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 10231 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 44, 'TRANS': 1277} Chain breaks: 10 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 151 Chain: "E" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2463 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 10231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 10231 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 44, 'TRANS': 1277} Chain breaks: 10 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 151 Chain: "G" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2463 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "H" Number of atoms: 10231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1322, 10231 Classifications: {'peptide': 1322} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 44, 'TRANS': 1277} Chain breaks: 10 Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 273 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 151 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' MG': 2, 'ADP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 26.02, per 1000 atoms: 0.51 Number of scatterers: 51108 At special positions: 0 Unit cell: (197.285, 197.285, 145.59, 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) S 272 16.00 P 24 15.00 Mg 8 11.99 O 8984 8.00 N 8672 7.00 C 33148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " 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=0, symmetry=0 Time building additional restraints: 20.39 Conformation dependent library (CDL) restraints added in 9.2 seconds 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12432 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 212 helices and 28 sheets defined 58.5% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.40 Creating SS restraints... Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 97 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.076A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.360A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'B' and resid 25 through 51 Proline residue: B 35 - end of helix removed outlier: 3.941A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 71 through 95 Processing helix chain 'B' and resid 104 through 129 Proline residue: B 109 - end of helix removed outlier: 3.758A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 159 removed outlier: 3.855A pdb=" N TYR B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 192 Processing helix chain 'B' and resid 208 through 211 No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 224 through 229 removed outlier: 4.493A pdb=" N GLY B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 229' Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.732A pdb=" N ALA B 235 " --> pdb=" O TRP B 232 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS B 241 " --> pdb=" O LYS B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 259 through 275 Processing helix chain 'B' and resid 284 through 295 removed outlier: 3.600A pdb=" N TRP B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 328 Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 356 through 401 removed outlier: 3.764A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 414 through 503 Proline residue: B 436 - end of helix removed outlier: 3.829A pdb=" N ALA B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Proline residue: B 442 - end of helix removed outlier: 4.388A pdb=" N TYR B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 455 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL B 458 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix removed outlier: 3.800A pdb=" N ALA B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 512 removed outlier: 3.900A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 563 Proline residue: B 551 - end of helix Processing helix chain 'B' and resid 573 through 614 Proline residue: B 589 - end of helix removed outlier: 3.820A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 599 " --> pdb=" O SER B 595 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS B 602 " --> pdb=" O ARG B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 726 Processing helix chain 'B' and resid 784 through 789 Processing helix chain 'B' and resid 796 through 805 removed outlier: 3.688A pdb=" N LYS B 800 " --> pdb=" O LYS B 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 832 through 845 removed outlier: 3.689A pdb=" N GLN B 836 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 871 Processing helix chain 'B' and resid 894 through 896 No H-bonds generated for 'chain 'B' and resid 894 through 896' Processing helix chain 'B' and resid 914 through 919 Processing helix chain 'B' and resid 1001 through 1008 Processing helix chain 'B' and resid 1012 through 1038 Processing helix chain 'B' and resid 1061 through 1106 removed outlier: 3.575A pdb=" N SER B1073 " --> pdb=" O THR B1069 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE B1076 " --> pdb=" O CYS B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1134 Processing helix chain 'B' and resid 1136 through 1160 Processing helix chain 'B' and resid 1164 through 1166 No H-bonds generated for 'chain 'B' and resid 1164 through 1166' Processing helix chain 'B' and resid 1168 through 1209 removed outlier: 3.817A pdb=" N VAL B1184 " --> pdb=" O LYS B1180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) Proline residue: B1199 - end of helix Processing helix chain 'B' and resid 1211 through 1217 Processing helix chain 'B' and resid 1220 through 1273 removed outlier: 4.209A pdb=" N LEU B1272 " --> pdb=" O ILE B1268 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1319 removed outlier: 3.826A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN B1293 " --> pdb=" O LEU B1289 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN B1296 " --> pdb=" O SER B1292 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1393 Processing helix chain 'B' and resid 1415 through 1419 Processing helix chain 'B' and resid 1436 through 1440 Processing helix chain 'B' and resid 1448 through 1457 Processing helix chain 'B' and resid 1461 through 1465 Processing helix chain 'B' and resid 1484 through 1498 Processing helix chain 'B' and resid 1514 through 1527 removed outlier: 4.041A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1544 Processing helix chain 'C' and resid 54 through 57 No H-bonds generated for 'chain 'C' and resid 54 through 57' Processing helix chain 'C' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU C 63 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 97 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 removed outlier: 4.076A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.360A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'D' and resid 25 through 51 Proline residue: D 35 - end of helix removed outlier: 3.941A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 71 through 95 Processing helix chain 'D' and resid 104 through 129 Proline residue: D 109 - end of helix removed outlier: 3.758A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 159 removed outlier: 3.855A pdb=" N TYR D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 192 Processing helix chain 'D' and resid 208 through 211 No H-bonds generated for 'chain 'D' and resid 208 through 211' Processing helix chain 'D' and resid 224 through 229 removed outlier: 4.493A pdb=" N GLY D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 229' Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.732A pdb=" N ALA D 235 " --> pdb=" O TRP D 232 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS D 241 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 259 through 275 Processing helix chain 'D' and resid 284 through 295 removed outlier: 3.600A pdb=" N TRP D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 328 Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 356 through 401 removed outlier: 3.764A pdb=" N MET D 400 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 408 Processing helix chain 'D' and resid 414 through 503 Proline residue: D 436 - end of helix removed outlier: 3.829A pdb=" N ALA D 440 " --> pdb=" O PRO D 436 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) Proline residue: D 442 - end of helix removed outlier: 4.388A pdb=" N TYR D 454 " --> pdb=" O ILE D 450 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 455 " --> pdb=" O LEU D 451 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY D 463 " --> pdb=" O SER D 459 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix removed outlier: 3.800A pdb=" N ALA D 484 " --> pdb=" O LYS D 480 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 487 " --> pdb=" O GLN D 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 497 " --> pdb=" O ASN D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 512 removed outlier: 3.900A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 563 Proline residue: D 551 - end of helix Processing helix chain 'D' and resid 573 through 614 Proline residue: D 589 - end of helix removed outlier: 3.820A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 598 " --> pdb=" O SER D 594 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER D 599 " --> pdb=" O SER D 595 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS D 602 " --> pdb=" O ARG D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 719 through 726 Processing helix chain 'D' and resid 784 through 789 Processing helix chain 'D' and resid 796 through 805 removed outlier: 3.688A pdb=" N LYS D 800 " --> pdb=" O LYS D 796 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 814 Processing helix chain 'D' and resid 832 through 845 removed outlier: 3.689A pdb=" N GLN D 836 " --> pdb=" O GLY D 832 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 871 Processing helix chain 'D' and resid 894 through 896 No H-bonds generated for 'chain 'D' and resid 894 through 896' Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 1001 through 1008 Processing helix chain 'D' and resid 1012 through 1038 Processing helix chain 'D' and resid 1061 through 1106 removed outlier: 3.575A pdb=" N SER D1073 " --> pdb=" O THR D1069 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE D1076 " --> pdb=" O CYS D1072 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1118 through 1134 Processing helix chain 'D' and resid 1136 through 1160 Processing helix chain 'D' and resid 1164 through 1166 No H-bonds generated for 'chain 'D' and resid 1164 through 1166' Processing helix chain 'D' and resid 1168 through 1209 removed outlier: 3.817A pdb=" N VAL D1184 " --> pdb=" O LYS D1180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D1185 " --> pdb=" O TYR D1181 " (cutoff:3.500A) Proline residue: D1199 - end of helix Processing helix chain 'D' and resid 1211 through 1217 Processing helix chain 'D' and resid 1220 through 1273 removed outlier: 4.209A pdb=" N LEU D1272 " --> pdb=" O ILE D1268 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1319 removed outlier: 3.826A pdb=" N LEU D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN D1293 " --> pdb=" O LEU D1289 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D1296 " --> pdb=" O SER D1292 " (cutoff:3.500A) Processing helix chain 'D' and resid 1385 through 1393 Processing helix chain 'D' and resid 1415 through 1419 Processing helix chain 'D' and resid 1436 through 1440 Processing helix chain 'D' and resid 1448 through 1457 Processing helix chain 'D' and resid 1461 through 1465 Processing helix chain 'D' and resid 1484 through 1498 Processing helix chain 'D' and resid 1514 through 1527 removed outlier: 4.041A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1540 through 1544 Processing helix chain 'E' and resid 54 through 57 No H-bonds generated for 'chain 'E' and resid 54 through 57' Processing helix chain 'E' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 97 Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 143 through 171 removed outlier: 4.076A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 266 through 269 removed outlier: 4.360A pdb=" N ASP E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 269' Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'F' and resid 25 through 51 Proline residue: F 35 - end of helix removed outlier: 3.941A pdb=" N PHE F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 71 through 95 Processing helix chain 'F' and resid 104 through 129 Proline residue: F 109 - end of helix removed outlier: 3.758A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 159 removed outlier: 3.855A pdb=" N TYR F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 192 Processing helix chain 'F' and resid 208 through 211 No H-bonds generated for 'chain 'F' and resid 208 through 211' Processing helix chain 'F' and resid 224 through 229 removed outlier: 4.493A pdb=" N GLY F 228 " --> pdb=" O LEU F 224 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 224 through 229' Processing helix chain 'F' and resid 231 through 242 removed outlier: 3.732A pdb=" N ALA F 235 " --> pdb=" O TRP F 232 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS F 241 " --> pdb=" O LYS F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 257 No H-bonds generated for 'chain 'F' and resid 255 through 257' Processing helix chain 'F' and resid 259 through 275 Processing helix chain 'F' and resid 284 through 295 removed outlier: 3.600A pdb=" N TRP F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 328 Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 356 through 401 removed outlier: 3.764A pdb=" N MET F 400 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 408 Processing helix chain 'F' and resid 414 through 503 Proline residue: F 436 - end of helix removed outlier: 3.829A pdb=" N ALA F 440 " --> pdb=" O PRO F 436 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET F 441 " --> pdb=" O ASN F 437 " (cutoff:3.500A) Proline residue: F 442 - end of helix removed outlier: 4.388A pdb=" N TYR F 454 " --> pdb=" O ILE F 450 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE F 455 " --> pdb=" O LEU F 451 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL F 458 " --> pdb=" O TYR F 454 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY F 463 " --> pdb=" O SER F 459 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix removed outlier: 3.800A pdb=" N ALA F 484 " --> pdb=" O LYS F 480 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER F 487 " --> pdb=" O GLN F 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS F 497 " --> pdb=" O ASN F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 512 removed outlier: 3.900A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 563 Proline residue: F 551 - end of helix Processing helix chain 'F' and resid 573 through 614 Proline residue: F 589 - end of helix removed outlier: 3.820A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG F 598 " --> pdb=" O SER F 594 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER F 599 " --> pdb=" O SER F 595 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS F 602 " --> pdb=" O ARG F 598 " (cutoff:3.500A) Processing helix chain 'F' and resid 719 through 726 Processing helix chain 'F' and resid 784 through 789 Processing helix chain 'F' and resid 796 through 805 removed outlier: 3.688A pdb=" N LYS F 800 " --> pdb=" O LYS F 796 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 814 Processing helix chain 'F' and resid 832 through 845 removed outlier: 3.689A pdb=" N GLN F 836 " --> pdb=" O GLY F 832 " (cutoff:3.500A) Processing helix chain 'F' and resid 862 through 871 Processing helix chain 'F' and resid 894 through 896 No H-bonds generated for 'chain 'F' and resid 894 through 896' Processing helix chain 'F' and resid 914 through 919 Processing helix chain 'F' and resid 1001 through 1008 Processing helix chain 'F' and resid 1012 through 1038 Processing helix chain 'F' and resid 1061 through 1106 removed outlier: 3.575A pdb=" N SER F1073 " --> pdb=" O THR F1069 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE F1076 " --> pdb=" O CYS F1072 " (cutoff:3.500A) Processing helix chain 'F' and resid 1110 through 1115 Processing helix chain 'F' and resid 1118 through 1134 Processing helix chain 'F' and resid 1136 through 1160 Processing helix chain 'F' and resid 1164 through 1166 No H-bonds generated for 'chain 'F' and resid 1164 through 1166' Processing helix chain 'F' and resid 1168 through 1209 removed outlier: 3.817A pdb=" N VAL F1184 " --> pdb=" O LYS F1180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA F1185 " --> pdb=" O TYR F1181 " (cutoff:3.500A) Proline residue: F1199 - end of helix Processing helix chain 'F' and resid 1211 through 1217 Processing helix chain 'F' and resid 1220 through 1273 removed outlier: 4.209A pdb=" N LEU F1272 " --> pdb=" O ILE F1268 " (cutoff:3.500A) Processing helix chain 'F' and resid 1279 through 1319 removed outlier: 3.826A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN F1293 " --> pdb=" O LEU F1289 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN F1296 " --> pdb=" O SER F1292 " (cutoff:3.500A) Processing helix chain 'F' and resid 1385 through 1393 Processing helix chain 'F' and resid 1415 through 1419 Processing helix chain 'F' and resid 1436 through 1440 Processing helix chain 'F' and resid 1448 through 1457 Processing helix chain 'F' and resid 1461 through 1465 Processing helix chain 'F' and resid 1484 through 1498 Processing helix chain 'F' and resid 1514 through 1527 removed outlier: 4.041A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1540 through 1544 Processing helix chain 'G' and resid 54 through 57 No H-bonds generated for 'chain 'G' and resid 54 through 57' Processing helix chain 'G' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU G 63 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 97 Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 143 through 171 removed outlier: 4.076A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 180 Processing helix chain 'G' and resid 266 through 269 removed outlier: 4.360A pdb=" N ASP G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 269' Processing helix chain 'G' and resid 346 through 355 Processing helix chain 'H' and resid 25 through 51 Proline residue: H 35 - end of helix removed outlier: 3.941A pdb=" N PHE H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 71 through 95 Processing helix chain 'H' and resid 104 through 129 Proline residue: H 109 - end of helix removed outlier: 3.758A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 159 removed outlier: 3.855A pdb=" N TYR H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 192 Processing helix chain 'H' and resid 208 through 211 No H-bonds generated for 'chain 'H' and resid 208 through 211' Processing helix chain 'H' and resid 224 through 229 removed outlier: 4.493A pdb=" N GLY H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 224 through 229' Processing helix chain 'H' and resid 231 through 242 removed outlier: 3.732A pdb=" N ALA H 235 " --> pdb=" O TRP H 232 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS H 241 " --> pdb=" O LYS H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 257 No H-bonds generated for 'chain 'H' and resid 255 through 257' Processing helix chain 'H' and resid 259 through 275 Processing helix chain 'H' and resid 284 through 295 removed outlier: 3.600A pdb=" N TRP H 288 " --> pdb=" O ALA H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 328 Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 356 through 401 removed outlier: 3.764A pdb=" N MET H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 408 Processing helix chain 'H' and resid 414 through 503 Proline residue: H 436 - end of helix removed outlier: 3.829A pdb=" N ALA H 440 " --> pdb=" O PRO H 436 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET H 441 " --> pdb=" O ASN H 437 " (cutoff:3.500A) Proline residue: H 442 - end of helix removed outlier: 4.388A pdb=" N TYR H 454 " --> pdb=" O ILE H 450 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE H 455 " --> pdb=" O LEU H 451 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N VAL H 458 " --> pdb=" O TYR H 454 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER H 459 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY H 463 " --> pdb=" O SER H 459 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix removed outlier: 3.800A pdb=" N ALA H 484 " --> pdb=" O LYS H 480 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER H 487 " --> pdb=" O GLN H 483 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS H 497 " --> pdb=" O ASN H 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 506 through 512 removed outlier: 3.900A pdb=" N TYR H 512 " --> pdb=" O LEU H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 563 Proline residue: H 551 - end of helix Processing helix chain 'H' and resid 573 through 614 Proline residue: H 589 - end of helix removed outlier: 3.820A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG H 598 " --> pdb=" O SER H 594 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER H 599 " --> pdb=" O SER H 595 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS H 602 " --> pdb=" O ARG H 598 " (cutoff:3.500A) Processing helix chain 'H' and resid 719 through 726 Processing helix chain 'H' and resid 784 through 789 Processing helix chain 'H' and resid 796 through 805 removed outlier: 3.688A pdb=" N LYS H 800 " --> pdb=" O LYS H 796 " (cutoff:3.500A) Processing helix chain 'H' and resid 809 through 814 Processing helix chain 'H' and resid 832 through 845 removed outlier: 3.689A pdb=" N GLN H 836 " --> pdb=" O GLY H 832 " (cutoff:3.500A) Processing helix chain 'H' and resid 862 through 871 Processing helix chain 'H' and resid 894 through 896 No H-bonds generated for 'chain 'H' and resid 894 through 896' Processing helix chain 'H' and resid 914 through 919 Processing helix chain 'H' and resid 1001 through 1008 Processing helix chain 'H' and resid 1012 through 1038 Processing helix chain 'H' and resid 1061 through 1106 removed outlier: 3.575A pdb=" N SER H1073 " --> pdb=" O THR H1069 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE H1076 " --> pdb=" O CYS H1072 " (cutoff:3.500A) Processing helix chain 'H' and resid 1110 through 1115 Processing helix chain 'H' and resid 1118 through 1134 Processing helix chain 'H' and resid 1136 through 1160 Processing helix chain 'H' and resid 1164 through 1166 No H-bonds generated for 'chain 'H' and resid 1164 through 1166' Processing helix chain 'H' and resid 1168 through 1209 removed outlier: 3.817A pdb=" N VAL H1184 " --> pdb=" O LYS H1180 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) Proline residue: H1199 - end of helix Processing helix chain 'H' and resid 1211 through 1217 Processing helix chain 'H' and resid 1220 through 1273 removed outlier: 4.209A pdb=" N LEU H1272 " --> pdb=" O ILE H1268 " (cutoff:3.500A) Processing helix chain 'H' and resid 1279 through 1319 removed outlier: 3.826A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASN H1293 " --> pdb=" O LEU H1289 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN H1296 " --> pdb=" O SER H1292 " (cutoff:3.500A) Processing helix chain 'H' and resid 1385 through 1393 Processing helix chain 'H' and resid 1415 through 1419 Processing helix chain 'H' and resid 1436 through 1440 Processing helix chain 'H' and resid 1448 through 1457 Processing helix chain 'H' and resid 1461 through 1465 Processing helix chain 'H' and resid 1484 through 1498 Processing helix chain 'H' and resid 1514 through 1527 removed outlier: 4.041A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1540 through 1544 Processing sheet with id= A, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS A 259 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 200 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 214 through 220 removed outlier: 3.662A pdb=" N GLU A 282 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= D, first strand: chain 'B' and resid 701 through 703 Processing sheet with id= E, first strand: chain 'B' and resid 911 through 913 removed outlier: 3.663A pdb=" N GLY B 912 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 884 " --> pdb=" O THR B 709 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE B 711 " --> pdb=" O VAL B 884 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU B 886 " --> pdb=" O ILE B 711 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N GLY B 713 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA B 773 " --> pdb=" O ASP B 854 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1367 through 1369 Processing sheet with id= G, first strand: chain 'B' and resid 1557 through 1560 removed outlier: 3.950A pdb=" N LEU B1548 " --> pdb=" O LYS B1374 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL B1533 " --> pdb=" O ILE B1375 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE B1377 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR B1535 " --> pdb=" O ILE B1377 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS C 259 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 200 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 214 through 220 removed outlier: 3.662A pdb=" N GLU C 282 " --> pdb=" O VAL C 220 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= K, first strand: chain 'D' and resid 701 through 703 Processing sheet with id= L, first strand: chain 'D' and resid 911 through 913 removed outlier: 3.663A pdb=" N GLY D 912 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL D 884 " --> pdb=" O THR D 709 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE D 711 " --> pdb=" O VAL D 884 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU D 886 " --> pdb=" O ILE D 711 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N GLY D 713 " --> pdb=" O LEU D 886 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA D 771 " --> pdb=" O PHE D 852 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP D 854 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA D 773 " --> pdb=" O ASP D 854 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 1367 through 1369 Processing sheet with id= N, first strand: chain 'D' and resid 1557 through 1560 removed outlier: 3.950A pdb=" N LEU D1548 " --> pdb=" O LYS D1374 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL D1533 " --> pdb=" O ILE D1375 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE D1377 " --> pdb=" O VAL D1533 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR D1535 " --> pdb=" O ILE D1377 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS E 259 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 200 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 214 through 220 removed outlier: 3.662A pdb=" N GLU E 282 " --> pdb=" O VAL E 220 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= R, first strand: chain 'F' and resid 701 through 703 Processing sheet with id= S, first strand: chain 'F' and resid 911 through 913 removed outlier: 3.663A pdb=" N GLY F 912 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL F 884 " --> pdb=" O THR F 709 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE F 711 " --> pdb=" O VAL F 884 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU F 886 " --> pdb=" O ILE F 711 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N GLY F 713 " --> pdb=" O LEU F 886 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 1367 through 1369 Processing sheet with id= U, first strand: chain 'F' and resid 1557 through 1560 removed outlier: 3.950A pdb=" N LEU F1548 " --> pdb=" O LYS F1374 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL F1533 " --> pdb=" O ILE F1375 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE F1377 " --> pdb=" O VAL F1533 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR F1535 " --> pdb=" O ILE F1377 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 188 through 192 removed outlier: 3.781A pdb=" N HIS G 259 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU G 200 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 214 through 220 removed outlier: 3.662A pdb=" N GLU G 282 " --> pdb=" O VAL G 220 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 313 through 315 Processing sheet with id= Y, first strand: chain 'H' and resid 701 through 703 Processing sheet with id= Z, first strand: chain 'H' and resid 911 through 913 removed outlier: 3.663A pdb=" N GLY H 912 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL H 884 " --> pdb=" O THR H 709 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE H 711 " --> pdb=" O VAL H 884 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU H 886 " --> pdb=" O ILE H 711 " (cutoff:3.500A) removed outlier: 9.282A pdb=" N GLY H 713 " --> pdb=" O LEU H 886 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 1367 through 1369 Processing sheet with id= AB, first strand: chain 'H' and resid 1557 through 1560 removed outlier: 3.950A pdb=" N LEU H1548 " --> pdb=" O LYS H1374 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL H1533 " --> pdb=" O ILE H1375 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE H1377 " --> pdb=" O VAL H1533 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR H1535 " --> pdb=" O ILE H1377 " (cutoff:3.500A) 2988 hydrogen bonds defined for protein. 8748 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: 20.23 Time building geometry restraints manager: 21.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 16052 1.34 - 1.47: 12284 1.47 - 1.59: 23356 1.59 - 1.71: 36 1.71 - 1.83: 436 Bond restraints: 52164 Sorted by residual: bond pdb=" CG HIS A 193 " pdb=" CD2 HIS A 193 " ideal model delta sigma weight residual 1.354 1.395 -0.041 1.10e-02 8.26e+03 1.36e+01 bond pdb=" CG HIS G 193 " pdb=" CD2 HIS G 193 " ideal model delta sigma weight residual 1.354 1.395 -0.041 1.10e-02 8.26e+03 1.36e+01 bond pdb=" CG HIS C 193 " pdb=" CD2 HIS C 193 " ideal model delta sigma weight residual 1.354 1.395 -0.041 1.10e-02 8.26e+03 1.36e+01 bond pdb=" CG HIS E 193 " pdb=" CD2 HIS E 193 " ideal model delta sigma weight residual 1.354 1.395 -0.041 1.10e-02 8.26e+03 1.36e+01 bond pdb=" CG HIS A 193 " pdb=" ND1 HIS A 193 " ideal model delta sigma weight residual 1.378 1.345 0.033 1.10e-02 8.26e+03 9.00e+00 ... (remaining 52159 not shown) Histogram of bond angle deviations from ideal: 98.77 - 106.25: 1256 106.25 - 113.74: 30952 113.74 - 121.22: 26760 121.22 - 128.71: 11540 128.71 - 136.19: 456 Bond angle restraints: 70964 Sorted by residual: angle pdb=" N GLY H 296 " pdb=" CA GLY H 296 " pdb=" C GLY H 296 " ideal model delta sigma weight residual 110.77 122.90 -12.13 1.93e+00 2.68e-01 3.95e+01 angle pdb=" N GLY B 296 " pdb=" CA GLY B 296 " pdb=" C GLY B 296 " ideal model delta sigma weight residual 110.77 122.90 -12.13 1.93e+00 2.68e-01 3.95e+01 angle pdb=" N GLY F 296 " pdb=" CA GLY F 296 " pdb=" C GLY F 296 " ideal model delta sigma weight residual 110.77 122.90 -12.13 1.93e+00 2.68e-01 3.95e+01 angle pdb=" N GLY D 296 " pdb=" CA GLY D 296 " pdb=" C GLY D 296 " ideal model delta sigma weight residual 110.77 122.90 -12.13 1.93e+00 2.68e-01 3.95e+01 angle pdb=" N ARG B 194 " pdb=" CA ARG B 194 " pdb=" C ARG B 194 " ideal model delta sigma weight residual 109.24 120.83 -11.59 1.89e+00 2.80e-01 3.76e+01 ... (remaining 70959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.72: 29696 28.72 - 57.45: 1084 57.45 - 86.17: 92 86.17 - 114.89: 12 114.89 - 143.62: 8 Dihedral angle restraints: 30892 sinusoidal: 11776 harmonic: 19116 Sorted by residual: dihedral pdb=" C5' ADP F2502 " pdb=" O5' ADP F2502 " pdb=" PA ADP F2502 " pdb=" O2A ADP F2502 " ideal model delta sinusoidal sigma weight residual -60.00 83.62 -143.62 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP B2502 " pdb=" O5' ADP B2502 " pdb=" PA ADP B2502 " pdb=" O2A ADP B2502 " ideal model delta sinusoidal sigma weight residual -60.00 83.62 -143.62 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP H2502 " pdb=" O5' ADP H2502 " pdb=" PA ADP H2502 " pdb=" O2A ADP H2502 " ideal model delta sinusoidal sigma weight residual -60.00 83.62 -143.62 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 30889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 7496 0.068 - 0.136: 1012 0.136 - 0.204: 48 0.204 - 0.272: 4 0.272 - 0.340: 8 Chirality restraints: 8568 Sorted by residual: chirality pdb=" CA ARG D 194 " pdb=" N ARG D 194 " pdb=" C ARG D 194 " pdb=" CB ARG D 194 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA ARG B 194 " pdb=" N ARG B 194 " pdb=" C ARG B 194 " pdb=" CB ARG B 194 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA ARG F 194 " pdb=" N ARG F 194 " pdb=" C ARG F 194 " pdb=" CB ARG F 194 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 8565 not shown) Planarity restraints: 8708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 200 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO D 201 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 201 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 201 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR H 200 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO H 201 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO H 201 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 201 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 200 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO F 201 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 201 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 201 " -0.039 5.00e-02 4.00e+02 ... (remaining 8705 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 456 2.60 - 3.18: 45500 3.18 - 3.75: 80688 3.75 - 4.33: 103380 4.33 - 4.90: 168992 Nonbonded interactions: 399016 Sorted by model distance: nonbonded pdb=" O ILE D 196 " pdb=" O PHE D 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE H 196 " pdb=" O PHE H 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE F 196 " pdb=" O PHE F 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE B 196 " pdb=" O PHE B 197 " model vdw 2.030 3.040 nonbonded pdb=" OE1 GLN H 775 " pdb="MG MG H2503 " model vdw 2.031 2.170 ... (remaining 399011 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 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 9.300 Check model and map are aligned: 0.770 Set scattering table: 0.460 Process input model: 130.790 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 52164 Z= 0.294 Angle : 0.805 12.134 70964 Z= 0.429 Chirality : 0.045 0.340 8568 Planarity : 0.005 0.073 8708 Dihedral : 14.467 143.618 18448 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.37 % Favored : 95.26 % Rotamer: Outliers : 7.97 % Allowed : 9.00 % Favored : 83.03 % 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: -1.76 (0.09), residues: 6492 helix: -0.29 (0.07), residues: 3896 sheet: -1.04 (0.21), residues: 564 loop : -2.83 (0.11), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1339 HIS 0.011 0.002 HIS G 175 PHE 0.034 0.002 PHE A 168 TYR 0.015 0.002 TYR B 512 ARG 0.009 0.001 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 432 poor density : 1176 time to evaluate : 5.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 MET cc_start: 0.8928 (mmt) cc_final: 0.8610 (tmm) REVERT: A 88 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8585 (tmm) REVERT: A 163 MET cc_start: 0.8581 (ttp) cc_final: 0.7800 (ttt) REVERT: A 219 VAL cc_start: 0.9437 (OUTLIER) cc_final: 0.9109 (m) REVERT: A 236 VAL cc_start: 0.9520 (OUTLIER) cc_final: 0.9062 (m) REVERT: A 283 ILE cc_start: 0.9302 (mm) cc_final: 0.8918 (tt) REVERT: A 329 ASP cc_start: 0.8804 (t0) cc_final: 0.7896 (t0) REVERT: A 332 LYS cc_start: 0.9178 (mtmt) cc_final: 0.8757 (mtmm) REVERT: A 352 ASP cc_start: 0.8829 (m-30) cc_final: 0.8482 (t0) REVERT: B 140 LEU cc_start: 0.9056 (tp) cc_final: 0.8800 (tp) REVERT: B 189 VAL cc_start: 0.8839 (t) cc_final: 0.8626 (t) REVERT: B 426 ASN cc_start: 0.8986 (m-40) cc_final: 0.8705 (m110) REVERT: B 432 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7612 (t80) REVERT: B 451 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8883 (tp) REVERT: B 530 MET cc_start: 0.8972 (tpp) cc_final: 0.8623 (mtt) REVERT: B 710 MET cc_start: 0.8617 (mmt) cc_final: 0.8245 (tpp) REVERT: B 737 VAL cc_start: 0.7761 (OUTLIER) cc_final: 0.7536 (t) REVERT: B 778 TRP cc_start: 0.7465 (p-90) cc_final: 0.7218 (p-90) REVERT: B 806 CYS cc_start: 0.9382 (m) cc_final: 0.8832 (p) REVERT: B 808 LEU cc_start: 0.8947 (tp) cc_final: 0.8691 (mt) REVERT: B 869 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9034 (tmm) REVERT: B 1136 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8478 (mm) REVERT: B 1176 TYR cc_start: 0.5845 (t80) cc_final: 0.5535 (m-80) REVERT: B 1197 GLN cc_start: 0.9140 (tt0) cc_final: 0.8616 (pt0) REVERT: B 1220 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8777 (mp0) REVERT: B 1222 ARG cc_start: 0.9043 (mmt-90) cc_final: 0.8760 (mpt-90) REVERT: B 1229 GLU cc_start: 0.9490 (tp30) cc_final: 0.9182 (tm-30) REVERT: B 1235 ASN cc_start: 0.9168 (m-40) cc_final: 0.8957 (m110) REVERT: B 1240 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: B 1252 MET cc_start: 0.9401 (mmm) cc_final: 0.9185 (tpp) REVERT: B 1395 MET cc_start: 0.7649 (mmt) cc_final: 0.7439 (mmm) REVERT: B 1409 ASP cc_start: 0.3673 (OUTLIER) cc_final: 0.3468 (p0) REVERT: B 1432 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6609 (p90) REVERT: B 1550 MET cc_start: 0.8047 (ptt) cc_final: 0.7686 (pmm) REVERT: B 1554 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8386 (mmp80) REVERT: B 1566 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6857 (pp) REVERT: B 1571 ASP cc_start: 0.7977 (m-30) cc_final: 0.7716 (t70) REVERT: C 77 MET cc_start: 0.8930 (mmt) cc_final: 0.8611 (tmm) REVERT: C 88 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8584 (tmm) REVERT: C 163 MET cc_start: 0.8579 (ttp) cc_final: 0.7834 (ttt) REVERT: C 219 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9105 (m) REVERT: C 236 VAL cc_start: 0.9521 (OUTLIER) cc_final: 0.9064 (m) REVERT: C 283 ILE cc_start: 0.9301 (mm) cc_final: 0.8917 (tt) REVERT: C 329 ASP cc_start: 0.8806 (t0) cc_final: 0.7895 (t0) REVERT: C 332 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8758 (mtmm) REVERT: C 352 ASP cc_start: 0.8829 (m-30) cc_final: 0.8481 (t0) REVERT: D 140 LEU cc_start: 0.9056 (tp) cc_final: 0.8799 (tp) REVERT: D 189 VAL cc_start: 0.8839 (t) cc_final: 0.8626 (t) REVERT: D 426 ASN cc_start: 0.8985 (m-40) cc_final: 0.8704 (m110) REVERT: D 432 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.7615 (t80) REVERT: D 451 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8884 (tp) REVERT: D 530 MET cc_start: 0.8973 (tpp) cc_final: 0.8623 (mtt) REVERT: D 710 MET cc_start: 0.8618 (mmt) cc_final: 0.8248 (tpp) REVERT: D 737 VAL cc_start: 0.7763 (OUTLIER) cc_final: 0.7536 (t) REVERT: D 778 TRP cc_start: 0.7462 (p-90) cc_final: 0.7214 (p-90) REVERT: D 806 CYS cc_start: 0.9382 (m) cc_final: 0.8833 (p) REVERT: D 808 LEU cc_start: 0.8946 (tp) cc_final: 0.8688 (mt) REVERT: D 869 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9038 (tmm) REVERT: D 1136 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8481 (mm) REVERT: D 1176 TYR cc_start: 0.5846 (t80) cc_final: 0.5534 (m-80) REVERT: D 1197 GLN cc_start: 0.9141 (tt0) cc_final: 0.8616 (pt0) REVERT: D 1220 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8780 (mp0) REVERT: D 1222 ARG cc_start: 0.9045 (mmt-90) cc_final: 0.8762 (mpt-90) REVERT: D 1229 GLU cc_start: 0.9490 (tp30) cc_final: 0.9184 (tm-30) REVERT: D 1235 ASN cc_start: 0.9164 (m-40) cc_final: 0.8953 (m110) REVERT: D 1240 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: D 1252 MET cc_start: 0.9401 (mmm) cc_final: 0.9186 (tpp) REVERT: D 1395 MET cc_start: 0.7647 (mmt) cc_final: 0.7436 (mmm) REVERT: D 1409 ASP cc_start: 0.3674 (OUTLIER) cc_final: 0.3464 (p0) REVERT: D 1432 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6601 (p90) REVERT: D 1550 MET cc_start: 0.8042 (ptt) cc_final: 0.7683 (pmm) REVERT: D 1554 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8389 (mmp80) REVERT: D 1566 LEU cc_start: 0.7088 (OUTLIER) cc_final: 0.6856 (pp) REVERT: D 1571 ASP cc_start: 0.7977 (m-30) cc_final: 0.7714 (t70) REVERT: E 77 MET cc_start: 0.8932 (mmt) cc_final: 0.8612 (tmm) REVERT: E 88 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8584 (tmm) REVERT: E 163 MET cc_start: 0.8580 (ttp) cc_final: 0.7831 (ttt) REVERT: E 219 VAL cc_start: 0.9436 (OUTLIER) cc_final: 0.9109 (m) REVERT: E 236 VAL cc_start: 0.9522 (OUTLIER) cc_final: 0.9062 (m) REVERT: E 283 ILE cc_start: 0.9300 (mm) cc_final: 0.8914 (tt) REVERT: E 329 ASP cc_start: 0.8802 (t0) cc_final: 0.7896 (t0) REVERT: E 332 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8757 (mtmm) REVERT: E 352 ASP cc_start: 0.8829 (m-30) cc_final: 0.8480 (t0) REVERT: F 140 LEU cc_start: 0.9056 (tp) cc_final: 0.8798 (tp) REVERT: F 189 VAL cc_start: 0.8835 (t) cc_final: 0.8625 (t) REVERT: F 426 ASN cc_start: 0.8985 (m-40) cc_final: 0.8703 (m110) REVERT: F 432 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7611 (t80) REVERT: F 451 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8884 (tp) REVERT: F 530 MET cc_start: 0.8974 (tpp) cc_final: 0.8620 (mtt) REVERT: F 710 MET cc_start: 0.8620 (mmt) cc_final: 0.8249 (tpp) REVERT: F 737 VAL cc_start: 0.7757 (OUTLIER) cc_final: 0.7532 (t) REVERT: F 778 TRP cc_start: 0.7462 (p-90) cc_final: 0.7215 (p-90) REVERT: F 806 CYS cc_start: 0.9379 (m) cc_final: 0.8831 (p) REVERT: F 808 LEU cc_start: 0.8946 (tp) cc_final: 0.8689 (mt) REVERT: F 869 MET cc_start: 0.9473 (OUTLIER) cc_final: 0.9040 (tmm) REVERT: F 1136 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8479 (mm) REVERT: F 1176 TYR cc_start: 0.5842 (t80) cc_final: 0.5537 (m-80) REVERT: F 1197 GLN cc_start: 0.9142 (tt0) cc_final: 0.8617 (pt0) REVERT: F 1220 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8779 (mp0) REVERT: F 1222 ARG cc_start: 0.9043 (mmt-90) cc_final: 0.8760 (mpt-90) REVERT: F 1229 GLU cc_start: 0.9490 (tp30) cc_final: 0.9182 (tm-30) REVERT: F 1235 ASN cc_start: 0.9165 (m-40) cc_final: 0.8955 (m110) REVERT: F 1240 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.8722 (m-80) REVERT: F 1252 MET cc_start: 0.9402 (mmm) cc_final: 0.9184 (tpp) REVERT: F 1395 MET cc_start: 0.7645 (mmt) cc_final: 0.7435 (mmm) REVERT: F 1409 ASP cc_start: 0.3670 (OUTLIER) cc_final: 0.3461 (p0) REVERT: F 1432 PHE cc_start: 0.7396 (OUTLIER) cc_final: 0.6609 (p90) REVERT: F 1550 MET cc_start: 0.8041 (ptt) cc_final: 0.7682 (pmm) REVERT: F 1554 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8388 (mmp80) REVERT: F 1566 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6856 (pp) REVERT: F 1571 ASP cc_start: 0.7977 (m-30) cc_final: 0.7716 (t70) REVERT: G 77 MET cc_start: 0.8929 (mmt) cc_final: 0.8613 (tmm) REVERT: G 88 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8589 (tmm) REVERT: G 163 MET cc_start: 0.8577 (ttp) cc_final: 0.7832 (ttt) REVERT: G 219 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9112 (m) REVERT: G 236 VAL cc_start: 0.9522 (OUTLIER) cc_final: 0.9065 (m) REVERT: G 283 ILE cc_start: 0.9301 (mm) cc_final: 0.8913 (tt) REVERT: G 301 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8454 (ptt180) REVERT: G 329 ASP cc_start: 0.8806 (t0) cc_final: 0.7895 (t0) REVERT: G 332 LYS cc_start: 0.9178 (mtmt) cc_final: 0.8753 (mtmm) REVERT: G 352 ASP cc_start: 0.8829 (m-30) cc_final: 0.8480 (t0) REVERT: H 140 LEU cc_start: 0.9055 (tp) cc_final: 0.8804 (tp) REVERT: H 189 VAL cc_start: 0.8837 (t) cc_final: 0.8618 (t) REVERT: H 426 ASN cc_start: 0.8985 (m-40) cc_final: 0.8702 (m110) REVERT: H 432 PHE cc_start: 0.8931 (OUTLIER) cc_final: 0.7610 (t80) REVERT: H 451 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8885 (tp) REVERT: H 530 MET cc_start: 0.8973 (tpp) cc_final: 0.8625 (mtt) REVERT: H 710 MET cc_start: 0.8619 (mmt) cc_final: 0.8246 (tpp) REVERT: H 737 VAL cc_start: 0.7764 (OUTLIER) cc_final: 0.7538 (t) REVERT: H 778 TRP cc_start: 0.7466 (p-90) cc_final: 0.7218 (p-90) REVERT: H 806 CYS cc_start: 0.9381 (m) cc_final: 0.8831 (p) REVERT: H 808 LEU cc_start: 0.8949 (tp) cc_final: 0.8692 (mt) REVERT: H 869 MET cc_start: 0.9471 (OUTLIER) cc_final: 0.9036 (tmm) REVERT: H 1136 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8479 (mm) REVERT: H 1176 TYR cc_start: 0.5844 (t80) cc_final: 0.5535 (m-80) REVERT: H 1197 GLN cc_start: 0.9139 (tt0) cc_final: 0.8614 (pt0) REVERT: H 1220 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8779 (mp0) REVERT: H 1222 ARG cc_start: 0.9043 (mmt-90) cc_final: 0.8760 (mpt-90) REVERT: H 1229 GLU cc_start: 0.9491 (tp30) cc_final: 0.9182 (tm-30) REVERT: H 1235 ASN cc_start: 0.9164 (m-40) cc_final: 0.8956 (m110) REVERT: H 1240 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: H 1252 MET cc_start: 0.9399 (mmm) cc_final: 0.9185 (tpp) REVERT: H 1395 MET cc_start: 0.7655 (mmt) cc_final: 0.7443 (mmm) REVERT: H 1409 ASP cc_start: 0.3680 (OUTLIER) cc_final: 0.3471 (p0) REVERT: H 1432 PHE cc_start: 0.7404 (OUTLIER) cc_final: 0.6620 (p90) REVERT: H 1550 MET cc_start: 0.8041 (ptt) cc_final: 0.7684 (pmm) REVERT: H 1554 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8388 (mmp80) REVERT: H 1566 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6856 (pp) REVERT: H 1571 ASP cc_start: 0.7977 (m-30) cc_final: 0.7716 (t70) outliers start: 432 outliers final: 104 residues processed: 1508 average time/residue: 0.5794 time to fit residues: 1492.3840 Evaluate side-chains 758 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 606 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 553 optimal weight: 8.9990 chunk 497 optimal weight: 0.9990 chunk 275 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 chunk 335 optimal weight: 7.9990 chunk 265 optimal weight: 20.0000 chunk 514 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 312 optimal weight: 20.0000 chunk 382 optimal weight: 9.9990 chunk 595 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN B 32 ASN B 374 GLN B 416 GLN B 437 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 GLN ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1245 ASN B1348 GLN C 46 HIS C 299 GLN D 32 ASN D 374 GLN D 416 GLN D 437 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 809 GLN ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1245 ASN D1301 ASN D1348 GLN E 46 HIS ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN F 32 ASN F 374 GLN F 416 GLN F 437 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 809 GLN ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1245 ASN F1301 ASN F1346 GLN F1348 GLN G 46 HIS G 173 GLN G 299 GLN H 32 ASN H 374 GLN H 416 GLN H 437 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 809 GLN ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 889 HIS H1245 ASN H1348 GLN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 52164 Z= 0.255 Angle : 0.714 10.180 70964 Z= 0.351 Chirality : 0.044 0.354 8568 Planarity : 0.004 0.052 8708 Dihedral : 7.659 129.783 7120 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: -0.35 (0.10), residues: 6492 helix: 0.88 (0.08), residues: 3896 sheet: -0.69 (0.21), residues: 572 loop : -2.30 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 899 HIS 0.008 0.001 HIS F 562 PHE 0.029 0.002 PHE D1018 TYR 0.031 0.002 TYR C 258 ARG 0.009 0.001 ARG D 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 742 time to evaluate : 5.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 CYS cc_start: 0.8347 (t) cc_final: 0.8075 (t) REVERT: A 88 MET cc_start: 0.9149 (tpt) cc_final: 0.8831 (tmm) REVERT: A 141 GLU cc_start: 0.8536 (tt0) cc_final: 0.8050 (tp30) REVERT: A 199 MET cc_start: 0.8519 (mmp) cc_final: 0.8150 (mmp) REVERT: A 329 ASP cc_start: 0.8427 (t0) cc_final: 0.7880 (t0) REVERT: A 332 LYS cc_start: 0.9241 (mtmt) cc_final: 0.9014 (mtmm) REVERT: A 338 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8416 (tptp) REVERT: B 169 PHE cc_start: 0.8437 (t80) cc_final: 0.8076 (p90) REVERT: B 187 VAL cc_start: 0.9327 (p) cc_final: 0.9049 (p) REVERT: B 230 TYR cc_start: 0.9173 (m-80) cc_final: 0.8868 (m-10) REVERT: B 451 LEU cc_start: 0.9195 (tt) cc_final: 0.8983 (mm) REVERT: B 530 MET cc_start: 0.9093 (tpp) cc_final: 0.8610 (mtt) REVERT: B 710 MET cc_start: 0.8495 (mmt) cc_final: 0.8242 (tpp) REVERT: B 778 TRP cc_start: 0.7417 (p-90) cc_final: 0.7172 (p-90) REVERT: B 806 CYS cc_start: 0.9416 (m) cc_final: 0.8992 (t) REVERT: B 869 MET cc_start: 0.9265 (tmm) cc_final: 0.8984 (tmm) REVERT: B 1176 TYR cc_start: 0.5950 (t80) cc_final: 0.5713 (m-80) REVERT: B 1197 GLN cc_start: 0.9191 (tt0) cc_final: 0.8884 (pt0) REVERT: B 1220 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8596 (mp0) REVERT: B 1222 ARG cc_start: 0.9061 (mmt-90) cc_final: 0.8811 (mtt90) REVERT: B 1229 GLU cc_start: 0.9393 (tp30) cc_final: 0.9076 (tm-30) REVERT: B 1235 ASN cc_start: 0.9244 (m-40) cc_final: 0.8909 (m110) REVERT: B 1253 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8476 (mm-30) REVERT: B 1451 LEU cc_start: 0.8676 (mp) cc_final: 0.8318 (tt) REVERT: B 1525 MET cc_start: 0.8998 (mmp) cc_final: 0.8767 (mmm) REVERT: B 1571 ASP cc_start: 0.7945 (m-30) cc_final: 0.7588 (t70) REVERT: C 42 CYS cc_start: 0.8347 (t) cc_final: 0.8071 (t) REVERT: C 88 MET cc_start: 0.9145 (tpt) cc_final: 0.8827 (tmm) REVERT: C 141 GLU cc_start: 0.8536 (tt0) cc_final: 0.8050 (tp30) REVERT: C 199 MET cc_start: 0.8517 (mmp) cc_final: 0.8150 (mmp) REVERT: C 251 LEU cc_start: 0.9124 (tt) cc_final: 0.8912 (tt) REVERT: C 329 ASP cc_start: 0.8421 (t0) cc_final: 0.7882 (t0) REVERT: C 332 LYS cc_start: 0.9239 (mtmt) cc_final: 0.9014 (mtmm) REVERT: C 338 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8413 (tptp) REVERT: D 169 PHE cc_start: 0.8433 (t80) cc_final: 0.8077 (p90) REVERT: D 187 VAL cc_start: 0.9326 (p) cc_final: 0.9047 (p) REVERT: D 189 VAL cc_start: 0.8639 (t) cc_final: 0.8437 (t) REVERT: D 230 TYR cc_start: 0.9173 (m-80) cc_final: 0.8869 (m-10) REVERT: D 451 LEU cc_start: 0.9196 (tt) cc_final: 0.8985 (mm) REVERT: D 530 MET cc_start: 0.9092 (tpp) cc_final: 0.8609 (mtt) REVERT: D 710 MET cc_start: 0.8493 (mmt) cc_final: 0.8240 (tpp) REVERT: D 778 TRP cc_start: 0.7418 (p-90) cc_final: 0.7171 (p-90) REVERT: D 806 CYS cc_start: 0.9415 (m) cc_final: 0.8994 (t) REVERT: D 869 MET cc_start: 0.9266 (tmm) cc_final: 0.8986 (tmm) REVERT: D 1176 TYR cc_start: 0.5947 (t80) cc_final: 0.5713 (m-80) REVERT: D 1197 GLN cc_start: 0.9193 (tt0) cc_final: 0.8885 (pt0) REVERT: D 1220 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8596 (mp0) REVERT: D 1222 ARG cc_start: 0.9061 (mmt-90) cc_final: 0.8812 (mtt90) REVERT: D 1229 GLU cc_start: 0.9393 (tp30) cc_final: 0.9078 (tm-30) REVERT: D 1235 ASN cc_start: 0.9243 (m-40) cc_final: 0.8909 (m110) REVERT: D 1253 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8475 (mm-30) REVERT: D 1451 LEU cc_start: 0.8674 (mp) cc_final: 0.8316 (tt) REVERT: D 1525 MET cc_start: 0.8998 (mmp) cc_final: 0.8767 (mmm) REVERT: D 1571 ASP cc_start: 0.7944 (m-30) cc_final: 0.7586 (t70) REVERT: E 42 CYS cc_start: 0.8350 (t) cc_final: 0.8066 (t) REVERT: E 88 MET cc_start: 0.9146 (tpt) cc_final: 0.8828 (tmm) REVERT: E 141 GLU cc_start: 0.8536 (tt0) cc_final: 0.8049 (tp30) REVERT: E 199 MET cc_start: 0.8521 (mmp) cc_final: 0.8153 (mmp) REVERT: E 251 LEU cc_start: 0.9126 (tt) cc_final: 0.8913 (tt) REVERT: E 329 ASP cc_start: 0.8415 (t0) cc_final: 0.7879 (t0) REVERT: E 332 LYS cc_start: 0.9241 (mtmt) cc_final: 0.9016 (mtmm) REVERT: E 338 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8415 (tptp) REVERT: F 169 PHE cc_start: 0.8434 (t80) cc_final: 0.8077 (p90) REVERT: F 187 VAL cc_start: 0.9326 (p) cc_final: 0.9050 (p) REVERT: F 189 VAL cc_start: 0.8633 (t) cc_final: 0.8432 (t) REVERT: F 230 TYR cc_start: 0.9172 (m-80) cc_final: 0.8869 (m-10) REVERT: F 451 LEU cc_start: 0.9195 (tt) cc_final: 0.8985 (mm) REVERT: F 530 MET cc_start: 0.9091 (tpp) cc_final: 0.8610 (mtt) REVERT: F 710 MET cc_start: 0.8496 (mmt) cc_final: 0.8239 (tpp) REVERT: F 778 TRP cc_start: 0.7424 (p-90) cc_final: 0.7177 (p-90) REVERT: F 806 CYS cc_start: 0.9418 (m) cc_final: 0.8992 (t) REVERT: F 869 MET cc_start: 0.9267 (tmm) cc_final: 0.8988 (tmm) REVERT: F 1176 TYR cc_start: 0.5947 (t80) cc_final: 0.5716 (m-80) REVERT: F 1197 GLN cc_start: 0.9191 (tt0) cc_final: 0.8884 (pt0) REVERT: F 1220 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8597 (mp0) REVERT: F 1222 ARG cc_start: 0.9061 (mmt-90) cc_final: 0.8810 (mtt90) REVERT: F 1229 GLU cc_start: 0.9393 (tp30) cc_final: 0.9077 (tm-30) REVERT: F 1235 ASN cc_start: 0.9246 (m-40) cc_final: 0.8910 (m110) REVERT: F 1253 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8474 (mm-30) REVERT: F 1451 LEU cc_start: 0.8675 (mp) cc_final: 0.8318 (tt) REVERT: F 1525 MET cc_start: 0.9001 (mmp) cc_final: 0.8771 (mmm) REVERT: F 1571 ASP cc_start: 0.7943 (m-30) cc_final: 0.7587 (t70) REVERT: G 42 CYS cc_start: 0.8332 (t) cc_final: 0.7925 (t) REVERT: G 88 MET cc_start: 0.9151 (tpt) cc_final: 0.8832 (tmm) REVERT: G 141 GLU cc_start: 0.8540 (tt0) cc_final: 0.8051 (tp30) REVERT: G 199 MET cc_start: 0.8521 (mmp) cc_final: 0.8151 (mmp) REVERT: G 251 LEU cc_start: 0.9123 (tt) cc_final: 0.8915 (tt) REVERT: G 301 ARG cc_start: 0.8762 (mtm180) cc_final: 0.8446 (ptt180) REVERT: G 329 ASP cc_start: 0.8416 (t0) cc_final: 0.7881 (t0) REVERT: G 332 LYS cc_start: 0.9240 (mtmt) cc_final: 0.9012 (mtmm) REVERT: G 338 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8414 (tptp) REVERT: H 169 PHE cc_start: 0.8436 (t80) cc_final: 0.8077 (p90) REVERT: H 187 VAL cc_start: 0.9326 (p) cc_final: 0.9048 (p) REVERT: H 189 VAL cc_start: 0.8633 (t) cc_final: 0.8432 (t) REVERT: H 230 TYR cc_start: 0.9170 (m-80) cc_final: 0.8865 (m-10) REVERT: H 451 LEU cc_start: 0.9194 (tt) cc_final: 0.8983 (mm) REVERT: H 530 MET cc_start: 0.9092 (tpp) cc_final: 0.8609 (mtt) REVERT: H 710 MET cc_start: 0.8496 (mmt) cc_final: 0.8240 (tpp) REVERT: H 778 TRP cc_start: 0.7419 (p-90) cc_final: 0.7173 (p-90) REVERT: H 806 CYS cc_start: 0.9412 (m) cc_final: 0.8992 (t) REVERT: H 869 MET cc_start: 0.9264 (tmm) cc_final: 0.8986 (tmm) REVERT: H 1176 TYR cc_start: 0.5949 (t80) cc_final: 0.5714 (m-80) REVERT: H 1197 GLN cc_start: 0.9189 (tt0) cc_final: 0.8881 (pt0) REVERT: H 1220 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8594 (mp0) REVERT: H 1222 ARG cc_start: 0.9061 (mmt-90) cc_final: 0.8810 (mtt90) REVERT: H 1229 GLU cc_start: 0.9393 (tp30) cc_final: 0.9075 (tm-30) REVERT: H 1235 ASN cc_start: 0.9245 (m-40) cc_final: 0.8910 (m110) REVERT: H 1253 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8479 (mm-30) REVERT: H 1451 LEU cc_start: 0.8675 (mp) cc_final: 0.8320 (tt) REVERT: H 1525 MET cc_start: 0.8999 (mmp) cc_final: 0.8769 (mmm) REVERT: H 1571 ASP cc_start: 0.7947 (m-30) cc_final: 0.7590 (t70) outliers start: 0 outliers final: 0 residues processed: 742 average time/residue: 0.5642 time to fit residues: 731.9685 Evaluate side-chains 495 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 6.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 331 optimal weight: 0.8980 chunk 184 optimal weight: 0.9990 chunk 495 optimal weight: 0.9990 chunk 405 optimal weight: 30.0000 chunk 164 optimal weight: 10.0000 chunk 596 optimal weight: 10.0000 chunk 644 optimal weight: 9.9990 chunk 531 optimal weight: 4.9990 chunk 591 optimal weight: 10.0000 chunk 203 optimal weight: 5.9990 chunk 478 optimal weight: 30.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 HIS A 235 GLN B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1245 ASN B1301 ASN C 216 HIS C 235 GLN D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1245 ASN ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 216 HIS E 235 GLN F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1245 ASN H1301 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52164 Z= 0.216 Angle : 0.657 10.218 70964 Z= 0.322 Chirality : 0.042 0.221 8568 Planarity : 0.004 0.054 8708 Dihedral : 6.924 127.571 7120 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.51 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % 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: 0.40 (0.10), residues: 6492 helix: 1.44 (0.08), residues: 3912 sheet: -0.52 (0.20), residues: 608 loop : -1.89 (0.12), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 899 HIS 0.005 0.001 HIS G 259 PHE 0.031 0.002 PHE E 168 TYR 0.014 0.001 TYR A 258 ARG 0.006 0.000 ARG F 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 649 time to evaluate : 5.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9120 (tpt) cc_final: 0.8838 (tmm) REVERT: A 163 MET cc_start: 0.9040 (ttt) cc_final: 0.8561 (tmm) REVERT: A 199 MET cc_start: 0.8644 (mmp) cc_final: 0.8158 (mmp) REVERT: A 329 ASP cc_start: 0.8393 (t0) cc_final: 0.7822 (t0) REVERT: B 169 PHE cc_start: 0.8472 (t80) cc_final: 0.8195 (p90) REVERT: B 230 TYR cc_start: 0.9156 (m-80) cc_final: 0.8928 (m-10) REVERT: B 530 MET cc_start: 0.9026 (tpp) cc_final: 0.8561 (mtt) REVERT: B 710 MET cc_start: 0.8513 (mmt) cc_final: 0.8236 (tpp) REVERT: B 781 ASN cc_start: 0.8800 (t0) cc_final: 0.8146 (m-40) REVERT: B 806 CYS cc_start: 0.9420 (m) cc_final: 0.8992 (t) REVERT: B 869 MET cc_start: 0.9184 (tmm) cc_final: 0.8943 (tmm) REVERT: B 1110 MET cc_start: 0.8313 (tpp) cc_final: 0.7484 (tpp) REVERT: B 1176 TYR cc_start: 0.5946 (t80) cc_final: 0.5675 (m-80) REVERT: B 1194 ASP cc_start: 0.9401 (m-30) cc_final: 0.9148 (m-30) REVERT: B 1220 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8509 (mp0) REVERT: B 1222 ARG cc_start: 0.9051 (mmt-90) cc_final: 0.8723 (tpp80) REVERT: B 1229 GLU cc_start: 0.9356 (tp30) cc_final: 0.9044 (tm-30) REVERT: B 1235 ASN cc_start: 0.9240 (m-40) cc_final: 0.8940 (m110) REVERT: B 1451 LEU cc_start: 0.8638 (mp) cc_final: 0.8305 (tt) REVERT: B 1525 MET cc_start: 0.9041 (mmp) cc_final: 0.8809 (mmm) REVERT: B 1571 ASP cc_start: 0.8207 (m-30) cc_final: 0.7910 (t70) REVERT: C 88 MET cc_start: 0.9121 (tpt) cc_final: 0.8836 (tmm) REVERT: C 199 MET cc_start: 0.8641 (mmp) cc_final: 0.8156 (mmp) REVERT: C 329 ASP cc_start: 0.8387 (t0) cc_final: 0.7824 (t0) REVERT: D 169 PHE cc_start: 0.8475 (t80) cc_final: 0.8198 (p90) REVERT: D 230 TYR cc_start: 0.9156 (m-80) cc_final: 0.8927 (m-10) REVERT: D 530 MET cc_start: 0.9024 (tpp) cc_final: 0.8559 (mtt) REVERT: D 710 MET cc_start: 0.8515 (mmt) cc_final: 0.8238 (tpp) REVERT: D 781 ASN cc_start: 0.8802 (t0) cc_final: 0.8146 (m-40) REVERT: D 806 CYS cc_start: 0.9416 (m) cc_final: 0.8993 (t) REVERT: D 869 MET cc_start: 0.9185 (tmm) cc_final: 0.8947 (tmm) REVERT: D 1110 MET cc_start: 0.8314 (tpp) cc_final: 0.7489 (tpp) REVERT: D 1176 TYR cc_start: 0.5943 (t80) cc_final: 0.5674 (m-80) REVERT: D 1194 ASP cc_start: 0.9402 (m-30) cc_final: 0.9149 (m-30) REVERT: D 1220 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8511 (mp0) REVERT: D 1222 ARG cc_start: 0.9052 (mmt-90) cc_final: 0.8726 (tpp80) REVERT: D 1229 GLU cc_start: 0.9356 (tp30) cc_final: 0.9046 (tm-30) REVERT: D 1235 ASN cc_start: 0.9239 (m-40) cc_final: 0.8940 (m110) REVERT: D 1451 LEU cc_start: 0.8637 (mp) cc_final: 0.8302 (tt) REVERT: D 1525 MET cc_start: 0.9039 (mmp) cc_final: 0.8808 (mmm) REVERT: D 1571 ASP cc_start: 0.8206 (m-30) cc_final: 0.7909 (t70) REVERT: E 88 MET cc_start: 0.9123 (tpt) cc_final: 0.8834 (tmm) REVERT: E 199 MET cc_start: 0.8645 (mmp) cc_final: 0.8159 (mmp) REVERT: E 329 ASP cc_start: 0.8379 (t0) cc_final: 0.7817 (t0) REVERT: F 169 PHE cc_start: 0.8472 (t80) cc_final: 0.8197 (p90) REVERT: F 230 TYR cc_start: 0.9155 (m-80) cc_final: 0.8926 (m-10) REVERT: F 530 MET cc_start: 0.9023 (tpp) cc_final: 0.8559 (mtt) REVERT: F 710 MET cc_start: 0.8518 (mmt) cc_final: 0.8237 (tpp) REVERT: F 781 ASN cc_start: 0.8799 (t0) cc_final: 0.8145 (m-40) REVERT: F 806 CYS cc_start: 0.9420 (m) cc_final: 0.8988 (t) REVERT: F 869 MET cc_start: 0.9188 (tmm) cc_final: 0.8949 (tmm) REVERT: F 1110 MET cc_start: 0.8310 (tpp) cc_final: 0.7480 (tpp) REVERT: F 1176 TYR cc_start: 0.5943 (t80) cc_final: 0.5675 (m-80) REVERT: F 1194 ASP cc_start: 0.9401 (m-30) cc_final: 0.9149 (m-30) REVERT: F 1220 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8512 (mp0) REVERT: F 1222 ARG cc_start: 0.9052 (mmt-90) cc_final: 0.8724 (tpp80) REVERT: F 1229 GLU cc_start: 0.9357 (tp30) cc_final: 0.9045 (tm-30) REVERT: F 1235 ASN cc_start: 0.9241 (m-40) cc_final: 0.8940 (m110) REVERT: F 1451 LEU cc_start: 0.8636 (mp) cc_final: 0.8304 (tt) REVERT: F 1525 MET cc_start: 0.9043 (mmp) cc_final: 0.8812 (mmm) REVERT: F 1571 ASP cc_start: 0.8207 (m-30) cc_final: 0.7910 (t70) REVERT: G 42 CYS cc_start: 0.8213 (t) cc_final: 0.7906 (t) REVERT: G 88 MET cc_start: 0.9126 (tpt) cc_final: 0.8836 (tmm) REVERT: G 199 MET cc_start: 0.8648 (mmp) cc_final: 0.8161 (mmp) REVERT: G 301 ARG cc_start: 0.8707 (mtm180) cc_final: 0.8357 (ptt180) REVERT: G 329 ASP cc_start: 0.8378 (t0) cc_final: 0.7822 (t0) REVERT: G 338 LYS cc_start: 0.8866 (mmmt) cc_final: 0.8626 (tptp) REVERT: H 169 PHE cc_start: 0.8473 (t80) cc_final: 0.8200 (p90) REVERT: H 230 TYR cc_start: 0.9155 (m-80) cc_final: 0.8924 (m-10) REVERT: H 530 MET cc_start: 0.9025 (tpp) cc_final: 0.8561 (mtt) REVERT: H 710 MET cc_start: 0.8518 (mmt) cc_final: 0.8237 (tpp) REVERT: H 781 ASN cc_start: 0.8799 (t0) cc_final: 0.8147 (m-40) REVERT: H 806 CYS cc_start: 0.9415 (m) cc_final: 0.8990 (t) REVERT: H 869 MET cc_start: 0.9185 (tmm) cc_final: 0.8946 (tmm) REVERT: H 1110 MET cc_start: 0.8311 (tpp) cc_final: 0.7485 (tpp) REVERT: H 1176 TYR cc_start: 0.5941 (t80) cc_final: 0.5675 (m-80) REVERT: H 1194 ASP cc_start: 0.9401 (m-30) cc_final: 0.9150 (m-30) REVERT: H 1220 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8511 (mp0) REVERT: H 1222 ARG cc_start: 0.9052 (mmt-90) cc_final: 0.8723 (tpp80) REVERT: H 1229 GLU cc_start: 0.9357 (tp30) cc_final: 0.9043 (tm-30) REVERT: H 1235 ASN cc_start: 0.9242 (m-40) cc_final: 0.8941 (m110) REVERT: H 1451 LEU cc_start: 0.8638 (mp) cc_final: 0.8306 (tt) REVERT: H 1525 MET cc_start: 0.9042 (mmp) cc_final: 0.8810 (mmm) REVERT: H 1571 ASP cc_start: 0.8209 (m-30) cc_final: 0.7912 (t70) outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.5654 time to fit residues: 646.3441 Evaluate side-chains 480 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 5.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 589 optimal weight: 20.0000 chunk 448 optimal weight: 8.9990 chunk 309 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 284 optimal weight: 8.9990 chunk 400 optimal weight: 9.9990 chunk 598 optimal weight: 1.9990 chunk 634 optimal weight: 50.0000 chunk 312 optimal weight: 20.0000 chunk 567 optimal weight: 9.9990 chunk 170 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS A 193 HIS A 216 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 HIS ** B1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 HIS B1346 GLN ** B1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1459 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 HIS C 193 HIS C 216 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 889 HIS ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 HIS D1346 GLN ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1459 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 HIS E 193 HIS E 216 HIS ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 889 HIS ** F1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1203 HIS F1245 ASN ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1459 GLN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 186 HIS G 193 HIS G 216 HIS H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H1203 HIS H1346 GLN ** H1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1459 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 52164 Z= 0.374 Angle : 0.772 9.917 70964 Z= 0.387 Chirality : 0.044 0.232 8568 Planarity : 0.005 0.094 8708 Dihedral : 6.662 111.452 7120 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.01 % 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: 0.41 (0.10), residues: 6492 helix: 1.37 (0.08), residues: 3944 sheet: -0.32 (0.21), residues: 528 loop : -1.78 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 90 HIS 0.006 0.001 HIS D1203 PHE 0.036 0.002 PHE G 75 TYR 0.025 0.002 TYR G 258 ARG 0.006 0.001 ARG H 370 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 539 time to evaluate : 6.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9201 (tpt) cc_final: 0.8837 (tmm) REVERT: A 163 MET cc_start: 0.9237 (ttt) cc_final: 0.8584 (tmm) REVERT: A 348 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9087 (tm-30) REVERT: B 530 MET cc_start: 0.8969 (tpp) cc_final: 0.8509 (mtt) REVERT: B 710 MET cc_start: 0.8513 (mmt) cc_final: 0.8228 (tpp) REVERT: B 731 GLN cc_start: 0.8343 (tp40) cc_final: 0.8055 (tt0) REVERT: B 781 ASN cc_start: 0.8979 (t0) cc_final: 0.8683 (m-40) REVERT: B 869 MET cc_start: 0.9152 (tmm) cc_final: 0.8889 (tmm) REVERT: B 1176 TYR cc_start: 0.6038 (t80) cc_final: 0.5663 (m-80) REVERT: B 1220 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8599 (mp0) REVERT: B 1229 GLU cc_start: 0.9243 (tp30) cc_final: 0.9022 (tm-30) REVERT: B 1305 MET cc_start: 0.8047 (tpp) cc_final: 0.7808 (tpp) REVERT: B 1451 LEU cc_start: 0.8648 (mp) cc_final: 0.8391 (tt) REVERT: B 1525 MET cc_start: 0.9025 (mmp) cc_final: 0.8797 (mmm) REVERT: B 1571 ASP cc_start: 0.8076 (m-30) cc_final: 0.7752 (t70) REVERT: C 88 MET cc_start: 0.9188 (tpt) cc_final: 0.8822 (tmm) REVERT: C 163 MET cc_start: 0.9227 (ttt) cc_final: 0.8938 (tmm) REVERT: C 348 GLN cc_start: 0.9392 (tm-30) cc_final: 0.9084 (tm-30) REVERT: D 530 MET cc_start: 0.8970 (tpp) cc_final: 0.8508 (mtt) REVERT: D 710 MET cc_start: 0.8510 (mmt) cc_final: 0.8226 (tpp) REVERT: D 731 GLN cc_start: 0.8341 (tp40) cc_final: 0.8052 (tt0) REVERT: D 781 ASN cc_start: 0.8983 (t0) cc_final: 0.8686 (m-40) REVERT: D 869 MET cc_start: 0.9155 (tmm) cc_final: 0.8892 (tmm) REVERT: D 1176 TYR cc_start: 0.6039 (t80) cc_final: 0.5662 (m-80) REVERT: D 1220 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8597 (mp0) REVERT: D 1229 GLU cc_start: 0.9242 (tp30) cc_final: 0.9022 (tm-30) REVERT: D 1305 MET cc_start: 0.8058 (tpp) cc_final: 0.7808 (tpp) REVERT: D 1451 LEU cc_start: 0.8648 (mp) cc_final: 0.8392 (tt) REVERT: D 1525 MET cc_start: 0.9023 (mmp) cc_final: 0.8795 (mmm) REVERT: D 1571 ASP cc_start: 0.8076 (m-30) cc_final: 0.7753 (t70) REVERT: E 88 MET cc_start: 0.9187 (tpt) cc_final: 0.8820 (tmm) REVERT: E 163 MET cc_start: 0.9235 (ttt) cc_final: 0.8941 (tmm) REVERT: E 348 GLN cc_start: 0.9394 (tm-30) cc_final: 0.9085 (tm-30) REVERT: F 530 MET cc_start: 0.8971 (tpp) cc_final: 0.8509 (mtt) REVERT: F 710 MET cc_start: 0.8511 (mmt) cc_final: 0.8226 (tpp) REVERT: F 731 GLN cc_start: 0.8342 (tp40) cc_final: 0.8054 (tt0) REVERT: F 781 ASN cc_start: 0.8978 (t0) cc_final: 0.8683 (m-40) REVERT: F 869 MET cc_start: 0.9154 (tmm) cc_final: 0.8893 (tmm) REVERT: F 1176 TYR cc_start: 0.6035 (t80) cc_final: 0.5659 (m-80) REVERT: F 1220 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8600 (mp0) REVERT: F 1229 GLU cc_start: 0.9243 (tp30) cc_final: 0.9021 (tm-30) REVERT: F 1305 MET cc_start: 0.8058 (tpp) cc_final: 0.7806 (tpp) REVERT: F 1451 LEU cc_start: 0.8647 (mp) cc_final: 0.8391 (tt) REVERT: F 1525 MET cc_start: 0.9025 (mmp) cc_final: 0.8796 (mmm) REVERT: F 1571 ASP cc_start: 0.8074 (m-30) cc_final: 0.7752 (t70) REVERT: G 88 MET cc_start: 0.9191 (tpt) cc_final: 0.8823 (tmm) REVERT: G 163 MET cc_start: 0.9242 (ttt) cc_final: 0.8953 (tmm) REVERT: G 348 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9194 (tm-30) REVERT: H 530 MET cc_start: 0.8970 (tpp) cc_final: 0.8508 (mtt) REVERT: H 710 MET cc_start: 0.8505 (mmt) cc_final: 0.8223 (tpp) REVERT: H 731 GLN cc_start: 0.8346 (tp40) cc_final: 0.8057 (tt0) REVERT: H 781 ASN cc_start: 0.8980 (t0) cc_final: 0.8684 (m-40) REVERT: H 869 MET cc_start: 0.9153 (tmm) cc_final: 0.8892 (tmm) REVERT: H 1176 TYR cc_start: 0.6038 (t80) cc_final: 0.5663 (m-80) REVERT: H 1220 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8598 (mp0) REVERT: H 1229 GLU cc_start: 0.9243 (tp30) cc_final: 0.9023 (tm-30) REVERT: H 1305 MET cc_start: 0.8048 (tpp) cc_final: 0.7809 (tpp) REVERT: H 1451 LEU cc_start: 0.8647 (mp) cc_final: 0.8392 (tt) REVERT: H 1525 MET cc_start: 0.9025 (mmp) cc_final: 0.8796 (mmm) REVERT: H 1571 ASP cc_start: 0.8078 (m-30) cc_final: 0.7756 (t70) outliers start: 4 outliers final: 4 residues processed: 543 average time/residue: 0.5680 time to fit residues: 537.8632 Evaluate side-chains 403 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 399 time to evaluate : 6.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 528 optimal weight: 10.0000 chunk 359 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 472 optimal weight: 40.0000 chunk 261 optimal weight: 5.9990 chunk 541 optimal weight: 10.0000 chunk 438 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 323 optimal weight: 6.9990 chunk 569 optimal weight: 30.0000 chunk 160 optimal weight: 50.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1203 HIS ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1203 HIS ** H1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 52164 Z= 0.342 Angle : 0.728 10.136 70964 Z= 0.364 Chirality : 0.043 0.231 8568 Planarity : 0.004 0.080 8708 Dihedral : 6.548 110.317 7120 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 0.49 (0.10), residues: 6492 helix: 1.38 (0.08), residues: 3956 sheet: -0.30 (0.21), residues: 528 loop : -1.66 (0.13), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 90 HIS 0.006 0.001 HIS B 67 PHE 0.032 0.002 PHE C 168 TYR 0.054 0.003 TYR F 123 ARG 0.003 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 5.864 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: A 88 MET cc_start: 0.9225 (tpt) cc_final: 0.8911 (tmm) REVERT: A 137 MET cc_start: 0.8590 (tpp) cc_final: 0.8358 (tpp) REVERT: A 163 MET cc_start: 0.9235 (ttt) cc_final: 0.8747 (tmm) REVERT: A 199 MET cc_start: 0.8957 (mmp) cc_final: 0.8438 (mmp) REVERT: A 348 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9021 (tm-30) REVERT: B 34 VAL cc_start: 0.9451 (t) cc_final: 0.9221 (t) REVERT: B 530 MET cc_start: 0.8877 (tpp) cc_final: 0.8426 (mtt) REVERT: B 710 MET cc_start: 0.8515 (mmt) cc_final: 0.8260 (tpp) REVERT: B 731 GLN cc_start: 0.8310 (tp40) cc_final: 0.8094 (tt0) REVERT: B 806 CYS cc_start: 0.9336 (m) cc_final: 0.8808 (t) REVERT: B 869 MET cc_start: 0.9091 (tmm) cc_final: 0.8839 (tmm) REVERT: B 1110 MET cc_start: 0.8238 (tpp) cc_final: 0.7994 (tpp) REVERT: B 1176 TYR cc_start: 0.5964 (t80) cc_final: 0.5500 (m-80) REVERT: B 1220 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8551 (mp0) REVERT: B 1229 GLU cc_start: 0.9327 (tp30) cc_final: 0.8995 (tm-30) REVERT: B 1248 LEU cc_start: 0.9479 (tp) cc_final: 0.9247 (tp) REVERT: B 1451 LEU cc_start: 0.8605 (mp) cc_final: 0.8337 (tt) REVERT: B 1525 MET cc_start: 0.8918 (mmp) cc_final: 0.8677 (mmm) REVERT: B 1571 ASP cc_start: 0.8097 (m-30) cc_final: 0.7805 (t70) REVERT: C 88 MET cc_start: 0.9220 (tpt) cc_final: 0.8911 (tmm) REVERT: C 137 MET cc_start: 0.8593 (tpp) cc_final: 0.8361 (tpp) REVERT: C 163 MET cc_start: 0.9324 (ttt) cc_final: 0.8766 (tmm) REVERT: C 199 MET cc_start: 0.8956 (mmp) cc_final: 0.8439 (mmp) REVERT: C 348 GLN cc_start: 0.9401 (tm-30) cc_final: 0.9020 (tm-30) REVERT: D 34 VAL cc_start: 0.9456 (t) cc_final: 0.9235 (t) REVERT: D 530 MET cc_start: 0.8876 (tpp) cc_final: 0.8421 (mtt) REVERT: D 710 MET cc_start: 0.8511 (mmt) cc_final: 0.8257 (tpp) REVERT: D 731 GLN cc_start: 0.8308 (tp40) cc_final: 0.8092 (tt0) REVERT: D 806 CYS cc_start: 0.9338 (m) cc_final: 0.8812 (t) REVERT: D 869 MET cc_start: 0.9091 (tmm) cc_final: 0.8839 (tmm) REVERT: D 1110 MET cc_start: 0.8235 (tpp) cc_final: 0.7991 (tpp) REVERT: D 1176 TYR cc_start: 0.5962 (t80) cc_final: 0.5500 (m-80) REVERT: D 1220 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8551 (mp0) REVERT: D 1229 GLU cc_start: 0.9329 (tp30) cc_final: 0.8995 (tm-30) REVERT: D 1248 LEU cc_start: 0.9478 (tp) cc_final: 0.9246 (tp) REVERT: D 1451 LEU cc_start: 0.8605 (mp) cc_final: 0.8337 (tt) REVERT: D 1525 MET cc_start: 0.8915 (mmp) cc_final: 0.8674 (mmm) REVERT: D 1571 ASP cc_start: 0.8096 (m-30) cc_final: 0.7804 (t70) REVERT: E 88 MET cc_start: 0.9220 (tpt) cc_final: 0.8910 (tmm) REVERT: E 137 MET cc_start: 0.8592 (tpp) cc_final: 0.8359 (tpp) REVERT: E 163 MET cc_start: 0.9326 (ttt) cc_final: 0.8765 (tmm) REVERT: E 199 MET cc_start: 0.8957 (mmp) cc_final: 0.8439 (mmp) REVERT: E 348 GLN cc_start: 0.9403 (tm-30) cc_final: 0.9022 (tm-30) REVERT: F 34 VAL cc_start: 0.9439 (t) cc_final: 0.9209 (t) REVERT: F 530 MET cc_start: 0.8875 (tpp) cc_final: 0.8419 (mtt) REVERT: F 710 MET cc_start: 0.8515 (mmt) cc_final: 0.8258 (tpp) REVERT: F 731 GLN cc_start: 0.8312 (tp40) cc_final: 0.8096 (tt0) REVERT: F 806 CYS cc_start: 0.9333 (m) cc_final: 0.8807 (t) REVERT: F 869 MET cc_start: 0.9094 (tmm) cc_final: 0.8843 (tmm) REVERT: F 1110 MET cc_start: 0.8241 (tpp) cc_final: 0.7997 (tpp) REVERT: F 1176 TYR cc_start: 0.5964 (t80) cc_final: 0.5500 (m-80) REVERT: F 1220 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8553 (mp0) REVERT: F 1229 GLU cc_start: 0.9327 (tp30) cc_final: 0.8994 (tm-30) REVERT: F 1248 LEU cc_start: 0.9478 (tp) cc_final: 0.9245 (tp) REVERT: F 1451 LEU cc_start: 0.8604 (mp) cc_final: 0.8337 (tt) REVERT: F 1525 MET cc_start: 0.8916 (mmp) cc_final: 0.8674 (mmm) REVERT: F 1571 ASP cc_start: 0.8094 (m-30) cc_final: 0.7802 (t70) REVERT: G 88 MET cc_start: 0.9225 (tpt) cc_final: 0.8914 (tmm) REVERT: G 137 MET cc_start: 0.8592 (tpp) cc_final: 0.8360 (tpp) REVERT: G 163 MET cc_start: 0.9327 (ttt) cc_final: 0.8758 (tmm) REVERT: G 199 MET cc_start: 0.8959 (mmp) cc_final: 0.8447 (mmp) REVERT: G 348 GLN cc_start: 0.9490 (tm-30) cc_final: 0.9192 (tm-30) REVERT: H 34 VAL cc_start: 0.9441 (t) cc_final: 0.9208 (t) REVERT: H 530 MET cc_start: 0.8873 (tpp) cc_final: 0.8422 (mtt) REVERT: H 710 MET cc_start: 0.8524 (mmt) cc_final: 0.8253 (tpp) REVERT: H 731 GLN cc_start: 0.8314 (tp40) cc_final: 0.8096 (tt0) REVERT: H 806 CYS cc_start: 0.9332 (m) cc_final: 0.8811 (t) REVERT: H 869 MET cc_start: 0.9098 (tmm) cc_final: 0.8843 (tmm) REVERT: H 1110 MET cc_start: 0.8242 (tpp) cc_final: 0.7996 (tpp) REVERT: H 1176 TYR cc_start: 0.5965 (t80) cc_final: 0.5502 (m-80) REVERT: H 1220 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8551 (mp0) REVERT: H 1229 GLU cc_start: 0.9328 (tp30) cc_final: 0.8995 (tm-30) REVERT: H 1248 LEU cc_start: 0.9480 (tp) cc_final: 0.9247 (tp) REVERT: H 1451 LEU cc_start: 0.8608 (mp) cc_final: 0.8339 (tt) REVERT: H 1525 MET cc_start: 0.8915 (mmp) cc_final: 0.8673 (mmm) REVERT: H 1571 ASP cc_start: 0.8096 (m-30) cc_final: 0.7805 (t70) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.5410 time to fit residues: 485.4350 Evaluate side-chains 376 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 5.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 213 optimal weight: 7.9990 chunk 571 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 156 optimal weight: 50.0000 chunk 634 optimal weight: 10.0000 chunk 526 optimal weight: 0.3980 chunk 293 optimal weight: 6.9990 chunk 52 optimal weight: 0.0370 chunk 209 optimal weight: 8.9990 chunk 333 optimal weight: 0.8980 overall best weight: 2.6662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 GLN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1427 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: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 52164 Z= 0.206 Angle : 0.662 11.114 70964 Z= 0.320 Chirality : 0.041 0.187 8568 Planarity : 0.004 0.070 8708 Dihedral : 6.231 102.139 7120 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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 (0.10), residues: 6492 helix: 1.66 (0.08), residues: 3948 sheet: -0.01 (0.22), residues: 508 loop : -1.54 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H1247 HIS 0.004 0.001 HIS D 562 PHE 0.026 0.001 PHE G 75 TYR 0.025 0.002 TYR B 123 ARG 0.003 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 6.047 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: A 88 MET cc_start: 0.9172 (tpt) cc_final: 0.8867 (tmm) REVERT: A 163 MET cc_start: 0.9191 (ttt) cc_final: 0.8560 (tmm) REVERT: A 199 MET cc_start: 0.8767 (mmp) cc_final: 0.8389 (mmp) REVERT: A 348 GLN cc_start: 0.9371 (tm-30) cc_final: 0.9066 (tm-30) REVERT: B 34 VAL cc_start: 0.9412 (t) cc_final: 0.9189 (t) REVERT: B 530 MET cc_start: 0.8899 (tpp) cc_final: 0.8453 (mtt) REVERT: B 710 MET cc_start: 0.8498 (mmt) cc_final: 0.8240 (tpp) REVERT: B 806 CYS cc_start: 0.9335 (m) cc_final: 0.8747 (t) REVERT: B 869 MET cc_start: 0.9075 (tmm) cc_final: 0.8863 (tmm) REVERT: B 1176 TYR cc_start: 0.6032 (t80) cc_final: 0.5595 (m-80) REVERT: B 1229 GLU cc_start: 0.9287 (tp30) cc_final: 0.8990 (tm-30) REVERT: B 1248 LEU cc_start: 0.9457 (tp) cc_final: 0.9251 (tp) REVERT: B 1451 LEU cc_start: 0.8610 (mp) cc_final: 0.8351 (tt) REVERT: B 1525 MET cc_start: 0.8922 (mmp) cc_final: 0.8682 (mmm) REVERT: B 1571 ASP cc_start: 0.8115 (m-30) cc_final: 0.7798 (t70) REVERT: C 88 MET cc_start: 0.9167 (tpt) cc_final: 0.8864 (tmm) REVERT: C 163 MET cc_start: 0.9178 (ttt) cc_final: 0.8589 (tmm) REVERT: C 199 MET cc_start: 0.8770 (mmp) cc_final: 0.8398 (mmp) REVERT: C 348 GLN cc_start: 0.9369 (tm-30) cc_final: 0.9063 (tm-30) REVERT: D 34 VAL cc_start: 0.9411 (t) cc_final: 0.9195 (t) REVERT: D 530 MET cc_start: 0.8899 (tpp) cc_final: 0.8452 (mtt) REVERT: D 710 MET cc_start: 0.8496 (mmt) cc_final: 0.8241 (tpp) REVERT: D 806 CYS cc_start: 0.9338 (m) cc_final: 0.8750 (t) REVERT: D 869 MET cc_start: 0.9076 (tmm) cc_final: 0.8866 (tmm) REVERT: D 1176 TYR cc_start: 0.6032 (t80) cc_final: 0.5594 (m-80) REVERT: D 1229 GLU cc_start: 0.9288 (tp30) cc_final: 0.8991 (tm-30) REVERT: D 1248 LEU cc_start: 0.9456 (tp) cc_final: 0.9251 (tp) REVERT: D 1451 LEU cc_start: 0.8608 (mp) cc_final: 0.8349 (tt) REVERT: D 1525 MET cc_start: 0.8918 (mmp) cc_final: 0.8679 (mmm) REVERT: D 1571 ASP cc_start: 0.8114 (m-30) cc_final: 0.7798 (t70) REVERT: E 88 MET cc_start: 0.9165 (tpt) cc_final: 0.8863 (tmm) REVERT: E 163 MET cc_start: 0.9135 (ttt) cc_final: 0.8561 (tmm) REVERT: E 199 MET cc_start: 0.8778 (mmp) cc_final: 0.8401 (mmp) REVERT: E 348 GLN cc_start: 0.9371 (tm-30) cc_final: 0.9065 (tm-30) REVERT: F 34 VAL cc_start: 0.9411 (t) cc_final: 0.9193 (t) REVERT: F 530 MET cc_start: 0.8896 (tpp) cc_final: 0.8447 (mtt) REVERT: F 710 MET cc_start: 0.8500 (mmt) cc_final: 0.8243 (tpp) REVERT: F 806 CYS cc_start: 0.9334 (m) cc_final: 0.8748 (t) REVERT: F 869 MET cc_start: 0.9077 (tmm) cc_final: 0.8865 (tmm) REVERT: F 1176 TYR cc_start: 0.6030 (t80) cc_final: 0.5594 (m-80) REVERT: F 1229 GLU cc_start: 0.9289 (tp30) cc_final: 0.8991 (tm-30) REVERT: F 1248 LEU cc_start: 0.9456 (tp) cc_final: 0.9251 (tp) REVERT: F 1451 LEU cc_start: 0.8609 (mp) cc_final: 0.8350 (tt) REVERT: F 1525 MET cc_start: 0.8918 (mmp) cc_final: 0.8680 (mmm) REVERT: F 1571 ASP cc_start: 0.8111 (m-30) cc_final: 0.7796 (t70) REVERT: G 88 MET cc_start: 0.9167 (tpt) cc_final: 0.8866 (tmm) REVERT: G 163 MET cc_start: 0.9138 (ttt) cc_final: 0.8560 (tmm) REVERT: G 199 MET cc_start: 0.8763 (mmp) cc_final: 0.8386 (mmp) REVERT: G 348 GLN cc_start: 0.9404 (tm-30) cc_final: 0.9090 (tm-30) REVERT: H 34 VAL cc_start: 0.9413 (t) cc_final: 0.9194 (t) REVERT: H 530 MET cc_start: 0.8899 (tpp) cc_final: 0.8450 (mtt) REVERT: H 710 MET cc_start: 0.8496 (mmt) cc_final: 0.8238 (tpp) REVERT: H 806 CYS cc_start: 0.9333 (m) cc_final: 0.8754 (t) REVERT: H 869 MET cc_start: 0.9078 (tmm) cc_final: 0.8866 (tmm) REVERT: H 1176 TYR cc_start: 0.6029 (t80) cc_final: 0.5595 (m-80) REVERT: H 1229 GLU cc_start: 0.9289 (tp30) cc_final: 0.8992 (tm-30) REVERT: H 1248 LEU cc_start: 0.9457 (tp) cc_final: 0.9251 (tp) REVERT: H 1451 LEU cc_start: 0.8611 (mp) cc_final: 0.8352 (tt) REVERT: H 1525 MET cc_start: 0.8919 (mmp) cc_final: 0.8680 (mmm) REVERT: H 1571 ASP cc_start: 0.8116 (m-30) cc_final: 0.7801 (t70) outliers start: 0 outliers final: 0 residues processed: 505 average time/residue: 0.5445 time to fit residues: 496.0540 Evaluate side-chains 378 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 378 time to evaluate : 5.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 611 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 361 optimal weight: 2.9990 chunk 463 optimal weight: 1.9990 chunk 359 optimal weight: 5.9990 chunk 534 optimal weight: 4.9990 chunk 354 optimal weight: 0.9980 chunk 632 optimal weight: 0.8980 chunk 395 optimal weight: 10.0000 chunk 385 optimal weight: 9.9990 chunk 291 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1203 HIS ** B1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1203 HIS ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 152 GLN ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 GLN ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52164 Z= 0.196 Angle : 0.642 11.381 70964 Z= 0.310 Chirality : 0.041 0.184 8568 Planarity : 0.004 0.066 8708 Dihedral : 6.035 95.224 7120 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % 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: 1.00 (0.10), residues: 6492 helix: 1.75 (0.08), residues: 3976 sheet: 0.26 (0.22), residues: 528 loop : -1.50 (0.13), residues: 1988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H1247 HIS 0.014 0.001 HIS C 259 PHE 0.025 0.001 PHE A 75 TYR 0.023 0.001 TYR B 123 ARG 0.002 0.000 ARG H1218 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 5.974 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: A 88 MET cc_start: 0.9163 (tpt) cc_final: 0.8886 (tmm) REVERT: A 163 MET cc_start: 0.9142 (ttt) cc_final: 0.8492 (tmm) REVERT: A 199 MET cc_start: 0.8839 (mmp) cc_final: 0.8409 (mmp) REVERT: A 348 GLN cc_start: 0.9341 (tm-30) cc_final: 0.9061 (tm-30) REVERT: B 233 MET cc_start: 0.9028 (mmm) cc_final: 0.8701 (mmt) REVERT: B 530 MET cc_start: 0.8933 (tpp) cc_final: 0.8533 (mtt) REVERT: B 710 MET cc_start: 0.8504 (mmt) cc_final: 0.8242 (tpp) REVERT: B 806 CYS cc_start: 0.9350 (m) cc_final: 0.8720 (t) REVERT: B 1176 TYR cc_start: 0.6208 (t80) cc_final: 0.5768 (m-80) REVERT: B 1229 GLU cc_start: 0.9279 (tp30) cc_final: 0.9001 (tm-30) REVERT: B 1248 LEU cc_start: 0.9493 (tp) cc_final: 0.9283 (tp) REVERT: B 1451 LEU cc_start: 0.8621 (mp) cc_final: 0.8371 (tt) REVERT: B 1525 MET cc_start: 0.8998 (mmp) cc_final: 0.8759 (mmm) REVERT: B 1571 ASP cc_start: 0.8119 (m-30) cc_final: 0.7815 (t70) REVERT: C 88 MET cc_start: 0.9131 (tpt) cc_final: 0.8842 (tmm) REVERT: C 163 MET cc_start: 0.9208 (ttt) cc_final: 0.8592 (tmm) REVERT: C 199 MET cc_start: 0.8832 (mmp) cc_final: 0.8406 (mmp) REVERT: C 348 GLN cc_start: 0.9340 (tm-30) cc_final: 0.9059 (tm-30) REVERT: D 233 MET cc_start: 0.9026 (mmm) cc_final: 0.8699 (mmt) REVERT: D 530 MET cc_start: 0.8930 (tpp) cc_final: 0.8530 (mtt) REVERT: D 710 MET cc_start: 0.8507 (mmt) cc_final: 0.8245 (tpp) REVERT: D 731 GLN cc_start: 0.8211 (tp40) cc_final: 0.8011 (tt0) REVERT: D 806 CYS cc_start: 0.9351 (m) cc_final: 0.8723 (t) REVERT: D 1176 TYR cc_start: 0.6208 (t80) cc_final: 0.5770 (m-80) REVERT: D 1229 GLU cc_start: 0.9278 (tp30) cc_final: 0.9002 (tm-30) REVERT: D 1248 LEU cc_start: 0.9491 (tp) cc_final: 0.9282 (tp) REVERT: D 1451 LEU cc_start: 0.8619 (mp) cc_final: 0.8370 (tt) REVERT: D 1525 MET cc_start: 0.8995 (mmp) cc_final: 0.8757 (mmm) REVERT: D 1571 ASP cc_start: 0.8118 (m-30) cc_final: 0.7815 (t70) REVERT: E 88 MET cc_start: 0.9130 (tpt) cc_final: 0.8840 (tmm) REVERT: E 163 MET cc_start: 0.9213 (ttt) cc_final: 0.8597 (tmm) REVERT: E 199 MET cc_start: 0.8841 (mmp) cc_final: 0.8412 (mmp) REVERT: E 348 GLN cc_start: 0.9339 (tm-30) cc_final: 0.9059 (tm-30) REVERT: F 233 MET cc_start: 0.9025 (mmm) cc_final: 0.8696 (mmt) REVERT: F 530 MET cc_start: 0.8930 (tpp) cc_final: 0.8526 (mtt) REVERT: F 710 MET cc_start: 0.8509 (mmt) cc_final: 0.8246 (tpp) REVERT: F 731 GLN cc_start: 0.8217 (tp40) cc_final: 0.8013 (tt0) REVERT: F 806 CYS cc_start: 0.9348 (m) cc_final: 0.8722 (t) REVERT: F 1176 TYR cc_start: 0.6206 (t80) cc_final: 0.5767 (m-80) REVERT: F 1229 GLU cc_start: 0.9280 (tp30) cc_final: 0.8993 (tm-30) REVERT: F 1248 LEU cc_start: 0.9493 (tp) cc_final: 0.9283 (tp) REVERT: F 1398 MET cc_start: 0.6950 (mtp) cc_final: 0.6739 (mtp) REVERT: F 1451 LEU cc_start: 0.8618 (mp) cc_final: 0.8370 (tt) REVERT: F 1525 MET cc_start: 0.8995 (mmp) cc_final: 0.8757 (mmm) REVERT: F 1571 ASP cc_start: 0.8117 (m-30) cc_final: 0.7814 (t70) REVERT: G 88 MET cc_start: 0.9136 (tpt) cc_final: 0.8842 (tmm) REVERT: G 163 MET cc_start: 0.9221 (ttt) cc_final: 0.8590 (tmm) REVERT: G 199 MET cc_start: 0.8836 (mmp) cc_final: 0.8405 (mmp) REVERT: G 348 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9024 (tm-30) REVERT: H 233 MET cc_start: 0.9024 (mmm) cc_final: 0.8696 (mmt) REVERT: H 530 MET cc_start: 0.8930 (tpp) cc_final: 0.8531 (mtt) REVERT: H 731 GLN cc_start: 0.8220 (tp40) cc_final: 0.8019 (tt0) REVERT: H 806 CYS cc_start: 0.9348 (m) cc_final: 0.8728 (t) REVERT: H 1176 TYR cc_start: 0.6206 (t80) cc_final: 0.5765 (m-80) REVERT: H 1229 GLU cc_start: 0.9280 (tp30) cc_final: 0.8994 (tm-30) REVERT: H 1248 LEU cc_start: 0.9493 (tp) cc_final: 0.9284 (tp) REVERT: H 1451 LEU cc_start: 0.8621 (mp) cc_final: 0.8372 (tt) REVERT: H 1525 MET cc_start: 0.8997 (mmp) cc_final: 0.8756 (mmm) REVERT: H 1571 ASP cc_start: 0.8121 (m-30) cc_final: 0.7818 (t70) outliers start: 0 outliers final: 0 residues processed: 513 average time/residue: 0.5594 time to fit residues: 510.4163 Evaluate side-chains 388 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 5.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 391 optimal weight: 7.9990 chunk 252 optimal weight: 0.7980 chunk 377 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 122 optimal weight: 0.0370 chunk 401 optimal weight: 50.0000 chunk 430 optimal weight: 6.9990 chunk 312 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 chunk 496 optimal weight: 0.9990 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 234 HIS ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 707 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 HIS ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 707 GLN ** H 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 52164 Z= 0.197 Angle : 0.662 11.423 70964 Z= 0.319 Chirality : 0.041 0.223 8568 Planarity : 0.004 0.062 8708 Dihedral : 5.855 89.762 7120 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 0.02 % Allowed : 1.09 % Favored : 98.89 % 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: 1.08 (0.10), residues: 6492 helix: 1.82 (0.08), residues: 3944 sheet: 0.20 (0.22), residues: 508 loop : -1.37 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 68 HIS 0.011 0.001 HIS G 259 PHE 0.032 0.001 PHE E 168 TYR 0.022 0.001 TYR B 123 ARG 0.003 0.000 ARG D1554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 512 time to evaluate : 6.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9165 (tpt) cc_final: 0.8907 (tmm) REVERT: A 163 MET cc_start: 0.9182 (ttt) cc_final: 0.8476 (tmm) REVERT: A 199 MET cc_start: 0.8819 (mmp) cc_final: 0.8344 (mmp) REVERT: A 234 HIS cc_start: 0.8964 (t-90) cc_final: 0.8245 (t-90) REVERT: A 348 GLN cc_start: 0.9286 (tm-30) cc_final: 0.8993 (tm-30) REVERT: B 233 MET cc_start: 0.9107 (mmm) cc_final: 0.8856 (mmt) REVERT: B 506 MET cc_start: 0.5941 (ppp) cc_final: 0.5684 (ppp) REVERT: B 530 MET cc_start: 0.8875 (tpp) cc_final: 0.8506 (mtt) REVERT: B 806 CYS cc_start: 0.9343 (m) cc_final: 0.8712 (t) REVERT: B 1176 TYR cc_start: 0.6857 (t80) cc_final: 0.6399 (m-80) REVERT: B 1229 GLU cc_start: 0.9247 (tp30) cc_final: 0.8981 (tm-30) REVERT: B 1248 LEU cc_start: 0.9502 (tp) cc_final: 0.9288 (tp) REVERT: B 1451 LEU cc_start: 0.8622 (mp) cc_final: 0.8381 (tt) REVERT: B 1525 MET cc_start: 0.8962 (mmp) cc_final: 0.8728 (mmm) REVERT: B 1571 ASP cc_start: 0.8127 (m-30) cc_final: 0.7816 (t70) REVERT: C 88 MET cc_start: 0.9167 (tpt) cc_final: 0.8906 (tmm) REVERT: C 163 MET cc_start: 0.8986 (ttt) cc_final: 0.8264 (tmm) REVERT: C 199 MET cc_start: 0.8813 (mmp) cc_final: 0.8332 (mmp) REVERT: C 234 HIS cc_start: 0.8968 (t-90) cc_final: 0.8245 (t-90) REVERT: C 348 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8992 (tm-30) REVERT: D 233 MET cc_start: 0.9106 (mmm) cc_final: 0.8855 (mmt) REVERT: D 506 MET cc_start: 0.5946 (ppp) cc_final: 0.5690 (ppp) REVERT: D 530 MET cc_start: 0.8927 (tpp) cc_final: 0.8537 (mtt) REVERT: D 806 CYS cc_start: 0.9344 (m) cc_final: 0.8710 (t) REVERT: D 1176 TYR cc_start: 0.6862 (t80) cc_final: 0.6400 (m-80) REVERT: D 1229 GLU cc_start: 0.9247 (tp30) cc_final: 0.8980 (tm-30) REVERT: D 1248 LEU cc_start: 0.9503 (tp) cc_final: 0.9287 (tp) REVERT: D 1451 LEU cc_start: 0.8622 (mp) cc_final: 0.8380 (tt) REVERT: D 1525 MET cc_start: 0.8960 (mmp) cc_final: 0.8726 (mmm) REVERT: D 1571 ASP cc_start: 0.8125 (m-30) cc_final: 0.7814 (t70) REVERT: E 88 MET cc_start: 0.9168 (tpt) cc_final: 0.8906 (tmm) REVERT: E 163 MET cc_start: 0.9042 (ttt) cc_final: 0.8319 (tmm) REVERT: E 199 MET cc_start: 0.8820 (mmp) cc_final: 0.8333 (mmp) REVERT: E 234 HIS cc_start: 0.8970 (t-90) cc_final: 0.8264 (t-90) REVERT: E 348 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8992 (tm-30) REVERT: F 233 MET cc_start: 0.9106 (mmm) cc_final: 0.8857 (mmt) REVERT: F 506 MET cc_start: 0.5953 (ppp) cc_final: 0.5692 (ppp) REVERT: F 530 MET cc_start: 0.8928 (tpp) cc_final: 0.8537 (mtt) REVERT: F 806 CYS cc_start: 0.9343 (m) cc_final: 0.8708 (t) REVERT: F 1176 TYR cc_start: 0.6855 (t80) cc_final: 0.6398 (m-80) REVERT: F 1229 GLU cc_start: 0.9253 (tp30) cc_final: 0.8985 (tm-30) REVERT: F 1248 LEU cc_start: 0.9501 (tp) cc_final: 0.9285 (tp) REVERT: F 1451 LEU cc_start: 0.8619 (mp) cc_final: 0.8378 (tt) REVERT: F 1525 MET cc_start: 0.8958 (mmp) cc_final: 0.8724 (mmm) REVERT: F 1571 ASP cc_start: 0.8125 (m-30) cc_final: 0.7814 (t70) REVERT: G 88 MET cc_start: 0.9166 (tpt) cc_final: 0.8910 (tmm) REVERT: G 163 MET cc_start: 0.8993 (ttt) cc_final: 0.8268 (tmm) REVERT: G 199 MET cc_start: 0.8803 (mmp) cc_final: 0.8371 (mmp) REVERT: G 234 HIS cc_start: 0.8903 (t-90) cc_final: 0.8235 (t-90) REVERT: G 348 GLN cc_start: 0.9427 (tm-30) cc_final: 0.9100 (tm-30) REVERT: H 233 MET cc_start: 0.9106 (mmm) cc_final: 0.8855 (mmt) REVERT: H 506 MET cc_start: 0.5936 (ppp) cc_final: 0.5677 (ppp) REVERT: H 530 MET cc_start: 0.8928 (tpp) cc_final: 0.8538 (mtt) REVERT: H 806 CYS cc_start: 0.9343 (m) cc_final: 0.8716 (t) REVERT: H 1176 TYR cc_start: 0.6857 (t80) cc_final: 0.6399 (m-80) REVERT: H 1229 GLU cc_start: 0.9255 (tp30) cc_final: 0.8987 (tm-30) REVERT: H 1248 LEU cc_start: 0.9501 (tp) cc_final: 0.9288 (tp) REVERT: H 1451 LEU cc_start: 0.8624 (mp) cc_final: 0.8383 (tt) REVERT: H 1525 MET cc_start: 0.8957 (mmp) cc_final: 0.8724 (mmm) REVERT: H 1571 ASP cc_start: 0.8128 (m-30) cc_final: 0.7819 (t70) outliers start: 1 outliers final: 0 residues processed: 513 average time/residue: 0.5371 time to fit residues: 496.0382 Evaluate side-chains 406 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 5.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 575 optimal weight: 6.9990 chunk 605 optimal weight: 30.0000 chunk 552 optimal weight: 4.9990 chunk 589 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 256 optimal weight: 50.0000 chunk 462 optimal weight: 0.0050 chunk 180 optimal weight: 0.9990 chunk 532 optimal weight: 0.8980 chunk 557 optimal weight: 40.0000 chunk 587 optimal weight: 40.0000 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 707 GLN ** B 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 707 GLN ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 707 GLN ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 52164 Z= 0.198 Angle : 0.654 11.827 70964 Z= 0.312 Chirality : 0.041 0.217 8568 Planarity : 0.004 0.075 8708 Dihedral : 5.724 84.890 7120 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.74 % Favored : 96.20 % Rotamer: Outliers : 0.06 % Allowed : 0.37 % Favored : 99.58 % 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: 1.12 (0.11), residues: 6492 helix: 1.85 (0.08), residues: 3936 sheet: 0.06 (0.21), residues: 528 loop : -1.32 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 68 HIS 0.010 0.001 HIS G 259 PHE 0.027 0.001 PHE A 75 TYR 0.027 0.002 TYR B 123 ARG 0.003 0.000 ARG E 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 517 time to evaluate : 6.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9194 (tpt) cc_final: 0.8895 (tmm) REVERT: A 163 MET cc_start: 0.9170 (ttt) cc_final: 0.8517 (tmm) REVERT: A 199 MET cc_start: 0.8804 (mmp) cc_final: 0.8377 (mmp) REVERT: A 234 HIS cc_start: 0.8916 (t-90) cc_final: 0.8309 (t-90) REVERT: A 348 GLN cc_start: 0.9301 (tm-30) cc_final: 0.9031 (tm-30) REVERT: B 184 LEU cc_start: 0.9123 (tt) cc_final: 0.8899 (mt) REVERT: B 218 LEU cc_start: 0.8700 (pp) cc_final: 0.8426 (mt) REVERT: B 506 MET cc_start: 0.5990 (ppp) cc_final: 0.5714 (ppp) REVERT: B 530 MET cc_start: 0.8841 (tpp) cc_final: 0.8465 (mtt) REVERT: B 730 MET cc_start: 0.1219 (ttt) cc_final: 0.0891 (ttt) REVERT: B 806 CYS cc_start: 0.9345 (m) cc_final: 0.8707 (t) REVERT: B 1176 TYR cc_start: 0.7094 (t80) cc_final: 0.6589 (m-80) REVERT: B 1229 GLU cc_start: 0.9241 (tp30) cc_final: 0.8970 (tm-30) REVERT: B 1248 LEU cc_start: 0.9511 (tp) cc_final: 0.9302 (tp) REVERT: B 1451 LEU cc_start: 0.8623 (mp) cc_final: 0.8390 (tt) REVERT: B 1525 MET cc_start: 0.8879 (mmp) cc_final: 0.8668 (mmm) REVERT: B 1571 ASP cc_start: 0.8138 (m-30) cc_final: 0.7823 (t70) REVERT: C 88 MET cc_start: 0.9186 (tpt) cc_final: 0.8887 (tmm) REVERT: C 163 MET cc_start: 0.9207 (ttt) cc_final: 0.8567 (tmm) REVERT: C 199 MET cc_start: 0.8788 (mmp) cc_final: 0.8384 (mmp) REVERT: C 234 HIS cc_start: 0.8916 (t-90) cc_final: 0.8306 (t-90) REVERT: C 292 GLU cc_start: 0.8865 (pm20) cc_final: 0.8599 (pm20) REVERT: C 348 GLN cc_start: 0.9302 (tm-30) cc_final: 0.9033 (tm-30) REVERT: D 184 LEU cc_start: 0.9121 (tt) cc_final: 0.8900 (mt) REVERT: D 218 LEU cc_start: 0.8704 (pp) cc_final: 0.8428 (mt) REVERT: D 506 MET cc_start: 0.5987 (ppp) cc_final: 0.5716 (ppp) REVERT: D 530 MET cc_start: 0.8837 (tpp) cc_final: 0.8461 (mtt) REVERT: D 806 CYS cc_start: 0.9347 (m) cc_final: 0.8706 (t) REVERT: D 1176 TYR cc_start: 0.7100 (t80) cc_final: 0.6590 (m-80) REVERT: D 1229 GLU cc_start: 0.9242 (tp30) cc_final: 0.8968 (tm-30) REVERT: D 1248 LEU cc_start: 0.9511 (tp) cc_final: 0.9301 (tp) REVERT: D 1451 LEU cc_start: 0.8621 (mp) cc_final: 0.8390 (tt) REVERT: D 1525 MET cc_start: 0.8876 (mmp) cc_final: 0.8664 (mmm) REVERT: D 1571 ASP cc_start: 0.8137 (m-30) cc_final: 0.7821 (t70) REVERT: E 88 MET cc_start: 0.9190 (tpt) cc_final: 0.8889 (tmm) REVERT: E 163 MET cc_start: 0.9228 (ttt) cc_final: 0.8593 (tmm) REVERT: E 199 MET cc_start: 0.8796 (mmp) cc_final: 0.8389 (mmp) REVERT: E 234 HIS cc_start: 0.8913 (t-90) cc_final: 0.8306 (t-90) REVERT: E 292 GLU cc_start: 0.8855 (pm20) cc_final: 0.8578 (pm20) REVERT: E 348 GLN cc_start: 0.9301 (tm-30) cc_final: 0.9031 (tm-30) REVERT: F 184 LEU cc_start: 0.9119 (tt) cc_final: 0.8896 (mt) REVERT: F 218 LEU cc_start: 0.8699 (pp) cc_final: 0.8423 (mt) REVERT: F 506 MET cc_start: 0.5995 (ppp) cc_final: 0.5722 (ppp) REVERT: F 530 MET cc_start: 0.8835 (tpp) cc_final: 0.8459 (mtt) REVERT: F 806 CYS cc_start: 0.9344 (m) cc_final: 0.8702 (t) REVERT: F 1176 TYR cc_start: 0.7094 (t80) cc_final: 0.6587 (m-80) REVERT: F 1229 GLU cc_start: 0.9236 (tp30) cc_final: 0.8969 (tm-30) REVERT: F 1248 LEU cc_start: 0.9509 (tp) cc_final: 0.9298 (tp) REVERT: F 1451 LEU cc_start: 0.8619 (mp) cc_final: 0.8388 (tt) REVERT: F 1525 MET cc_start: 0.8879 (mmp) cc_final: 0.8669 (mmm) REVERT: F 1571 ASP cc_start: 0.8138 (m-30) cc_final: 0.7824 (t70) REVERT: G 88 MET cc_start: 0.9197 (tpt) cc_final: 0.8897 (tmm) REVERT: G 163 MET cc_start: 0.9204 (ttt) cc_final: 0.8576 (tmm) REVERT: G 199 MET cc_start: 0.8803 (mmp) cc_final: 0.8379 (mmp) REVERT: G 234 HIS cc_start: 0.8837 (t-90) cc_final: 0.8241 (t-90) REVERT: G 292 GLU cc_start: 0.8877 (pm20) cc_final: 0.8584 (pm20) REVERT: G 348 GLN cc_start: 0.9325 (tm-30) cc_final: 0.8976 (tm-30) REVERT: H 184 LEU cc_start: 0.9121 (tt) cc_final: 0.8899 (mt) REVERT: H 218 LEU cc_start: 0.8699 (pp) cc_final: 0.8423 (mt) REVERT: H 506 MET cc_start: 0.5980 (ppp) cc_final: 0.5706 (ppp) REVERT: H 530 MET cc_start: 0.8836 (tpp) cc_final: 0.8459 (mtt) REVERT: H 806 CYS cc_start: 0.9346 (m) cc_final: 0.8712 (t) REVERT: H 1176 TYR cc_start: 0.7098 (t80) cc_final: 0.6590 (m-80) REVERT: H 1229 GLU cc_start: 0.9237 (tp30) cc_final: 0.8972 (tm-30) REVERT: H 1248 LEU cc_start: 0.9509 (tp) cc_final: 0.9299 (tp) REVERT: H 1451 LEU cc_start: 0.8625 (mp) cc_final: 0.8392 (tt) REVERT: H 1525 MET cc_start: 0.8877 (mmp) cc_final: 0.8665 (mmm) REVERT: H 1571 ASP cc_start: 0.8142 (m-30) cc_final: 0.7827 (t70) outliers start: 3 outliers final: 0 residues processed: 520 average time/residue: 0.5294 time to fit residues: 497.3383 Evaluate side-chains 412 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 412 time to evaluate : 6.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 386 optimal weight: 6.9990 chunk 623 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 chunk 295 optimal weight: 10.0000 chunk 433 optimal weight: 7.9990 chunk 653 optimal weight: 8.9990 chunk 601 optimal weight: 20.0000 chunk 520 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 401 optimal weight: 4.9990 chunk 319 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 846 GLN B1203 HIS ** B1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 846 GLN D1203 HIS ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 846 GLN F1203 HIS ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 731 GLN ** H 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 846 GLN H1203 HIS ** H1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 52164 Z= 0.386 Angle : 0.782 11.079 70964 Z= 0.390 Chirality : 0.045 0.226 8568 Planarity : 0.005 0.068 8708 Dihedral : 6.138 83.025 7120 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.51 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: 0.70 (0.10), residues: 6492 helix: 1.50 (0.08), residues: 3960 sheet: -0.14 (0.21), residues: 536 loop : -1.49 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 232 HIS 0.028 0.002 HIS E 259 PHE 0.052 0.002 PHE E 168 TYR 0.067 0.003 TYR F 123 ARG 0.008 0.001 ARG F 620 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12984 Ramachandran restraints generated. 6492 Oldfield, 0 Emsley, 6492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 5.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 MET cc_start: 0.9208 (tpt) cc_final: 0.8961 (tmm) REVERT: A 163 MET cc_start: 0.9420 (ttt) cc_final: 0.9011 (tmm) REVERT: A 199 MET cc_start: 0.8891 (mmp) cc_final: 0.8425 (mmp) REVERT: A 234 HIS cc_start: 0.9122 (t-90) cc_final: 0.8453 (t-170) REVERT: A 348 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8966 (tm-30) REVERT: B 506 MET cc_start: 0.5982 (ppp) cc_final: 0.5707 (ppp) REVERT: B 530 MET cc_start: 0.8846 (tpp) cc_final: 0.8455 (mtt) REVERT: B 801 MET cc_start: 0.8957 (ttp) cc_final: 0.8751 (ptm) REVERT: B 1176 TYR cc_start: 0.7279 (t80) cc_final: 0.6723 (m-80) REVERT: B 1229 GLU cc_start: 0.9254 (tp30) cc_final: 0.8983 (tm-30) REVERT: B 1451 LEU cc_start: 0.8616 (mp) cc_final: 0.8374 (tt) REVERT: B 1525 MET cc_start: 0.8840 (mmp) cc_final: 0.8596 (mmm) REVERT: B 1571 ASP cc_start: 0.8157 (m-30) cc_final: 0.7794 (t70) REVERT: C 88 MET cc_start: 0.9200 (tpt) cc_final: 0.8950 (tmm) REVERT: C 163 MET cc_start: 0.9265 (ttt) cc_final: 0.8586 (tmm) REVERT: C 199 MET cc_start: 0.8912 (mmp) cc_final: 0.8400 (mmp) REVERT: C 234 HIS cc_start: 0.9125 (t-90) cc_final: 0.8458 (t-170) REVERT: C 348 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8965 (tm-30) REVERT: D 506 MET cc_start: 0.5984 (ppp) cc_final: 0.5708 (ppp) REVERT: D 530 MET cc_start: 0.8843 (tpp) cc_final: 0.8452 (mtt) REVERT: D 801 MET cc_start: 0.8952 (ttp) cc_final: 0.8749 (ptm) REVERT: D 1176 TYR cc_start: 0.7285 (t80) cc_final: 0.6716 (m-80) REVERT: D 1229 GLU cc_start: 0.9254 (tp30) cc_final: 0.8981 (tm-30) REVERT: D 1451 LEU cc_start: 0.8617 (mp) cc_final: 0.8379 (tt) REVERT: D 1525 MET cc_start: 0.8838 (mmp) cc_final: 0.8593 (mmm) REVERT: D 1571 ASP cc_start: 0.8155 (m-30) cc_final: 0.7793 (t70) REVERT: E 88 MET cc_start: 0.9200 (tpt) cc_final: 0.8951 (tmm) REVERT: E 163 MET cc_start: 0.9302 (ttt) cc_final: 0.8744 (tmm) REVERT: E 199 MET cc_start: 0.8917 (mmp) cc_final: 0.8410 (mmp) REVERT: E 234 HIS cc_start: 0.9130 (t-90) cc_final: 0.8482 (t-170) REVERT: E 348 GLN cc_start: 0.9266 (tm-30) cc_final: 0.8966 (tm-30) REVERT: F 506 MET cc_start: 0.5989 (ppp) cc_final: 0.5709 (ppp) REVERT: F 530 MET cc_start: 0.8842 (tpp) cc_final: 0.8451 (mtt) REVERT: F 801 MET cc_start: 0.8954 (ttp) cc_final: 0.8748 (ptm) REVERT: F 1176 TYR cc_start: 0.7282 (t80) cc_final: 0.6717 (m-80) REVERT: F 1229 GLU cc_start: 0.9259 (tp30) cc_final: 0.8982 (tm-30) REVERT: F 1451 LEU cc_start: 0.8615 (mp) cc_final: 0.8374 (tt) REVERT: F 1525 MET cc_start: 0.8838 (mmp) cc_final: 0.8594 (mmm) REVERT: F 1571 ASP cc_start: 0.8156 (m-30) cc_final: 0.7793 (t70) REVERT: G 88 MET cc_start: 0.9207 (tpt) cc_final: 0.8955 (tmm) REVERT: G 163 MET cc_start: 0.9276 (ttt) cc_final: 0.8745 (tmm) REVERT: G 199 MET cc_start: 0.8922 (mmp) cc_final: 0.8402 (mmp) REVERT: G 348 GLN cc_start: 0.9330 (tm-30) cc_final: 0.8990 (tm-30) REVERT: H 506 MET cc_start: 0.5980 (ppp) cc_final: 0.5709 (ppp) REVERT: H 530 MET cc_start: 0.8844 (tpp) cc_final: 0.8453 (mtt) REVERT: H 801 MET cc_start: 0.8952 (ttp) cc_final: 0.8746 (ptm) REVERT: H 1176 TYR cc_start: 0.7283 (t80) cc_final: 0.6720 (m-80) REVERT: H 1229 GLU cc_start: 0.9259 (tp30) cc_final: 0.8986 (tm-30) REVERT: H 1451 LEU cc_start: 0.8622 (mp) cc_final: 0.8382 (tt) REVERT: H 1525 MET cc_start: 0.8837 (mmp) cc_final: 0.8594 (mmm) REVERT: H 1571 ASP cc_start: 0.8148 (m-30) cc_final: 0.7797 (t70) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.5459 time to fit residues: 438.9994 Evaluate side-chains 348 residues out of total 5724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 348 time to evaluate : 6.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 656 random chunks: chunk 413 optimal weight: 9.9990 chunk 554 optimal weight: 9.9990 chunk 159 optimal weight: 50.0000 chunk 479 optimal weight: 3.9990 chunk 76 optimal weight: 30.0000 chunk 144 optimal weight: 40.0000 chunk 521 optimal weight: 0.9990 chunk 218 optimal weight: 20.0000 chunk 535 optimal weight: 0.7980 chunk 65 optimal weight: 40.0000 chunk 96 optimal weight: 20.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.080115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.059720 restraints weight = 285638.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.059986 restraints weight = 167255.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.059715 restraints weight = 122935.159| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 52164 Z= 0.286 Angle : 0.709 11.499 70964 Z= 0.348 Chirality : 0.043 0.217 8568 Planarity : 0.005 0.064 8708 Dihedral : 6.035 83.642 7120 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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 (0.10), residues: 6492 helix: 1.57 (0.08), residues: 3952 sheet: 0.01 (0.22), residues: 504 loop : -1.53 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 68 HIS 0.019 0.001 HIS G 259 PHE 0.037 0.002 PHE A 75 TYR 0.069 0.002 TYR B 123 ARG 0.014 0.000 ARG F1353 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11008.50 seconds wall clock time: 199 minutes 41.70 seconds (11981.70 seconds total)