Starting phenix.real_space_refine on Sun Feb 25 09:34:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/02_2024/5yw8_6848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/02_2024/5yw8_6848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/02_2024/5yw8_6848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/02_2024/5yw8_6848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/02_2024/5yw8_6848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yw8_6848/02_2024/5yw8_6848_updated.pdb" } resolution = 4.4 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= 0.002 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 272 5.16 5 C 32848 2.51 5 N 8540 2.21 5 O 8840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 598": "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 999": "NH1" <-> "NH2" Residue "B ARG 1099": "NH1" <-> "NH2" Residue "B ARG 1104": "NH1" <-> "NH2" Residue "B ARG 1145": "NH1" <-> "NH2" Residue "B TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1531": "NH1" <-> "NH2" Residue "B ARG 1539": "NH1" <-> "NH2" Residue "B ARG 1554": "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 PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 598": "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 999": "NH1" <-> "NH2" Residue "D ARG 1099": "NH1" <-> "NH2" Residue "D ARG 1104": "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 1531": "NH1" <-> "NH2" Residue "D ARG 1539": "NH1" <-> "NH2" Residue "D ARG 1554": "NH1" <-> "NH2" Residue "E TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 248": "NH1" <-> "NH2" Residue "F ARG 258": "NH1" <-> "NH2" Residue "F ARG 265": "NH1" <-> "NH2" Residue "F PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 598": "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 999": "NH1" <-> "NH2" Residue "F ARG 1099": "NH1" <-> "NH2" Residue "F ARG 1104": "NH1" <-> "NH2" Residue "F ARG 1145": "NH1" <-> "NH2" Residue "F TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1531": "NH1" <-> "NH2" Residue "F ARG 1539": "NH1" <-> "NH2" Residue "F ARG 1554": "NH1" <-> "NH2" Residue "G TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 248": "NH1" <-> "NH2" Residue "H ARG 258": "NH1" <-> "NH2" Residue "H ARG 265": "NH1" <-> "NH2" Residue "H PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 598": "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 999": "NH1" <-> "NH2" Residue "H ARG 1099": "NH1" <-> "NH2" Residue "H ARG 1104": "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 1531": "NH1" <-> "NH2" Residue "H ARG 1539": "NH1" <-> "NH2" Residue "H ARG 1554": "NH1" <-> "NH2" Time to flip residues: 0.34s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 50524 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "C" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "D" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "F" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "G" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2457 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "H" Number of atoms: 10112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1305, 10112 Classifications: {'peptide': 1305} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 45, 'TRANS': 1259} Chain breaks: 12 Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 26.20, per 1000 atoms: 0.52 Number of scatterers: 50524 At special positions: 0 Unit cell: (210.38, 210.38, 143.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 272 16.00 P 24 15.00 O 8840 8.00 N 8540 7.00 C 32848 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: 20.26 Conformation dependent library (CDL) restraints added in 12.4 seconds 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 32 sheets defined 58.7% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 16.33 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: 3.631A 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: 4.075A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 4.155A 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: 3.757A 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 226 through 229 No H-bonds generated for 'chain 'B' and resid 226 through 229' Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.943A pdb=" N ALA B 235 " --> pdb=" O TRP B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 299 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Proline residue: B 317 - end of helix Processing helix chain 'B' and resid 356 through 401 removed outlier: 3.630A pdb=" N MET B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N HIS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 422 Processing helix chain 'B' and resid 424 through 500 Proline residue: B 436 - end of helix removed outlier: 3.536A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix removed outlier: 8.212A pdb=" N VAL B 458 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER B 459 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 461 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 468 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA B 471 " --> pdb=" O ILE B 467 " (cutoff:3.500A) Proline residue: B 472 - end of helix Processing helix chain 'B' and resid 506 through 512 removed outlier: 4.017A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 559 removed outlier: 3.654A pdb=" N ARG B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 528 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR B 548 " --> pdb=" O ILE B 544 " (cutoff:3.500A) Proline residue: B 551 - end of helix removed outlier: 3.554A pdb=" N VAL B 555 " --> pdb=" O PRO B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 614 Proline residue: B 589 - end of helix removed outlier: 4.446A pdb=" N LEU B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 593 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 594 " --> pdb=" O LEU B 590 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER B 595 " --> pdb=" O PHE B 591 " (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 797 through 806 Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 832 through 845 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 918 Processing helix chain 'B' and resid 998 through 1008 removed outlier: 3.804A pdb=" N ALA B1008 " --> pdb=" O TYR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1038 removed outlier: 4.194A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU B1015 " --> pdb=" O LEU B1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER B1019 " --> pdb=" O LEU B1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP B1031 " --> pdb=" O LEU B1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B1036 " --> pdb=" O TYR B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1061 through 1106 Processing helix chain 'B' and resid 1110 through 1115 Processing helix chain 'B' and resid 1118 through 1126 removed outlier: 4.264A pdb=" N PHE B1125 " --> pdb=" O ILE B1121 " (cutoff:3.500A) Processing helix chain 'B' and resid 1128 through 1160 Proline residue: B1137 - end of helix Processing helix chain 'B' and resid 1162 through 1216 removed outlier: 4.302A pdb=" N VAL B1166 " --> pdb=" O PRO B1162 " (cutoff:3.500A) Proline residue: B1170 - end of helix removed outlier: 3.539A pdb=" N PHE B1177 " --> pdb=" O VAL B1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE B1182 " --> pdb=" O ILE B1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA B1185 " --> pdb=" O TYR B1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP B1188 " --> pdb=" O VAL B1184 " (cutoff:3.500A) Proline residue: B1199 - end of helix removed outlier: 3.525A pdb=" N GLY B1210 " --> pdb=" O GLU B1206 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR B1212 " --> pdb=" O VAL B1208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B1213 " --> pdb=" O GLU B1209 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1270 removed outlier: 3.723A pdb=" N ALA B1237 " --> pdb=" O SER B1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1242 " --> pdb=" O SER B1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B1260 " --> pdb=" O GLY B1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER B1269 " --> pdb=" O ALA B1265 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1288 removed outlier: 4.139A pdb=" N LEU B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1291 through 1319 removed outlier: 4.140A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS B1316 " --> pdb=" O VAL B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1385 through 1392 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: 4.096A pdb=" N ILE B1519 " --> pdb=" O ALA B1515 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1545 Processing helix chain 'B' and resid 1563 through 1569 removed outlier: 4.307A pdb=" N SER B1568 " --> pdb=" O GLU B1564 " (cutoff:3.500A) 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: 4.373A 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: 3.757A 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 226 through 229 No H-bonds generated for 'chain 'D' and resid 226 through 229' Processing helix chain 'D' and resid 231 through 242 removed outlier: 3.942A pdb=" N ALA D 235 " --> pdb=" O TRP D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG D 297 " --> pdb=" O HIS D 293 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 300 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Proline residue: D 317 - end of helix Processing helix chain 'D' and resid 356 through 401 removed outlier: 3.631A pdb=" N MET D 400 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 422 Processing helix chain 'D' and resid 424 through 500 Proline residue: D 436 - end of helix removed outlier: 3.535A pdb=" N TRP D 439 " --> pdb=" O CYS D 435 " (cutoff:3.500A) Proline residue: D 442 - end of helix removed outlier: 8.211A pdb=" N VAL D 458 " --> pdb=" O TYR D 454 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N SER D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU D 461 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 462 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 468 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA D 471 " --> pdb=" O ILE D 467 " (cutoff:3.500A) Proline residue: D 472 - end of helix Processing helix chain 'D' and resid 506 through 512 removed outlier: 4.017A pdb=" N TYR D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG D 521 " --> pdb=" O ILE D 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR D 548 " --> pdb=" O ILE D 544 " (cutoff:3.500A) Proline residue: D 551 - end of helix removed outlier: 3.554A pdb=" N VAL D 555 " --> pdb=" O PRO D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 614 Proline residue: D 589 - end of helix removed outlier: 4.446A pdb=" N LEU D 592 " --> pdb=" O THR D 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 593 " --> pdb=" O PRO D 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER D 594 " --> pdb=" O LEU D 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 595 " --> pdb=" O PHE D 591 " (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 797 through 806 Processing helix chain 'D' and resid 809 through 814 Processing helix chain 'D' and resid 832 through 845 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 918 Processing helix chain 'D' and resid 998 through 1008 removed outlier: 3.804A pdb=" N ALA D1008 " --> pdb=" O TYR D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU D1015 " --> pdb=" O LEU D1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER D1019 " --> pdb=" O LEU D1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D1031 " --> pdb=" O LEU D1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS D1036 " --> pdb=" O TYR D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1061 through 1106 Processing helix chain 'D' and resid 1110 through 1115 Processing helix chain 'D' and resid 1118 through 1126 removed outlier: 4.264A pdb=" N PHE D1125 " --> pdb=" O ILE D1121 " (cutoff:3.500A) Processing helix chain 'D' and resid 1128 through 1160 Proline residue: D1137 - end of helix Processing helix chain 'D' and resid 1162 through 1216 removed outlier: 4.301A pdb=" N VAL D1166 " --> pdb=" O PRO D1162 " (cutoff:3.500A) Proline residue: D1170 - end of helix removed outlier: 3.539A pdb=" N PHE D1177 " --> pdb=" O VAL D1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR D1181 " --> pdb=" O PHE D1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D1182 " --> pdb=" O ILE D1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA D1185 " --> pdb=" O TYR D1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP D1188 " --> pdb=" O VAL D1184 " (cutoff:3.500A) Proline residue: D1199 - end of helix removed outlier: 3.525A pdb=" N GLY D1210 " --> pdb=" O GLU D1206 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR D1212 " --> pdb=" O VAL D1208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR D1213 " --> pdb=" O GLU D1209 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1270 removed outlier: 3.723A pdb=" N ALA D1237 " --> pdb=" O SER D1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D1242 " --> pdb=" O SER D1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER D1269 " --> pdb=" O ALA D1265 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1288 removed outlier: 4.139A pdb=" N LEU D1283 " --> pdb=" O GLY D1279 " (cutoff:3.500A) Processing helix chain 'D' and resid 1291 through 1319 removed outlier: 4.141A pdb=" N ARG D1314 " --> pdb=" O GLY D1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS D1316 " --> pdb=" O VAL D1312 " (cutoff:3.500A) Processing helix chain 'D' and resid 1385 through 1392 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: 4.095A pdb=" N ILE D1519 " --> pdb=" O ALA D1515 " (cutoff:3.500A) Processing helix chain 'D' and resid 1540 through 1545 Processing helix chain 'D' and resid 1563 through 1569 removed outlier: 3.500A pdb=" N LEU D1567 " --> pdb=" O PRO D1563 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER D1568 " --> pdb=" O GLU D1564 " (cutoff:3.500A) 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: 3.631A 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: 4.075A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.155A 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 226 through 229 No H-bonds generated for 'chain 'F' and resid 226 through 229' Processing helix chain 'F' and resid 231 through 242 removed outlier: 3.941A pdb=" N ALA F 235 " --> pdb=" O TRP F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 284 through 328 removed outlier: 6.309A pdb=" N ARG F 297 " --> pdb=" O HIS F 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU F 299 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE F 300 " --> pdb=" O GLY F 296 " (cutoff:3.500A) Proline residue: F 317 - end of helix Processing helix chain 'F' and resid 356 through 401 removed outlier: 3.630A pdb=" N MET F 400 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 422 Processing helix chain 'F' and resid 424 through 500 Proline residue: F 436 - end of helix removed outlier: 3.536A pdb=" N TRP F 439 " --> pdb=" O CYS F 435 " (cutoff:3.500A) Proline residue: F 442 - end of helix removed outlier: 8.211A pdb=" N VAL F 458 " --> pdb=" O TYR F 454 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N SER F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 461 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE F 462 " --> pdb=" O VAL F 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE F 468 " --> pdb=" O ALA F 464 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 471 " --> pdb=" O ILE F 467 " (cutoff:3.500A) Proline residue: F 472 - end of helix Processing helix chain 'F' and resid 506 through 512 removed outlier: 4.017A pdb=" N TYR F 512 " --> pdb=" O LEU F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 559 removed outlier: 3.655A pdb=" N ARG F 521 " --> pdb=" O ILE F 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS F 528 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR F 548 " --> pdb=" O ILE F 544 " (cutoff:3.500A) Proline residue: F 551 - end of helix removed outlier: 3.554A pdb=" N VAL F 555 " --> pdb=" O PRO F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 614 Proline residue: F 589 - end of helix removed outlier: 4.446A pdb=" N LEU F 592 " --> pdb=" O THR F 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU F 593 " --> pdb=" O PRO F 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER F 594 " --> pdb=" O LEU F 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER F 595 " --> pdb=" O PHE F 591 " (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 797 through 806 Processing helix chain 'F' and resid 809 through 814 Processing helix chain 'F' and resid 832 through 845 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 918 Processing helix chain 'F' and resid 998 through 1008 removed outlier: 3.804A pdb=" N ALA F1008 " --> pdb=" O TYR F1004 " (cutoff:3.500A) Processing helix chain 'F' and resid 1010 through 1038 removed outlier: 4.194A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU F1015 " --> pdb=" O LEU F1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER F1019 " --> pdb=" O LEU F1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP F1031 " --> pdb=" O LEU F1027 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS F1036 " --> pdb=" O TYR F1032 " (cutoff:3.500A) Processing helix chain 'F' and resid 1061 through 1106 Processing helix chain 'F' and resid 1110 through 1115 Processing helix chain 'F' and resid 1118 through 1126 removed outlier: 4.264A pdb=" N PHE F1125 " --> pdb=" O ILE F1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 1128 through 1160 Proline residue: F1137 - end of helix Processing helix chain 'F' and resid 1162 through 1216 removed outlier: 4.301A pdb=" N VAL F1166 " --> pdb=" O PRO F1162 " (cutoff:3.500A) Proline residue: F1170 - end of helix removed outlier: 3.539A pdb=" N PHE F1177 " --> pdb=" O VAL F1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR F1181 " --> pdb=" O PHE F1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE F1182 " --> pdb=" O ILE F1178 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA F1185 " --> pdb=" O TYR F1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP F1188 " --> pdb=" O VAL F1184 " (cutoff:3.500A) Proline residue: F1199 - end of helix removed outlier: 3.526A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR F1212 " --> pdb=" O VAL F1208 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR F1213 " --> pdb=" O GLU F1209 " (cutoff:3.500A) Processing helix chain 'F' and resid 1220 through 1270 removed outlier: 3.724A pdb=" N ALA F1237 " --> pdb=" O SER F1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR F1242 " --> pdb=" O SER F1238 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL F1260 " --> pdb=" O GLY F1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER F1269 " --> pdb=" O ALA F1265 " (cutoff:3.500A) Processing helix chain 'F' and resid 1279 through 1288 removed outlier: 4.140A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1291 through 1319 removed outlier: 4.140A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS F1316 " --> pdb=" O VAL F1312 " (cutoff:3.500A) Processing helix chain 'F' and resid 1385 through 1392 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: 4.096A pdb=" N ILE F1519 " --> pdb=" O ALA F1515 " (cutoff:3.500A) Processing helix chain 'F' and resid 1540 through 1545 Processing helix chain 'F' and resid 1563 through 1569 removed outlier: 3.500A pdb=" N LEU F1567 " --> pdb=" O PRO F1563 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F1568 " --> pdb=" O GLU F1564 " (cutoff:3.500A) 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: 4.373A 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: 4.155A 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: 3.757A 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 226 through 229 No H-bonds generated for 'chain 'H' and resid 226 through 229' Processing helix chain 'H' and resid 231 through 242 removed outlier: 3.941A pdb=" N ALA H 235 " --> pdb=" O TRP H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 Processing helix chain 'H' and resid 284 through 328 removed outlier: 6.308A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU H 299 " --> pdb=" O PHE H 295 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE H 300 " --> pdb=" O GLY H 296 " (cutoff:3.500A) Proline residue: H 317 - end of helix Processing helix chain 'H' and resid 356 through 401 removed outlier: 3.630A pdb=" N MET H 400 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS H 401 " --> pdb=" O ASN H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 422 Processing helix chain 'H' and resid 424 through 500 Proline residue: H 436 - end of helix removed outlier: 3.536A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix removed outlier: 8.212A pdb=" N VAL H 458 " --> pdb=" O TYR H 454 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N SER H 459 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA H 460 " --> pdb=" O LEU H 456 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU H 461 " --> pdb=" O GLY H 457 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE H 462 " --> pdb=" O VAL H 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE H 468 " --> pdb=" O ALA H 464 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA H 471 " --> pdb=" O ILE H 467 " (cutoff:3.500A) Proline residue: H 472 - end of helix Processing helix chain 'H' and resid 506 through 512 removed outlier: 4.018A pdb=" N TYR H 512 " --> pdb=" O LEU H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 559 removed outlier: 3.654A pdb=" N ARG H 521 " --> pdb=" O ILE H 517 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS H 528 " --> pdb=" O VAL H 524 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.553A pdb=" N VAL H 555 " --> pdb=" O PRO H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 614 Proline residue: H 589 - end of helix removed outlier: 4.446A pdb=" N LEU H 592 " --> pdb=" O THR H 588 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 593 " --> pdb=" O PRO H 589 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER H 594 " --> pdb=" O LEU H 590 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER H 595 " --> pdb=" O PHE H 591 " (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 797 through 806 Processing helix chain 'H' and resid 809 through 814 Processing helix chain 'H' and resid 832 through 845 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 918 Processing helix chain 'H' and resid 998 through 1008 removed outlier: 3.804A pdb=" N ALA H1008 " --> pdb=" O TYR H1004 " (cutoff:3.500A) Processing helix chain 'H' and resid 1010 through 1038 removed outlier: 4.194A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU H1015 " --> pdb=" O LEU H1011 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER H1019 " --> pdb=" O LEU H1015 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP H1031 " --> pdb=" O LEU H1027 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS H1036 " --> pdb=" O TYR H1032 " (cutoff:3.500A) Processing helix chain 'H' and resid 1061 through 1106 Processing helix chain 'H' and resid 1110 through 1115 Processing helix chain 'H' and resid 1118 through 1126 removed outlier: 4.264A pdb=" N PHE H1125 " --> pdb=" O ILE H1121 " (cutoff:3.500A) Processing helix chain 'H' and resid 1128 through 1160 Proline residue: H1137 - end of helix Processing helix chain 'H' and resid 1162 through 1216 removed outlier: 4.301A pdb=" N VAL H1166 " --> pdb=" O PRO H1162 " (cutoff:3.500A) Proline residue: H1170 - end of helix removed outlier: 3.539A pdb=" N PHE H1177 " --> pdb=" O VAL H1173 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR H1181 " --> pdb=" O PHE H1177 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE H1182 " --> pdb=" O ILE H1178 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA H1185 " --> pdb=" O TYR H1181 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ASP H1188 " --> pdb=" O VAL H1184 " (cutoff:3.500A) Proline residue: H1199 - end of helix removed outlier: 3.525A pdb=" N GLY H1210 " --> pdb=" O GLU H1206 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR H1212 " --> pdb=" O VAL H1208 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR H1213 " --> pdb=" O GLU H1209 " (cutoff:3.500A) Processing helix chain 'H' and resid 1220 through 1270 removed outlier: 3.723A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL H1260 " --> pdb=" O GLY H1256 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER H1269 " --> pdb=" O ALA H1265 " (cutoff:3.500A) Processing helix chain 'H' and resid 1279 through 1288 removed outlier: 4.139A pdb=" N LEU H1283 " --> pdb=" O GLY H1279 " (cutoff:3.500A) Processing helix chain 'H' and resid 1291 through 1319 removed outlier: 4.140A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE H1315 " --> pdb=" O ALA H1311 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS H1316 " --> pdb=" O VAL H1312 " (cutoff:3.500A) Processing helix chain 'H' and resid 1385 through 1392 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: 4.096A pdb=" N ILE H1519 " --> pdb=" O ALA H1515 " (cutoff:3.500A) Processing helix chain 'H' and resid 1540 through 1545 Processing helix chain 'H' and resid 1563 through 1569 removed outlier: 4.307A pdb=" N SER H1568 " --> pdb=" O GLU H1564 " (cutoff:3.500A) 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: 3.639A 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: 3.661A 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: 3.671A pdb=" N GLY B 912 " --> pdb=" O ILE B 900 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 771 " --> pdb=" O PHE B 852 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.494A 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 removed outlier: 3.602A pdb=" N GLN B1346 " --> pdb=" O ILE B1404 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B1348 " --> pdb=" O ARG B1402 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG B1402 " --> pdb=" O GLN B1348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET B1398 " --> pdb=" O ARG B1353 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1557 through 1560 removed outlier: 3.774A pdb=" N MET B1550 " --> pdb=" O GLY B1376 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE B1503 " --> pdb=" O VAL B1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE B1536 " --> pdb=" O PHE B1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET B1505 " --> pdb=" O ILE B1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B1425 " --> pdb=" O ASP B1506 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 188 through 192 removed outlier: 3.782A pdb=" N HIS C 259 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU C 200 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id= J, 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= K, first strand: chain 'C' and resid 313 through 315 Processing sheet with id= L, first strand: chain 'D' and resid 701 through 703 Processing sheet with id= M, first strand: chain 'D' and resid 911 through 913 removed outlier: 3.670A pdb=" N GLY D 912 " --> pdb=" O ILE D 900 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA D 771 " --> pdb=" O PHE D 852 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASP D 854 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA D 773 " --> pdb=" O ASP D 854 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 1367 through 1369 removed outlier: 3.602A pdb=" N GLN D1346 " --> pdb=" O ILE D1404 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN D1348 " --> pdb=" O ARG D1402 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG D1402 " --> pdb=" O GLN D1348 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET D1398 " --> pdb=" O ARG D1353 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 1557 through 1560 removed outlier: 3.775A pdb=" N MET D1550 " --> pdb=" O GLY D1376 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE D1503 " --> pdb=" O VAL D1534 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE D1536 " --> pdb=" O PHE D1503 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET D1505 " --> pdb=" O ILE D1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER D1423 " --> pdb=" O ILE D1504 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ASP D1506 " --> pdb=" O SER D1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE D1425 " --> pdb=" O ASP D1506 " (cutoff:3.500A) Processing sheet with id= Q, 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: 3.639A pdb=" N LEU E 200 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id= R, 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= S, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= T, first strand: chain 'F' and resid 701 through 703 Processing sheet with id= U, first strand: chain 'F' and resid 911 through 913 removed outlier: 3.669A pdb=" N GLY F 912 " --> pdb=" O ILE F 900 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA F 771 " --> pdb=" O PHE F 852 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ASP F 854 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA F 773 " --> pdb=" O ASP F 854 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 1367 through 1369 removed outlier: 3.602A pdb=" N GLN F1346 " --> pdb=" O ILE F1404 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F1348 " --> pdb=" O ARG F1402 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG F1402 " --> pdb=" O GLN F1348 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET F1398 " --> pdb=" O ARG F1353 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 1557 through 1560 removed outlier: 3.774A pdb=" N MET F1550 " --> pdb=" O GLY F1376 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE F1503 " --> pdb=" O VAL F1534 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE F1536 " --> pdb=" O PHE F1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET F1505 " --> pdb=" O ILE F1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER F1423 " --> pdb=" O ILE F1504 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP F1506 " --> pdb=" O SER F1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE F1425 " --> pdb=" O ASP F1506 " (cutoff:3.500A) Processing sheet with id= Y, 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: 3.639A pdb=" N LEU G 200 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing sheet with id= Z, 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= AA, first strand: chain 'G' and resid 313 through 315 Processing sheet with id= AB, first strand: chain 'H' and resid 701 through 703 Processing sheet with id= AC, first strand: chain 'H' and resid 911 through 913 removed outlier: 3.670A pdb=" N GLY H 912 " --> pdb=" O ILE H 900 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA H 771 " --> pdb=" O PHE H 852 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N ASP H 854 " --> pdb=" O ALA H 771 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ALA H 773 " --> pdb=" O ASP H 854 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 1367 through 1369 removed outlier: 3.601A pdb=" N GLN H1346 " --> pdb=" O ILE H1404 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN H1348 " --> pdb=" O ARG H1402 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG H1402 " --> pdb=" O GLN H1348 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 1351 through 1353 removed outlier: 3.547A pdb=" N MET H1398 " --> pdb=" O ARG H1353 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 1557 through 1560 removed outlier: 3.774A pdb=" N MET H1550 " --> pdb=" O GLY H1376 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE H1503 " --> pdb=" O VAL H1534 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE H1536 " --> pdb=" O PHE H1503 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N MET H1505 " --> pdb=" O ILE H1536 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N SER H1423 " --> pdb=" O ILE H1504 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ASP H1506 " --> pdb=" O SER H1423 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE H1425 " --> pdb=" O ASP H1506 " (cutoff:3.500A) 2882 hydrogen bonds defined for protein. 8406 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: 21.56 Time building geometry restraints manager: 21.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.39: 20094 1.39 - 1.58: 31022 1.58 - 1.76: 32 1.76 - 1.94: 420 1.94 - 2.12: 8 Bond restraints: 51576 Sorted by residual: bond pdb=" PG AGS A 401 " pdb=" S1G AGS A 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS G 401 " pdb=" S1G AGS G 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS E 401 " pdb=" S1G AGS E 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" PG AGS C 401 " pdb=" S1G AGS C 401 " ideal model delta sigma weight residual 1.949 2.122 -0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C4 AGS F2501 " pdb=" C5 AGS F2501 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.26e+01 ... (remaining 51571 not shown) Histogram of bond angle deviations from ideal: 98.78 - 106.22: 1233 106.22 - 113.65: 30492 113.65 - 121.09: 25660 121.09 - 128.52: 12331 128.52 - 135.95: 456 Bond angle restraints: 70172 Sorted by residual: angle pdb=" C5 AGS F2501 " pdb=" C4 AGS F2501 " pdb=" N3 AGS F2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS D2501 " pdb=" C4 AGS D2501 " pdb=" N3 AGS D2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS B2501 " pdb=" C4 AGS B2501 " pdb=" N3 AGS B2501 " ideal model delta sigma weight residual 126.80 118.60 8.20 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS H2501 " pdb=" C4 AGS H2501 " pdb=" N3 AGS H2501 " ideal model delta sigma weight residual 126.80 118.61 8.19 7.41e-01 1.82e+00 1.22e+02 angle pdb=" C5 AGS G 401 " pdb=" C4 AGS G 401 " pdb=" N3 AGS G 401 " ideal model delta sigma weight residual 126.80 119.10 7.70 7.41e-01 1.82e+00 1.08e+02 ... (remaining 70167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.24: 29654 31.24 - 62.49: 918 62.49 - 93.73: 12 93.73 - 124.97: 8 124.97 - 156.22: 4 Dihedral angle restraints: 30596 sinusoidal: 11668 harmonic: 18928 Sorted by residual: dihedral pdb=" CA ASP B 212 " pdb=" C ASP B 212 " pdb=" N LEU B 213 " pdb=" CA LEU B 213 " ideal model delta harmonic sigma weight residual -180.00 -153.56 -26.44 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA ASP H 212 " pdb=" C ASP H 212 " pdb=" N LEU H 213 " pdb=" CA LEU H 213 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA ASP D 212 " pdb=" C ASP D 212 " pdb=" N LEU D 213 " pdb=" CA LEU D 213 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 30593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 8424 0.158 - 0.316: 72 0.316 - 0.474: 16 0.474 - 0.632: 0 0.632 - 0.790: 4 Chirality restraints: 8516 Sorted by residual: chirality pdb=" PB AGS A 401 " pdb=" O2B AGS A 401 " pdb=" O3A AGS A 401 " pdb=" O3B AGS A 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" PB AGS C 401 " pdb=" O2B AGS C 401 " pdb=" O3A AGS C 401 " pdb=" O3B AGS C 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" PB AGS G 401 " pdb=" O2B AGS G 401 " pdb=" O3A AGS G 401 " pdb=" O3B AGS G 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.39 0.79 2.00e-01 2.50e+01 1.55e+01 ... (remaining 8513 not shown) Planarity restraints: 8588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS F1273 " 0.020 2.00e-02 2.50e+03 4.08e-02 1.67e+01 pdb=" C HIS F1273 " -0.071 2.00e-02 2.50e+03 pdb=" O HIS F1273 " 0.027 2.00e-02 2.50e+03 pdb=" N ARG F1274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D1273 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C HIS D1273 " -0.070 2.00e-02 2.50e+03 pdb=" O HIS D1273 " 0.026 2.00e-02 2.50e+03 pdb=" N ARG D1274 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H1273 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C HIS H1273 " 0.070 2.00e-02 2.50e+03 pdb=" O HIS H1273 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG H1274 " -0.023 2.00e-02 2.50e+03 ... (remaining 8585 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 492 2.60 - 3.18: 45721 3.18 - 3.75: 80070 3.75 - 4.33: 102660 4.33 - 4.90: 167822 Nonbonded interactions: 396765 Sorted by model distance: nonbonded pdb=" O ILE B 196 " pdb=" O PHE B 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE D 196 " pdb=" O PHE D 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 H 196 " pdb=" O PHE H 197 " model vdw 2.030 3.040 nonbonded pdb=" CD1 LEU C 200 " pdb=" N ARG C 201 " model vdw 2.049 3.540 ... (remaining 396760 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: 0.010 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 5.960 Check model and map are aligned: 0.740 Set scattering table: 0.460 Process input model: 132.560 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.400 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.005 0.173 51576 Z= 0.351 Angle : 0.804 11.538 70172 Z= 0.504 Chirality : 0.052 0.790 8516 Planarity : 0.005 0.074 8588 Dihedral : 13.785 156.217 18272 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.43 % Favored : 95.13 % Rotamer: Outliers : 8.11 % Allowed : 9.38 % Favored : 82.51 % Cbeta Deviations : 0.06 % 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: -2.46 (0.09), residues: 6408 helix: -1.03 (0.07), residues: 3948 sheet: -1.58 (0.20), residues: 536 loop : -2.64 (0.12), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D1339 HIS 0.012 0.001 HIS C 175 PHE 0.035 0.002 PHE G 168 TYR 0.015 0.002 TYR B 378 ARG 0.003 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1576 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 436 poor density : 1140 time to evaluate : 5.644 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: A 77 MET cc_start: 0.8703 (mmt) cc_final: 0.8378 (tpt) REVERT: A 78 SER cc_start: 0.9341 (OUTLIER) cc_final: 0.8778 (p) REVERT: A 81 CYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7697 (p) REVERT: A 88 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8642 (tmm) REVERT: A 92 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9405 (tt) REVERT: A 95 PHE cc_start: 0.8860 (t80) cc_final: 0.8646 (t80) REVERT: A 163 MET cc_start: 0.7818 (ttp) cc_final: 0.7241 (ttt) REVERT: A 182 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7684 (pt) REVERT: A 204 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7771 (t0) REVERT: A 238 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.6990 (tt) REVERT: A 286 ILE cc_start: 0.4594 (OUTLIER) cc_final: 0.3925 (tt) REVERT: A 293 THR cc_start: 0.5405 (OUTLIER) cc_final: 0.5182 (t) REVERT: A 332 LYS cc_start: 0.8171 (mtmt) cc_final: 0.7529 (mtmm) REVERT: B 89 ILE cc_start: 0.9164 (mt) cc_final: 0.8844 (mm) REVERT: B 91 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8175 (tm-30) REVERT: B 135 LEU cc_start: 0.8255 (mt) cc_final: 0.7834 (mt) REVERT: B 175 LEU cc_start: 0.9072 (mt) cc_final: 0.8698 (tt) REVERT: B 233 MET cc_start: 0.9398 (mmm) cc_final: 0.8902 (mmm) REVERT: B 253 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8872 (mt) REVERT: B 319 CYS cc_start: 0.9056 (m) cc_final: 0.8748 (p) REVERT: B 327 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8403 (tt) REVERT: B 432 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.9116 (t80) REVERT: B 710 MET cc_start: 0.6727 (mmt) cc_final: 0.6047 (tpp) REVERT: B 727 LEU cc_start: 0.7894 (tp) cc_final: 0.7488 (mt) REVERT: B 1020 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8370 (mp10) REVERT: B 1031 ASP cc_start: 0.8228 (m-30) cc_final: 0.7388 (t0) REVERT: B 1246 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8401 (mmp80) REVERT: B 1251 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8492 (mmt180) REVERT: B 1252 MET cc_start: 0.8900 (ttm) cc_final: 0.8476 (tpp) REVERT: B 1432 PHE cc_start: 0.2989 (OUTLIER) cc_final: 0.2234 (p90) REVERT: B 1536 ILE cc_start: 0.0379 (OUTLIER) cc_final: -0.0020 (pt) REVERT: B 1561 ASP cc_start: 0.6779 (OUTLIER) cc_final: 0.6337 (t0) REVERT: B 1566 LEU cc_start: 0.1664 (OUTLIER) cc_final: 0.1152 (pt) REVERT: C 74 ILE cc_start: 0.9432 (tt) cc_final: 0.9227 (tt) REVERT: C 77 MET cc_start: 0.8697 (mmt) cc_final: 0.8377 (tpt) REVERT: C 78 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8789 (p) REVERT: C 81 CYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7678 (p) REVERT: C 88 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8647 (tmm) REVERT: C 92 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9409 (tt) REVERT: C 95 PHE cc_start: 0.8870 (t80) cc_final: 0.8659 (t80) REVERT: C 122 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (tt) REVERT: C 163 MET cc_start: 0.7894 (ttp) cc_final: 0.7240 (ttt) REVERT: C 182 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7690 (pt) REVERT: C 204 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7733 (t0) REVERT: C 238 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.6978 (tt) REVERT: C 286 ILE cc_start: 0.4390 (OUTLIER) cc_final: 0.3740 (tt) REVERT: C 293 THR cc_start: 0.5385 (OUTLIER) cc_final: 0.5156 (t) REVERT: C 332 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7599 (mtmm) REVERT: D 89 ILE cc_start: 0.9121 (mt) cc_final: 0.8785 (mm) REVERT: D 91 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8189 (tm-30) REVERT: D 126 ASN cc_start: 0.8361 (m-40) cc_final: 0.7919 (t0) REVERT: D 135 LEU cc_start: 0.8266 (mt) cc_final: 0.7785 (mt) REVERT: D 175 LEU cc_start: 0.9070 (mt) cc_final: 0.8700 (tt) REVERT: D 233 MET cc_start: 0.9401 (mmm) cc_final: 0.8909 (mmm) REVERT: D 253 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8871 (mt) REVERT: D 319 CYS cc_start: 0.9067 (m) cc_final: 0.8750 (p) REVERT: D 327 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 432 PHE cc_start: 0.9360 (OUTLIER) cc_final: 0.9105 (t80) REVERT: D 710 MET cc_start: 0.6732 (mmt) cc_final: 0.6053 (tpp) REVERT: D 727 LEU cc_start: 0.7903 (tp) cc_final: 0.7495 (mt) REVERT: D 1020 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8366 (mp10) REVERT: D 1031 ASP cc_start: 0.8146 (m-30) cc_final: 0.7259 (t0) REVERT: D 1165 LEU cc_start: 0.8538 (tt) cc_final: 0.8297 (tt) REVERT: D 1246 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.8464 (mmp80) REVERT: D 1251 ARG cc_start: 0.9218 (OUTLIER) cc_final: 0.8488 (mmt180) REVERT: D 1252 MET cc_start: 0.8909 (ttm) cc_final: 0.8342 (tpp) REVERT: D 1432 PHE cc_start: 0.2940 (OUTLIER) cc_final: 0.2146 (p90) REVERT: D 1536 ILE cc_start: 0.0407 (OUTLIER) cc_final: -0.0008 (pt) REVERT: D 1561 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6353 (t0) REVERT: D 1566 LEU cc_start: 0.1848 (OUTLIER) cc_final: 0.1189 (pt) REVERT: E 74 ILE cc_start: 0.9437 (tt) cc_final: 0.9236 (tt) REVERT: E 77 MET cc_start: 0.8706 (mmt) cc_final: 0.8376 (tpt) REVERT: E 78 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.8777 (p) REVERT: E 81 CYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7664 (p) REVERT: E 88 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8658 (tmm) REVERT: E 92 LEU cc_start: 0.9630 (OUTLIER) cc_final: 0.9411 (tt) REVERT: E 95 PHE cc_start: 0.8867 (t80) cc_final: 0.8658 (t80) REVERT: E 122 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9034 (tt) REVERT: E 163 MET cc_start: 0.7874 (ttp) cc_final: 0.7375 (ttt) REVERT: E 182 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7732 (pt) REVERT: E 204 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7727 (t0) REVERT: E 238 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.6974 (tt) REVERT: E 286 ILE cc_start: 0.4402 (OUTLIER) cc_final: 0.3732 (tt) REVERT: E 293 THR cc_start: 0.5372 (OUTLIER) cc_final: 0.5162 (t) REVERT: E 332 LYS cc_start: 0.8236 (mtmt) cc_final: 0.7877 (mtmm) REVERT: F 89 ILE cc_start: 0.9103 (mt) cc_final: 0.8756 (mm) REVERT: F 91 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8174 (tm-30) REVERT: F 135 LEU cc_start: 0.8271 (mt) cc_final: 0.7838 (mt) REVERT: F 175 LEU cc_start: 0.9077 (mt) cc_final: 0.8695 (tt) REVERT: F 233 MET cc_start: 0.9424 (mmm) cc_final: 0.8967 (mmm) REVERT: F 253 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8888 (mt) REVERT: F 319 CYS cc_start: 0.9065 (m) cc_final: 0.8742 (p) REVERT: F 327 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8414 (tt) REVERT: F 432 PHE cc_start: 0.9357 (OUTLIER) cc_final: 0.9099 (t80) REVERT: F 710 MET cc_start: 0.6729 (mmt) cc_final: 0.6046 (tpp) REVERT: F 727 LEU cc_start: 0.7888 (tp) cc_final: 0.7480 (mt) REVERT: F 1020 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8330 (mp10) REVERT: F 1031 ASP cc_start: 0.8206 (m-30) cc_final: 0.7377 (t0) REVERT: F 1165 LEU cc_start: 0.8539 (tt) cc_final: 0.8294 (tt) REVERT: F 1246 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8455 (mmp80) REVERT: F 1251 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8498 (mmt180) REVERT: F 1252 MET cc_start: 0.8901 (ttm) cc_final: 0.8410 (tpp) REVERT: F 1432 PHE cc_start: 0.2928 (OUTLIER) cc_final: 0.2137 (p90) REVERT: F 1536 ILE cc_start: 0.0414 (OUTLIER) cc_final: -0.0004 (pt) REVERT: F 1561 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6353 (t0) REVERT: F 1566 LEU cc_start: 0.2135 (OUTLIER) cc_final: 0.1464 (pt) REVERT: G 74 ILE cc_start: 0.9434 (tt) cc_final: 0.9233 (tt) REVERT: G 77 MET cc_start: 0.8714 (mmt) cc_final: 0.8373 (tpt) REVERT: G 78 SER cc_start: 0.9346 (OUTLIER) cc_final: 0.8770 (p) REVERT: G 81 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7653 (p) REVERT: G 88 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8635 (tmm) REVERT: G 92 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9406 (tt) REVERT: G 95 PHE cc_start: 0.8861 (t80) cc_final: 0.8643 (t80) REVERT: G 122 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9033 (tt) REVERT: G 163 MET cc_start: 0.7807 (ttp) cc_final: 0.7356 (ttt) REVERT: G 182 ILE cc_start: 0.7929 (OUTLIER) cc_final: 0.7726 (pt) REVERT: G 204 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7741 (t0) REVERT: G 238 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.6964 (tt) REVERT: G 286 ILE cc_start: 0.4597 (OUTLIER) cc_final: 0.3908 (tt) REVERT: G 293 THR cc_start: 0.5367 (OUTLIER) cc_final: 0.5159 (t) REVERT: G 332 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7823 (mtmm) REVERT: H 89 ILE cc_start: 0.9171 (mt) cc_final: 0.8956 (mm) REVERT: H 91 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8159 (tm-30) REVERT: H 135 LEU cc_start: 0.8264 (mt) cc_final: 0.7825 (mt) REVERT: H 175 LEU cc_start: 0.9081 (mt) cc_final: 0.8698 (tt) REVERT: H 233 MET cc_start: 0.9402 (mmm) cc_final: 0.8907 (mmm) REVERT: H 253 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8889 (mt) REVERT: H 319 CYS cc_start: 0.9056 (m) cc_final: 0.8742 (p) REVERT: H 327 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8407 (tt) REVERT: H 710 MET cc_start: 0.6721 (mmt) cc_final: 0.6041 (tpp) REVERT: H 727 LEU cc_start: 0.7899 (tp) cc_final: 0.7488 (mt) REVERT: H 1020 GLN cc_start: 0.8663 (mm-40) cc_final: 0.8341 (mp10) REVERT: H 1031 ASP cc_start: 0.8223 (m-30) cc_final: 0.7388 (t0) REVERT: H 1103 ASN cc_start: 0.8002 (m-40) cc_final: 0.7675 (m-40) REVERT: H 1165 LEU cc_start: 0.8539 (tt) cc_final: 0.8291 (tt) REVERT: H 1246 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8387 (mmp80) REVERT: H 1251 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8497 (mmt180) REVERT: H 1252 MET cc_start: 0.8892 (ttm) cc_final: 0.8409 (tpp) REVERT: H 1432 PHE cc_start: 0.2922 (OUTLIER) cc_final: 0.2133 (p90) REVERT: H 1536 ILE cc_start: 0.0558 (OUTLIER) cc_final: 0.0166 (pt) REVERT: H 1561 ASP cc_start: 0.6778 (OUTLIER) cc_final: 0.6334 (t0) REVERT: H 1566 LEU cc_start: 0.2070 (OUTLIER) cc_final: 0.1411 (pt) outliers start: 436 outliers final: 58 residues processed: 1493 average time/residue: 0.6000 time to fit residues: 1490.1163 Evaluate side-chains 702 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 570 time to evaluate : 5.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 9.9990 chunk 491 optimal weight: 7.9990 chunk 272 optimal weight: 20.0000 chunk 167 optimal weight: 0.5980 chunk 331 optimal weight: 8.9990 chunk 262 optimal weight: 40.0000 chunk 507 optimal weight: 30.0000 chunk 196 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 378 optimal weight: 7.9990 chunk 588 optimal weight: 10.0000 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 48 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN A 348 GLN B 397 ASN ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 485 GLN B 809 GLN B1135 HIS C 46 HIS C 48 ASN C 173 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN C 348 GLN D 397 ASN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 485 GLN D 809 GLN D 863 HIS D1135 HIS E 46 HIS ** E 48 ASN ** 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 173 GLN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN E 348 GLN F 397 ASN F 485 GLN F 809 GLN F1135 HIS G 46 HIS G 48 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 299 GLN G 348 GLN H 397 ASN H 485 GLN H 809 GLN H1135 HIS H1296 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 51576 Z= 0.312 Angle : 0.739 9.148 70172 Z= 0.385 Chirality : 0.046 0.204 8516 Planarity : 0.005 0.052 8588 Dihedral : 8.833 161.473 7064 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 0.17 % Allowed : 4.13 % Favored : 95.70 % 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: -0.92 (0.10), residues: 6408 helix: 0.28 (0.08), residues: 3944 sheet: -1.29 (0.20), residues: 552 loop : -2.17 (0.13), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 514 HIS 0.012 0.001 HIS D 863 PHE 0.025 0.002 PHE B 295 TYR 0.025 0.002 TYR F 124 ARG 0.010 0.001 ARG H1421 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 714 time to evaluate : 6.242 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: A 81 CYS cc_start: 0.8629 (t) cc_final: 0.7141 (t) REVERT: A 88 MET cc_start: 0.8984 (tpt) cc_final: 0.8704 (tmm) REVERT: A 95 PHE cc_start: 0.8932 (t80) cc_final: 0.8542 (t80) REVERT: A 199 MET cc_start: 0.7617 (mmp) cc_final: 0.6490 (mmm) REVERT: A 329 ASP cc_start: 0.7084 (p0) cc_final: 0.6480 (p0) REVERT: A 332 LYS cc_start: 0.8211 (mtmt) cc_final: 0.7712 (mtmm) REVERT: B 88 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8679 (tm-30) REVERT: B 89 ILE cc_start: 0.9214 (mt) cc_final: 0.8898 (mp) REVERT: B 91 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7948 (tt0) REVERT: B 108 MET cc_start: 0.8524 (mmt) cc_final: 0.8269 (mmp) REVERT: B 233 MET cc_start: 0.9573 (mmm) cc_final: 0.9109 (mmm) REVERT: B 319 CYS cc_start: 0.9202 (m) cc_final: 0.8948 (m) REVERT: B 429 MET cc_start: 0.8857 (ppp) cc_final: 0.8440 (ppp) REVERT: B 710 MET cc_start: 0.6357 (mmt) cc_final: 0.5865 (tpt) REVERT: B 869 MET cc_start: 0.8253 (ppp) cc_final: 0.8010 (tpt) REVERT: B 903 MET cc_start: 0.6868 (mmp) cc_final: 0.5981 (mmm) REVERT: B 1031 ASP cc_start: 0.8600 (m-30) cc_final: 0.7749 (t0) REVERT: B 1142 CYS cc_start: 0.9311 (t) cc_final: 0.8701 (m) REVERT: B 1223 PHE cc_start: 0.8661 (m-10) cc_final: 0.8368 (m-10) REVERT: B 1252 MET cc_start: 0.8919 (ttm) cc_final: 0.8443 (tpp) REVERT: B 1395 MET cc_start: 0.8272 (mmp) cc_final: 0.8047 (mmm) REVERT: C 81 CYS cc_start: 0.8500 (t) cc_final: 0.7265 (t) REVERT: C 88 MET cc_start: 0.8982 (tpt) cc_final: 0.8701 (tmm) REVERT: C 95 PHE cc_start: 0.8972 (t80) cc_final: 0.8592 (t80) REVERT: C 199 MET cc_start: 0.7561 (mmp) cc_final: 0.6405 (mmm) REVERT: C 329 ASP cc_start: 0.7187 (p0) cc_final: 0.6560 (p0) REVERT: C 332 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7714 (mtmm) REVERT: D 88 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8672 (tm-30) REVERT: D 89 ILE cc_start: 0.9213 (mt) cc_final: 0.8898 (mp) REVERT: D 91 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7972 (tt0) REVERT: D 108 MET cc_start: 0.8532 (mmt) cc_final: 0.8269 (mmp) REVERT: D 126 ASN cc_start: 0.8577 (m-40) cc_final: 0.7762 (t0) REVERT: D 233 MET cc_start: 0.9582 (mmm) cc_final: 0.9129 (mmm) REVERT: D 257 MET cc_start: 0.8896 (pmm) cc_final: 0.8456 (ptm) REVERT: D 319 CYS cc_start: 0.9208 (m) cc_final: 0.8951 (m) REVERT: D 429 MET cc_start: 0.8851 (ppp) cc_final: 0.8438 (ppp) REVERT: D 710 MET cc_start: 0.6309 (mmt) cc_final: 0.5853 (tpt) REVERT: D 877 LEU cc_start: 0.9075 (mt) cc_final: 0.8866 (mt) REVERT: D 903 MET cc_start: 0.6862 (mmp) cc_final: 0.5969 (mmm) REVERT: D 1031 ASP cc_start: 0.8595 (m-30) cc_final: 0.7745 (t0) REVERT: D 1142 CYS cc_start: 0.9284 (t) cc_final: 0.8672 (m) REVERT: D 1223 PHE cc_start: 0.8677 (m-10) cc_final: 0.8377 (m-10) REVERT: D 1252 MET cc_start: 0.8891 (ttm) cc_final: 0.8359 (tpp) REVERT: E 81 CYS cc_start: 0.8484 (t) cc_final: 0.8209 (t) REVERT: E 83 TRP cc_start: 0.8442 (m-10) cc_final: 0.8239 (m-10) REVERT: E 88 MET cc_start: 0.8985 (tpt) cc_final: 0.8707 (tmm) REVERT: E 95 PHE cc_start: 0.8973 (t80) cc_final: 0.8587 (t80) REVERT: E 199 MET cc_start: 0.7570 (mmp) cc_final: 0.6503 (mmm) REVERT: E 329 ASP cc_start: 0.7125 (p0) cc_final: 0.6201 (p0) REVERT: E 332 LYS cc_start: 0.8405 (mtmt) cc_final: 0.7800 (mtmm) REVERT: F 88 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8669 (tm-30) REVERT: F 89 ILE cc_start: 0.9198 (mt) cc_final: 0.8854 (mp) REVERT: F 91 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7968 (tt0) REVERT: F 108 MET cc_start: 0.8523 (mmt) cc_final: 0.8266 (mmp) REVERT: F 233 MET cc_start: 0.9583 (mmm) cc_final: 0.9134 (mmm) REVERT: F 319 CYS cc_start: 0.9208 (m) cc_final: 0.8951 (m) REVERT: F 429 MET cc_start: 0.8852 (ppp) cc_final: 0.8426 (ppp) REVERT: F 710 MET cc_start: 0.6322 (mmt) cc_final: 0.5855 (tpt) REVERT: F 877 LEU cc_start: 0.9109 (mt) cc_final: 0.8908 (mt) REVERT: F 903 MET cc_start: 0.6858 (mmp) cc_final: 0.6000 (mmm) REVERT: F 1031 ASP cc_start: 0.8498 (m-30) cc_final: 0.7713 (t0) REVERT: F 1142 CYS cc_start: 0.9285 (t) cc_final: 0.8671 (m) REVERT: F 1223 PHE cc_start: 0.8676 (m-10) cc_final: 0.8370 (m-10) REVERT: F 1252 MET cc_start: 0.8903 (ttm) cc_final: 0.8382 (tpp) REVERT: G 81 CYS cc_start: 0.8479 (t) cc_final: 0.8204 (t) REVERT: G 88 MET cc_start: 0.8986 (tpt) cc_final: 0.8709 (tmm) REVERT: G 95 PHE cc_start: 0.8968 (t80) cc_final: 0.8578 (t80) REVERT: G 199 MET cc_start: 0.7593 (mmp) cc_final: 0.6563 (mmm) REVERT: G 329 ASP cc_start: 0.7149 (p0) cc_final: 0.6232 (p0) REVERT: G 332 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7746 (mtmm) REVERT: H 88 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8675 (tm-30) REVERT: H 89 ILE cc_start: 0.9195 (mt) cc_final: 0.8850 (mp) REVERT: H 91 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7945 (tt0) REVERT: H 108 MET cc_start: 0.8520 (mmt) cc_final: 0.8263 (mmp) REVERT: H 233 MET cc_start: 0.9570 (mmm) cc_final: 0.9116 (mmm) REVERT: H 319 CYS cc_start: 0.9200 (m) cc_final: 0.8945 (m) REVERT: H 429 MET cc_start: 0.8844 (ppp) cc_final: 0.8408 (ppp) REVERT: H 710 MET cc_start: 0.6389 (mmt) cc_final: 0.5751 (tpt) REVERT: H 903 MET cc_start: 0.6876 (mmp) cc_final: 0.5989 (mmm) REVERT: H 1031 ASP cc_start: 0.8504 (m-30) cc_final: 0.7717 (t0) REVERT: H 1103 ASN cc_start: 0.7860 (m-40) cc_final: 0.7545 (m-40) REVERT: H 1142 CYS cc_start: 0.9269 (t) cc_final: 0.8660 (m) REVERT: H 1223 PHE cc_start: 0.8664 (m-10) cc_final: 0.8364 (m-10) REVERT: H 1252 MET cc_start: 0.8902 (ttm) cc_final: 0.8377 (tpp) outliers start: 9 outliers final: 0 residues processed: 723 average time/residue: 0.5377 time to fit residues: 684.0173 Evaluate side-chains 497 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 497 time to evaluate : 6.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 7.9990 chunk 182 optimal weight: 30.0000 chunk 489 optimal weight: 8.9990 chunk 400 optimal weight: 7.9990 chunk 162 optimal weight: 20.0000 chunk 589 optimal weight: 20.0000 chunk 636 optimal weight: 30.0000 chunk 525 optimal weight: 9.9990 chunk 584 optimal weight: 20.0000 chunk 200 optimal weight: 10.0000 chunk 472 optimal weight: 6.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 HIS B 822 GLN B 863 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 822 GLN ** D1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1416 HIS E 48 ASN E 152 GLN ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN F 562 HIS F 822 GLN F 863 HIS ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 152 GLN ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 822 GLN H 863 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 51576 Z= 0.395 Angle : 0.788 11.861 70172 Z= 0.411 Chirality : 0.048 0.293 8516 Planarity : 0.005 0.044 8588 Dihedral : 8.820 149.729 7064 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.09 % Allowed : 5.93 % Favored : 93.97 % 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: -0.51 (0.10), residues: 6408 helix: 0.52 (0.08), residues: 3940 sheet: -1.26 (0.20), residues: 536 loop : -1.74 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP B1452 HIS 0.015 0.002 HIS F 863 PHE 0.037 0.003 PHE C 168 TYR 0.021 0.002 TYR B 124 ARG 0.014 0.001 ARG A 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 609 time to evaluate : 5.432 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: A 81 CYS cc_start: 0.8530 (t) cc_final: 0.7185 (t) REVERT: A 150 ILE cc_start: 0.9251 (tp) cc_final: 0.9050 (tp) REVERT: A 163 MET cc_start: 0.8009 (ttt) cc_final: 0.7300 (ttt) REVERT: A 329 ASP cc_start: 0.7482 (p0) cc_final: 0.6487 (p0) REVERT: A 332 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7794 (mtmm) REVERT: B 89 ILE cc_start: 0.9291 (mt) cc_final: 0.8905 (mp) REVERT: B 233 MET cc_start: 0.9626 (mmm) cc_final: 0.9118 (mmm) REVERT: B 319 CYS cc_start: 0.9164 (m) cc_final: 0.8902 (m) REVERT: B 429 MET cc_start: 0.8865 (ppp) cc_final: 0.8461 (ppp) REVERT: B 710 MET cc_start: 0.6420 (mmt) cc_final: 0.5660 (tpt) REVERT: B 1025 MET cc_start: 0.7939 (mmm) cc_final: 0.7719 (mmm) REVERT: B 1031 ASP cc_start: 0.8568 (m-30) cc_final: 0.7556 (t0) REVERT: B 1142 CYS cc_start: 0.9293 (t) cc_final: 0.8720 (m) REVERT: B 1165 LEU cc_start: 0.8709 (tt) cc_final: 0.8376 (pp) REVERT: B 1223 PHE cc_start: 0.8594 (m-10) cc_final: 0.8311 (m-10) REVERT: B 1252 MET cc_start: 0.8731 (ttm) cc_final: 0.8452 (tpp) REVERT: B 1283 LEU cc_start: 0.9200 (mp) cc_final: 0.8859 (mp) REVERT: C 81 CYS cc_start: 0.8337 (t) cc_final: 0.7685 (t) REVERT: C 83 TRP cc_start: 0.8478 (m-10) cc_final: 0.8164 (m-10) REVERT: C 122 LEU cc_start: 0.9510 (tt) cc_final: 0.9307 (tt) REVERT: C 163 MET cc_start: 0.8226 (ttt) cc_final: 0.7689 (ttt) REVERT: C 329 ASP cc_start: 0.7449 (p0) cc_final: 0.6449 (p0) REVERT: C 332 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7799 (mtmm) REVERT: D 89 ILE cc_start: 0.9290 (mt) cc_final: 0.8935 (mp) REVERT: D 126 ASN cc_start: 0.9051 (m-40) cc_final: 0.8753 (t0) REVERT: D 186 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8687 (mm-30) REVERT: D 233 MET cc_start: 0.9622 (mmm) cc_final: 0.9097 (mmm) REVERT: D 257 MET cc_start: 0.8778 (pmm) cc_final: 0.8391 (ptm) REVERT: D 319 CYS cc_start: 0.9168 (m) cc_final: 0.8905 (m) REVERT: D 429 MET cc_start: 0.8864 (ppp) cc_final: 0.8470 (ppp) REVERT: D 710 MET cc_start: 0.6424 (mmt) cc_final: 0.5607 (tpt) REVERT: D 1025 MET cc_start: 0.7925 (mmm) cc_final: 0.7684 (mmm) REVERT: D 1031 ASP cc_start: 0.8564 (m-30) cc_final: 0.7585 (t0) REVERT: D 1142 CYS cc_start: 0.9297 (t) cc_final: 0.8758 (m) REVERT: D 1165 LEU cc_start: 0.8771 (tt) cc_final: 0.8419 (pp) REVERT: D 1223 PHE cc_start: 0.8610 (m-10) cc_final: 0.8323 (m-10) REVERT: D 1252 MET cc_start: 0.8695 (ttm) cc_final: 0.8466 (tpp) REVERT: D 1283 LEU cc_start: 0.9203 (mp) cc_final: 0.8860 (mp) REVERT: D 1395 MET cc_start: 0.8411 (mmp) cc_final: 0.8154 (mmm) REVERT: E 81 CYS cc_start: 0.8484 (t) cc_final: 0.7018 (t) REVERT: E 122 LEU cc_start: 0.9511 (tt) cc_final: 0.9305 (tt) REVERT: E 163 MET cc_start: 0.8025 (ttt) cc_final: 0.7285 (ttt) REVERT: E 199 MET cc_start: 0.7443 (mmp) cc_final: 0.6806 (mmm) REVERT: E 329 ASP cc_start: 0.7389 (p0) cc_final: 0.6374 (p0) REVERT: E 332 LYS cc_start: 0.8570 (mtmt) cc_final: 0.7846 (mtmm) REVERT: F 89 ILE cc_start: 0.9269 (mt) cc_final: 0.8904 (mp) REVERT: F 233 MET cc_start: 0.9614 (mmm) cc_final: 0.9082 (mmm) REVERT: F 319 CYS cc_start: 0.9158 (m) cc_final: 0.8902 (m) REVERT: F 429 MET cc_start: 0.8867 (ppp) cc_final: 0.8460 (ppp) REVERT: F 710 MET cc_start: 0.6521 (mmt) cc_final: 0.5678 (tpt) REVERT: F 1025 MET cc_start: 0.7934 (mmm) cc_final: 0.7689 (mmm) REVERT: F 1031 ASP cc_start: 0.8632 (m-30) cc_final: 0.7594 (t0) REVERT: F 1142 CYS cc_start: 0.9294 (t) cc_final: 0.8752 (m) REVERT: F 1165 LEU cc_start: 0.8775 (tt) cc_final: 0.8427 (pp) REVERT: F 1223 PHE cc_start: 0.8614 (m-10) cc_final: 0.8326 (m-10) REVERT: F 1252 MET cc_start: 0.8687 (ttm) cc_final: 0.8408 (tpp) REVERT: F 1283 LEU cc_start: 0.9201 (mp) cc_final: 0.8857 (mp) REVERT: F 1395 MET cc_start: 0.8401 (mmp) cc_final: 0.8109 (mmm) REVERT: G 81 CYS cc_start: 0.8497 (t) cc_final: 0.8156 (t) REVERT: G 83 TRP cc_start: 0.8475 (m-10) cc_final: 0.8163 (m-10) REVERT: G 122 LEU cc_start: 0.9505 (tt) cc_final: 0.9295 (tt) REVERT: G 163 MET cc_start: 0.8169 (ttt) cc_final: 0.7460 (ttt) REVERT: G 329 ASP cc_start: 0.7515 (p0) cc_final: 0.6506 (p0) REVERT: G 332 LYS cc_start: 0.8554 (mtmt) cc_final: 0.7863 (mtmm) REVERT: H 89 ILE cc_start: 0.9287 (mt) cc_final: 0.8902 (mp) REVERT: H 233 MET cc_start: 0.9624 (mmm) cc_final: 0.9111 (mmm) REVERT: H 257 MET cc_start: 0.8964 (pmm) cc_final: 0.8629 (ptm) REVERT: H 319 CYS cc_start: 0.9161 (m) cc_final: 0.8900 (m) REVERT: H 429 MET cc_start: 0.8855 (ppp) cc_final: 0.8433 (ppp) REVERT: H 710 MET cc_start: 0.6513 (mmt) cc_final: 0.5725 (tpt) REVERT: H 1025 MET cc_start: 0.7950 (mmm) cc_final: 0.7731 (mmm) REVERT: H 1031 ASP cc_start: 0.8561 (m-30) cc_final: 0.7558 (t0) REVERT: H 1103 ASN cc_start: 0.7786 (m-40) cc_final: 0.7498 (m-40) REVERT: H 1142 CYS cc_start: 0.9296 (t) cc_final: 0.8744 (m) REVERT: H 1165 LEU cc_start: 0.8775 (tt) cc_final: 0.8427 (pp) REVERT: H 1223 PHE cc_start: 0.8598 (m-10) cc_final: 0.8309 (m-10) REVERT: H 1252 MET cc_start: 0.8682 (ttm) cc_final: 0.8412 (tpp) REVERT: H 1283 LEU cc_start: 0.9199 (mp) cc_final: 0.8859 (mp) REVERT: H 1395 MET cc_start: 0.8411 (mmp) cc_final: 0.8122 (mmm) REVERT: H 1398 MET cc_start: 0.6238 (ttm) cc_final: 0.5991 (ttm) outliers start: 5 outliers final: 5 residues processed: 610 average time/residue: 0.5431 time to fit residues: 585.7896 Evaluate side-chains 443 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 438 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 20.0000 chunk 443 optimal weight: 30.0000 chunk 305 optimal weight: 30.0000 chunk 65 optimal weight: 0.2980 chunk 281 optimal weight: 20.0000 chunk 395 optimal weight: 20.0000 chunk 591 optimal weight: 30.0000 chunk 626 optimal weight: 8.9990 chunk 309 optimal weight: 5.9990 chunk 560 optimal weight: 30.0000 chunk 168 optimal weight: 1.9990 overall best weight: 7.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B1245 ASN C 41 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 562 HIS D 863 HIS D1245 ASN E 41 ASN ** E 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN F1245 ASN G 41 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 259 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN H 562 HIS H1245 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 51576 Z= 0.357 Angle : 0.741 11.641 70172 Z= 0.391 Chirality : 0.046 0.213 8516 Planarity : 0.005 0.073 8588 Dihedral : 8.743 147.933 7064 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.45 % Favored : 95.43 % Rotamer: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.27 (0.10), residues: 6408 helix: 0.66 (0.08), residues: 3936 sheet: -0.97 (0.21), residues: 508 loop : -1.56 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 83 HIS 0.010 0.002 HIS C 259 PHE 0.038 0.003 PHE E 168 TYR 0.058 0.003 TYR D1254 ARG 0.005 0.001 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 572 time to evaluate : 6.268 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: A 81 CYS cc_start: 0.8469 (t) cc_final: 0.7208 (t) REVERT: A 88 MET cc_start: 0.8970 (tmm) cc_final: 0.8619 (tmm) REVERT: A 163 MET cc_start: 0.8292 (ttt) cc_final: 0.7682 (tmm) REVERT: A 332 LYS cc_start: 0.8502 (mtmt) cc_final: 0.8279 (mtpt) REVERT: B 233 MET cc_start: 0.9604 (mmm) cc_final: 0.9225 (ttm) REVERT: B 257 MET cc_start: 0.8891 (pmm) cc_final: 0.8580 (ptm) REVERT: B 319 CYS cc_start: 0.9169 (m) cc_final: 0.8916 (m) REVERT: B 433 PHE cc_start: 0.8641 (m-10) cc_final: 0.8384 (m-80) REVERT: B 468 ILE cc_start: 0.9143 (tp) cc_final: 0.8915 (pt) REVERT: B 710 MET cc_start: 0.6205 (mmt) cc_final: 0.5248 (tpt) REVERT: B 1025 MET cc_start: 0.7864 (mmm) cc_final: 0.7607 (mmm) REVERT: B 1031 ASP cc_start: 0.8657 (m-30) cc_final: 0.7610 (t0) REVERT: B 1142 CYS cc_start: 0.9272 (t) cc_final: 0.8803 (m) REVERT: B 1252 MET cc_start: 0.8818 (ttm) cc_final: 0.8387 (tpp) REVERT: B 1283 LEU cc_start: 0.9152 (mp) cc_final: 0.8628 (mp) REVERT: B 1305 MET cc_start: 0.8805 (mmm) cc_final: 0.8500 (mmm) REVERT: B 1395 MET cc_start: 0.8356 (mmp) cc_final: 0.8057 (mmm) REVERT: B 1398 MET cc_start: 0.5914 (ttm) cc_final: 0.5597 (ttm) REVERT: C 81 CYS cc_start: 0.8747 (t) cc_final: 0.7550 (t) REVERT: C 88 MET cc_start: 0.9002 (tmm) cc_final: 0.8739 (tmm) REVERT: C 199 MET cc_start: 0.7233 (mmp) cc_final: 0.6677 (mmp) REVERT: C 332 LYS cc_start: 0.8514 (mtmt) cc_final: 0.8291 (mtpt) REVERT: D 186 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8576 (mm-30) REVERT: D 233 MET cc_start: 0.9584 (mmm) cc_final: 0.9041 (mmm) REVERT: D 319 CYS cc_start: 0.9173 (m) cc_final: 0.8915 (m) REVERT: D 433 PHE cc_start: 0.8643 (m-10) cc_final: 0.8378 (m-80) REVERT: D 468 ILE cc_start: 0.9142 (tp) cc_final: 0.8913 (pt) REVERT: D 710 MET cc_start: 0.6448 (mmt) cc_final: 0.5409 (tpt) REVERT: D 801 MET cc_start: 0.8785 (ptt) cc_final: 0.8517 (ptt) REVERT: D 1025 MET cc_start: 0.7828 (mmm) cc_final: 0.7579 (mmm) REVERT: D 1031 ASP cc_start: 0.8652 (m-30) cc_final: 0.7600 (t0) REVERT: D 1142 CYS cc_start: 0.9265 (t) cc_final: 0.8809 (m) REVERT: D 1248 LEU cc_start: 0.9251 (tp) cc_final: 0.8777 (tp) REVERT: D 1283 LEU cc_start: 0.9154 (mp) cc_final: 0.8632 (mp) REVERT: D 1395 MET cc_start: 0.8346 (mmp) cc_final: 0.8081 (mmm) REVERT: D 1398 MET cc_start: 0.5919 (ttm) cc_final: 0.5598 (ttm) REVERT: E 81 CYS cc_start: 0.8496 (t) cc_final: 0.7120 (t) REVERT: E 88 MET cc_start: 0.8990 (tmm) cc_final: 0.8654 (tmm) REVERT: E 163 MET cc_start: 0.8242 (ttt) cc_final: 0.7812 (tmm) REVERT: F 41 PHE cc_start: 0.8231 (m-10) cc_final: 0.8023 (m-80) REVERT: F 233 MET cc_start: 0.9584 (mmm) cc_final: 0.9039 (mmm) REVERT: F 257 MET cc_start: 0.8865 (pmm) cc_final: 0.8617 (ptm) REVERT: F 319 CYS cc_start: 0.9134 (m) cc_final: 0.8872 (m) REVERT: F 433 PHE cc_start: 0.8640 (m-10) cc_final: 0.8377 (m-80) REVERT: F 468 ILE cc_start: 0.9144 (tp) cc_final: 0.8916 (pt) REVERT: F 710 MET cc_start: 0.6537 (mmt) cc_final: 0.5498 (tpt) REVERT: F 801 MET cc_start: 0.8779 (ptt) cc_final: 0.8515 (ptt) REVERT: F 1025 MET cc_start: 0.7835 (mmm) cc_final: 0.7583 (mmm) REVERT: F 1031 ASP cc_start: 0.8642 (m-30) cc_final: 0.7605 (t0) REVERT: F 1118 LEU cc_start: 0.8520 (tp) cc_final: 0.8319 (mp) REVERT: F 1142 CYS cc_start: 0.9262 (t) cc_final: 0.8811 (m) REVERT: F 1252 MET cc_start: 0.8871 (ttm) cc_final: 0.8405 (tpp) REVERT: F 1283 LEU cc_start: 0.9153 (mp) cc_final: 0.8629 (mp) REVERT: F 1395 MET cc_start: 0.8344 (mmp) cc_final: 0.8078 (mmm) REVERT: F 1398 MET cc_start: 0.5853 (ttm) cc_final: 0.5632 (ttm) REVERT: G 81 CYS cc_start: 0.8724 (t) cc_final: 0.7323 (t) REVERT: G 83 TRP cc_start: 0.8512 (m-10) cc_final: 0.8209 (m-10) REVERT: G 88 MET cc_start: 0.8974 (tmm) cc_final: 0.8626 (tmm) REVERT: G 163 MET cc_start: 0.8288 (ttt) cc_final: 0.7929 (tmm) REVERT: G 332 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8434 (mtpt) REVERT: H 233 MET cc_start: 0.9600 (mmm) cc_final: 0.9224 (ttm) REVERT: H 319 CYS cc_start: 0.9108 (m) cc_final: 0.8835 (m) REVERT: H 433 PHE cc_start: 0.8678 (m-10) cc_final: 0.8427 (m-80) REVERT: H 468 ILE cc_start: 0.9145 (tp) cc_final: 0.8917 (pt) REVERT: H 710 MET cc_start: 0.6546 (mmt) cc_final: 0.5515 (tpt) REVERT: H 1025 MET cc_start: 0.7832 (mmm) cc_final: 0.7583 (mmm) REVERT: H 1031 ASP cc_start: 0.8651 (m-30) cc_final: 0.7606 (t0) REVERT: H 1103 ASN cc_start: 0.7908 (m-40) cc_final: 0.7631 (m-40) REVERT: H 1142 CYS cc_start: 0.9262 (t) cc_final: 0.8793 (m) REVERT: H 1252 MET cc_start: 0.8834 (ttm) cc_final: 0.8332 (tpp) REVERT: H 1283 LEU cc_start: 0.9153 (mp) cc_final: 0.8633 (mp) REVERT: H 1395 MET cc_start: 0.8332 (mmp) cc_final: 0.8062 (mmm) outliers start: 4 outliers final: 0 residues processed: 576 average time/residue: 0.6036 time to fit residues: 610.3000 Evaluate side-chains 404 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 404 time to evaluate : 6.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 10.0000 chunk 355 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 466 optimal weight: 7.9990 chunk 258 optimal weight: 0.9980 chunk 534 optimal weight: 0.9990 chunk 432 optimal weight: 0.0970 chunk 0 optimal weight: 20.0000 chunk 319 optimal weight: 30.0000 chunk 562 optimal weight: 40.0000 chunk 158 optimal weight: 40.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN C 41 ASN C 48 ASN C 259 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN E 41 ASN E 48 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 HIS ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN G 41 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 51576 Z= 0.176 Angle : 0.632 8.874 70172 Z= 0.317 Chirality : 0.042 0.204 8516 Planarity : 0.004 0.066 8588 Dihedral : 8.340 141.533 7064 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.28 (0.11), residues: 6408 helix: 1.15 (0.08), residues: 3948 sheet: -0.99 (0.20), residues: 572 loop : -1.43 (0.14), residues: 1888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 83 HIS 0.006 0.001 HIS F 71 PHE 0.030 0.002 PHE A 75 TYR 0.020 0.001 TYR D 123 ARG 0.007 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 624 time to evaluate : 5.815 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 73 LEU cc_start: 0.9150 (tt) cc_final: 0.8870 (pp) REVERT: A 81 CYS cc_start: 0.8425 (t) cc_final: 0.7123 (t) REVERT: A 88 MET cc_start: 0.8959 (tmm) cc_final: 0.8610 (tmm) REVERT: A 95 PHE cc_start: 0.9052 (t80) cc_final: 0.8675 (t80) REVERT: A 152 GLN cc_start: 0.9244 (tp40) cc_final: 0.8935 (tp40) REVERT: A 329 ASP cc_start: 0.7378 (p0) cc_final: 0.6620 (p0) REVERT: A 332 LYS cc_start: 0.8438 (mtmt) cc_final: 0.7899 (mtmm) REVERT: B 233 MET cc_start: 0.9567 (mmm) cc_final: 0.8987 (mmm) REVERT: B 319 CYS cc_start: 0.9092 (m) cc_final: 0.8803 (m) REVERT: B 710 MET cc_start: 0.6560 (mmt) cc_final: 0.5982 (tpt) REVERT: B 1025 MET cc_start: 0.7792 (mmm) cc_final: 0.7535 (mmm) REVERT: B 1031 ASP cc_start: 0.8621 (m-30) cc_final: 0.7530 (t0) REVERT: B 1118 LEU cc_start: 0.8498 (tp) cc_final: 0.8268 (pt) REVERT: B 1142 CYS cc_start: 0.9221 (t) cc_final: 0.8870 (m) REVERT: B 1149 LEU cc_start: 0.8992 (mt) cc_final: 0.8785 (mt) REVERT: B 1283 LEU cc_start: 0.9141 (mp) cc_final: 0.8571 (mp) REVERT: B 1395 MET cc_start: 0.8321 (mmp) cc_final: 0.8047 (mmm) REVERT: C 73 LEU cc_start: 0.9122 (tt) cc_final: 0.8893 (pp) REVERT: C 81 CYS cc_start: 0.8472 (t) cc_final: 0.7050 (t) REVERT: C 83 TRP cc_start: 0.8547 (m-10) cc_final: 0.8283 (m-10) REVERT: C 88 MET cc_start: 0.8982 (tmm) cc_final: 0.8700 (tmm) REVERT: C 95 PHE cc_start: 0.9063 (t80) cc_final: 0.8676 (t80) REVERT: C 152 GLN cc_start: 0.9228 (tp40) cc_final: 0.8951 (tp40) REVERT: C 199 MET cc_start: 0.7028 (mmp) cc_final: 0.6538 (mmp) REVERT: C 329 ASP cc_start: 0.7430 (p0) cc_final: 0.6663 (p0) REVERT: C 332 LYS cc_start: 0.8435 (mtmt) cc_final: 0.7894 (mtmm) REVERT: D 186 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8538 (mm-30) REVERT: D 233 MET cc_start: 0.9561 (mmm) cc_final: 0.9083 (ttm) REVERT: D 257 MET cc_start: 0.8814 (pmm) cc_final: 0.8454 (ptm) REVERT: D 319 CYS cc_start: 0.9095 (m) cc_final: 0.8808 (m) REVERT: D 710 MET cc_start: 0.6555 (mmt) cc_final: 0.5968 (tpt) REVERT: D 801 MET cc_start: 0.8861 (ptt) cc_final: 0.8505 (tmm) REVERT: D 903 MET cc_start: 0.6688 (mmp) cc_final: 0.5656 (tmm) REVERT: D 1025 MET cc_start: 0.7808 (mmm) cc_final: 0.7550 (mmm) REVERT: D 1031 ASP cc_start: 0.8622 (m-30) cc_final: 0.7505 (t0) REVERT: D 1142 CYS cc_start: 0.9210 (t) cc_final: 0.8825 (m) REVERT: D 1283 LEU cc_start: 0.9146 (mp) cc_final: 0.8574 (mp) REVERT: E 73 LEU cc_start: 0.9123 (tt) cc_final: 0.8849 (pp) REVERT: E 81 CYS cc_start: 0.8221 (t) cc_final: 0.7615 (t) REVERT: E 88 MET cc_start: 0.8981 (tmm) cc_final: 0.8668 (tmm) REVERT: E 95 PHE cc_start: 0.9065 (t80) cc_final: 0.8670 (t80) REVERT: E 163 MET cc_start: 0.8248 (ttt) cc_final: 0.7924 (tmm) REVERT: E 332 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8222 (mtpp) REVERT: F 233 MET cc_start: 0.9562 (mmm) cc_final: 0.9088 (ttm) REVERT: F 319 CYS cc_start: 0.9093 (m) cc_final: 0.8806 (m) REVERT: F 710 MET cc_start: 0.6737 (mmt) cc_final: 0.5977 (tpt) REVERT: F 801 MET cc_start: 0.8886 (ptt) cc_final: 0.8558 (tmm) REVERT: F 903 MET cc_start: 0.6684 (mmp) cc_final: 0.5681 (tmm) REVERT: F 1025 MET cc_start: 0.7814 (mmm) cc_final: 0.7554 (mmm) REVERT: F 1031 ASP cc_start: 0.8615 (m-30) cc_final: 0.7508 (t0) REVERT: F 1118 LEU cc_start: 0.8519 (tp) cc_final: 0.8298 (mp) REVERT: F 1142 CYS cc_start: 0.9205 (t) cc_final: 0.8826 (m) REVERT: F 1283 LEU cc_start: 0.9145 (mp) cc_final: 0.8570 (mp) REVERT: G 73 LEU cc_start: 0.9144 (tt) cc_final: 0.8872 (pp) REVERT: G 81 CYS cc_start: 0.8559 (t) cc_final: 0.7214 (t) REVERT: G 88 MET cc_start: 0.8972 (tmm) cc_final: 0.8681 (tmm) REVERT: G 95 PHE cc_start: 0.9062 (t80) cc_final: 0.8675 (t80) REVERT: G 152 GLN cc_start: 0.9272 (tp40) cc_final: 0.8963 (tp40) REVERT: G 329 ASP cc_start: 0.7375 (p0) cc_final: 0.6561 (p0) REVERT: G 332 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8055 (mtmm) REVERT: H 233 MET cc_start: 0.9566 (mmm) cc_final: 0.8989 (mmm) REVERT: H 319 CYS cc_start: 0.9086 (m) cc_final: 0.8800 (m) REVERT: H 710 MET cc_start: 0.6735 (mmt) cc_final: 0.5973 (tpt) REVERT: H 1025 MET cc_start: 0.7811 (mmm) cc_final: 0.7543 (mmm) REVERT: H 1031 ASP cc_start: 0.8613 (m-30) cc_final: 0.7540 (t0) REVERT: H 1103 ASN cc_start: 0.7674 (m-40) cc_final: 0.7386 (m-40) REVERT: H 1118 LEU cc_start: 0.8692 (tp) cc_final: 0.8451 (pt) REVERT: H 1142 CYS cc_start: 0.9222 (t) cc_final: 0.8866 (m) REVERT: H 1149 LEU cc_start: 0.9012 (mt) cc_final: 0.8773 (mt) REVERT: H 1283 LEU cc_start: 0.9137 (mp) cc_final: 0.8580 (mp) REVERT: H 1395 MET cc_start: 0.8321 (mmp) cc_final: 0.8103 (mmm) outliers start: 4 outliers final: 4 residues processed: 624 average time/residue: 0.5299 time to fit residues: 584.3190 Evaluate side-chains 464 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 460 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 3.9990 chunk 564 optimal weight: 30.0000 chunk 123 optimal weight: 0.6980 chunk 367 optimal weight: 6.9990 chunk 154 optimal weight: 0.0770 chunk 626 optimal weight: 10.0000 chunk 520 optimal weight: 1.9990 chunk 290 optimal weight: 10.0000 chunk 52 optimal weight: 0.0370 chunk 207 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 48 ASN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN C 41 ASN C 48 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN E 41 ASN E 48 ASN ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN G 41 ASN G 48 ASN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 51576 Z= 0.172 Angle : 0.620 8.802 70172 Z= 0.314 Chirality : 0.042 0.192 8516 Planarity : 0.004 0.061 8588 Dihedral : 8.083 145.890 7064 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.50 (0.11), residues: 6408 helix: 1.28 (0.08), residues: 3948 sheet: -0.95 (0.21), residues: 536 loop : -1.22 (0.14), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP G 83 HIS 0.005 0.001 HIS D 71 PHE 0.039 0.002 PHE B1204 TYR 0.016 0.001 TYR H 123 ARG 0.005 0.000 ARG H 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 596 time to evaluate : 5.821 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 73 LEU cc_start: 0.9092 (tt) cc_final: 0.8840 (pp) REVERT: A 77 MET cc_start: 0.8787 (tpt) cc_final: 0.8502 (tpp) REVERT: A 81 CYS cc_start: 0.8192 (t) cc_final: 0.7521 (t) REVERT: A 88 MET cc_start: 0.9037 (tmm) cc_final: 0.8715 (tmm) REVERT: A 95 PHE cc_start: 0.9064 (t80) cc_final: 0.8670 (t80) REVERT: A 159 ILE cc_start: 0.9069 (tp) cc_final: 0.8827 (pt) REVERT: A 332 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7776 (mtmm) REVERT: B 233 MET cc_start: 0.9551 (mmm) cc_final: 0.9002 (mmm) REVERT: B 257 MET cc_start: 0.8532 (ptm) cc_final: 0.8185 (ppp) REVERT: B 319 CYS cc_start: 0.8982 (m) cc_final: 0.8732 (m) REVERT: B 710 MET cc_start: 0.6743 (mmt) cc_final: 0.6122 (tpt) REVERT: B 1025 MET cc_start: 0.7853 (mmm) cc_final: 0.7535 (mmm) REVERT: B 1031 ASP cc_start: 0.8704 (m-30) cc_final: 0.7564 (t0) REVERT: B 1142 CYS cc_start: 0.9211 (t) cc_final: 0.8849 (m) REVERT: B 1252 MET cc_start: 0.9016 (tpp) cc_final: 0.8813 (tpp) REVERT: B 1283 LEU cc_start: 0.9208 (mp) cc_final: 0.8818 (mp) REVERT: B 1398 MET cc_start: 0.5162 (ttm) cc_final: 0.4912 (ttp) REVERT: C 81 CYS cc_start: 0.8455 (t) cc_final: 0.7380 (t) REVERT: C 88 MET cc_start: 0.8989 (tmm) cc_final: 0.8652 (tmm) REVERT: C 95 PHE cc_start: 0.9071 (t80) cc_final: 0.8691 (t80) REVERT: C 199 MET cc_start: 0.6988 (mmp) cc_final: 0.6449 (mmp) REVERT: C 256 ILE cc_start: 0.8951 (mp) cc_final: 0.8634 (tt) REVERT: C 332 LYS cc_start: 0.8369 (mtmt) cc_final: 0.7885 (mtmm) REVERT: D 233 MET cc_start: 0.9547 (mmm) cc_final: 0.9093 (ttm) REVERT: D 257 MET cc_start: 0.8760 (pmm) cc_final: 0.8528 (ptm) REVERT: D 319 CYS cc_start: 0.8998 (m) cc_final: 0.8746 (m) REVERT: D 710 MET cc_start: 0.6554 (mmt) cc_final: 0.5956 (tpt) REVERT: D 801 MET cc_start: 0.8884 (ptt) cc_final: 0.8518 (tmm) REVERT: D 903 MET cc_start: 0.6635 (mmp) cc_final: 0.5727 (mmm) REVERT: D 1025 MET cc_start: 0.7866 (mmm) cc_final: 0.7551 (mmm) REVERT: D 1031 ASP cc_start: 0.8695 (m-30) cc_final: 0.7568 (t0) REVERT: D 1142 CYS cc_start: 0.9208 (t) cc_final: 0.8848 (m) REVERT: D 1252 MET cc_start: 0.8978 (ttm) cc_final: 0.8768 (tpp) REVERT: D 1283 LEU cc_start: 0.9209 (mp) cc_final: 0.8815 (mp) REVERT: D 1398 MET cc_start: 0.5170 (ttm) cc_final: 0.4933 (ttp) REVERT: E 73 LEU cc_start: 0.9130 (tt) cc_final: 0.8823 (pp) REVERT: E 77 MET cc_start: 0.8888 (tpt) cc_final: 0.8458 (tpp) REVERT: E 81 CYS cc_start: 0.8719 (t) cc_final: 0.7427 (t) REVERT: E 88 MET cc_start: 0.9035 (tmm) cc_final: 0.8709 (tmm) REVERT: E 95 PHE cc_start: 0.9056 (t80) cc_final: 0.8675 (t80) REVERT: E 163 MET cc_start: 0.8187 (ttt) cc_final: 0.7978 (tmm) REVERT: E 199 MET cc_start: 0.7818 (mmm) cc_final: 0.7446 (mmm) REVERT: E 332 LYS cc_start: 0.8667 (mtpt) cc_final: 0.8317 (mtpp) REVERT: F 233 MET cc_start: 0.9549 (mmm) cc_final: 0.9095 (ttm) REVERT: F 257 MET cc_start: 0.8561 (ptm) cc_final: 0.8193 (ppp) REVERT: F 319 CYS cc_start: 0.8985 (m) cc_final: 0.8739 (m) REVERT: F 710 MET cc_start: 0.6567 (mmt) cc_final: 0.5971 (tpt) REVERT: F 801 MET cc_start: 0.8881 (ptt) cc_final: 0.8521 (tmm) REVERT: F 903 MET cc_start: 0.6648 (mmp) cc_final: 0.5726 (mmm) REVERT: F 1025 MET cc_start: 0.7809 (mmm) cc_final: 0.7482 (mmm) REVERT: F 1031 ASP cc_start: 0.8672 (m-30) cc_final: 0.7603 (t0) REVERT: F 1142 CYS cc_start: 0.9207 (t) cc_final: 0.8842 (m) REVERT: F 1252 MET cc_start: 0.8980 (tpp) cc_final: 0.8766 (tpp) REVERT: F 1398 MET cc_start: 0.5161 (ttm) cc_final: 0.4907 (ttp) REVERT: G 73 LEU cc_start: 0.9105 (tt) cc_final: 0.8877 (pp) REVERT: G 77 MET cc_start: 0.8889 (tpt) cc_final: 0.8562 (tpp) REVERT: G 81 CYS cc_start: 0.8740 (t) cc_final: 0.7625 (t) REVERT: G 83 TRP cc_start: 0.8557 (m-10) cc_final: 0.7668 (m-10) REVERT: G 88 MET cc_start: 0.9031 (tmm) cc_final: 0.8770 (tmm) REVERT: G 95 PHE cc_start: 0.9063 (t80) cc_final: 0.8689 (t80) REVERT: G 199 MET cc_start: 0.7331 (mmp) cc_final: 0.7097 (mmm) REVERT: G 329 ASP cc_start: 0.7359 (p0) cc_final: 0.6148 (p0) REVERT: G 332 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8022 (mtmm) REVERT: H 233 MET cc_start: 0.9547 (mmm) cc_final: 0.8999 (mmm) REVERT: H 257 MET cc_start: 0.8737 (pmm) cc_final: 0.8200 (ppp) REVERT: H 319 CYS cc_start: 0.8981 (m) cc_final: 0.8732 (m) REVERT: H 429 MET cc_start: 0.8427 (ppp) cc_final: 0.8168 (ppp) REVERT: H 710 MET cc_start: 0.6567 (mmt) cc_final: 0.5971 (tpt) REVERT: H 903 MET cc_start: 0.6770 (mmp) cc_final: 0.5691 (tmm) REVERT: H 1025 MET cc_start: 0.7830 (mmm) cc_final: 0.7502 (mmm) REVERT: H 1031 ASP cc_start: 0.8680 (m-30) cc_final: 0.7590 (t0) REVERT: H 1103 ASN cc_start: 0.7612 (m-40) cc_final: 0.7338 (m-40) REVERT: H 1118 LEU cc_start: 0.8711 (tp) cc_final: 0.8448 (pt) REVERT: H 1142 CYS cc_start: 0.9208 (t) cc_final: 0.8837 (m) REVERT: H 1149 LEU cc_start: 0.9019 (mt) cc_final: 0.8804 (mt) REVERT: H 1252 MET cc_start: 0.8931 (tpp) cc_final: 0.8719 (tpp) REVERT: H 1283 LEU cc_start: 0.9212 (mp) cc_final: 0.8816 (mp) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 0.5286 time to fit residues: 556.3330 Evaluate side-chains 433 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 357 optimal weight: 4.9990 chunk 457 optimal weight: 20.0000 chunk 354 optimal weight: 20.0000 chunk 527 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 624 optimal weight: 0.8980 chunk 390 optimal weight: 10.0000 chunk 380 optimal weight: 9.9990 chunk 288 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN E 41 ASN E 48 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN G 41 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 51576 Z= 0.265 Angle : 0.667 10.212 70172 Z= 0.342 Chirality : 0.043 0.190 8516 Planarity : 0.004 0.061 8588 Dihedral : 8.015 151.045 7064 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.47 (0.11), residues: 6408 helix: 1.26 (0.08), residues: 3936 sheet: -0.91 (0.20), residues: 576 loop : -1.22 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP G 83 HIS 0.006 0.001 HIS E 259 PHE 0.033 0.002 PHE E 168 TYR 0.021 0.002 TYR H 124 ARG 0.018 0.001 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 5.977 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 73 LEU cc_start: 0.9154 (tt) cc_final: 0.8877 (pp) REVERT: A 81 CYS cc_start: 0.8775 (t) cc_final: 0.8456 (t) REVERT: A 88 MET cc_start: 0.9075 (tmm) cc_final: 0.8780 (tmm) REVERT: A 95 PHE cc_start: 0.9132 (t80) cc_final: 0.8771 (t80) REVERT: A 164 LEU cc_start: 0.9417 (tt) cc_final: 0.9159 (tt) REVERT: A 332 LYS cc_start: 0.8486 (mtmt) cc_final: 0.7996 (mtmm) REVERT: B 233 MET cc_start: 0.9561 (mmm) cc_final: 0.9025 (mmm) REVERT: B 257 MET cc_start: 0.8826 (ptm) cc_final: 0.8294 (ppp) REVERT: B 319 CYS cc_start: 0.8849 (m) cc_final: 0.8537 (m) REVERT: B 1025 MET cc_start: 0.7818 (mmm) cc_final: 0.7516 (mmm) REVERT: B 1031 ASP cc_start: 0.8569 (m-30) cc_final: 0.7461 (t0) REVERT: B 1066 MET cc_start: 0.7828 (mtm) cc_final: 0.7063 (mmm) REVERT: B 1142 CYS cc_start: 0.9215 (t) cc_final: 0.8870 (m) REVERT: B 1283 LEU cc_start: 0.9128 (mp) cc_final: 0.8686 (mp) REVERT: C 77 MET cc_start: 0.8797 (tpt) cc_final: 0.8522 (tpp) REVERT: C 81 CYS cc_start: 0.8415 (t) cc_final: 0.7264 (t) REVERT: C 88 MET cc_start: 0.9096 (tmm) cc_final: 0.8839 (tmm) REVERT: C 95 PHE cc_start: 0.9140 (t80) cc_final: 0.8775 (t80) REVERT: C 164 LEU cc_start: 0.9440 (tt) cc_final: 0.9224 (tt) REVERT: C 256 ILE cc_start: 0.8949 (mp) cc_final: 0.8454 (tt) REVERT: C 332 LYS cc_start: 0.8468 (mtmt) cc_final: 0.7986 (mtmm) REVERT: D 233 MET cc_start: 0.9550 (mmm) cc_final: 0.9019 (mmm) REVERT: D 257 MET cc_start: 0.8786 (pmm) cc_final: 0.8573 (ptm) REVERT: D 319 CYS cc_start: 0.8854 (m) cc_final: 0.8544 (m) REVERT: D 502 MET cc_start: 0.8368 (mtt) cc_final: 0.7803 (mmm) REVERT: D 801 MET cc_start: 0.8867 (ptt) cc_final: 0.8462 (tmm) REVERT: D 903 MET cc_start: 0.6618 (mmp) cc_final: 0.5711 (mmm) REVERT: D 1025 MET cc_start: 0.7834 (mmm) cc_final: 0.7529 (mmm) REVERT: D 1031 ASP cc_start: 0.8575 (m-30) cc_final: 0.7470 (t0) REVERT: D 1066 MET cc_start: 0.7754 (mtm) cc_final: 0.6994 (mmm) REVERT: D 1142 CYS cc_start: 0.9207 (t) cc_final: 0.8867 (m) REVERT: D 1252 MET cc_start: 0.8945 (ttm) cc_final: 0.8578 (tpp) REVERT: D 1283 LEU cc_start: 0.9155 (mp) cc_final: 0.8737 (mp) REVERT: E 73 LEU cc_start: 0.9151 (tt) cc_final: 0.8868 (pp) REVERT: E 81 CYS cc_start: 0.8795 (t) cc_final: 0.7563 (t) REVERT: E 83 TRP cc_start: 0.8655 (m-10) cc_final: 0.8317 (m-10) REVERT: E 88 MET cc_start: 0.9075 (tmm) cc_final: 0.8812 (tmm) REVERT: E 95 PHE cc_start: 0.9131 (t80) cc_final: 0.8774 (t80) REVERT: E 163 MET cc_start: 0.8613 (ttt) cc_final: 0.8384 (tmm) REVERT: E 199 MET cc_start: 0.7877 (mmm) cc_final: 0.7632 (mmm) REVERT: E 332 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8333 (mtpp) REVERT: F 233 MET cc_start: 0.9549 (mmm) cc_final: 0.9022 (mmm) REVERT: F 257 MET cc_start: 0.8852 (ptm) cc_final: 0.8269 (ppp) REVERT: F 319 CYS cc_start: 0.8859 (m) cc_final: 0.8542 (m) REVERT: F 502 MET cc_start: 0.8436 (mtt) cc_final: 0.7998 (mmm) REVERT: F 801 MET cc_start: 0.8873 (ptt) cc_final: 0.8465 (tmm) REVERT: F 903 MET cc_start: 0.6627 (mmp) cc_final: 0.5720 (mmm) REVERT: F 1025 MET cc_start: 0.7840 (mmm) cc_final: 0.7531 (mmm) REVERT: F 1031 ASP cc_start: 0.8708 (m-30) cc_final: 0.7614 (t0) REVERT: F 1066 MET cc_start: 0.7756 (mtm) cc_final: 0.7000 (mmm) REVERT: F 1142 CYS cc_start: 0.9195 (t) cc_final: 0.8815 (m) REVERT: F 1252 MET cc_start: 0.8997 (tpp) cc_final: 0.8761 (tpp) REVERT: F 1283 LEU cc_start: 0.9224 (mp) cc_final: 0.8959 (mp) REVERT: G 73 LEU cc_start: 0.9109 (tt) cc_final: 0.8808 (pp) REVERT: G 77 MET cc_start: 0.8937 (tpt) cc_final: 0.8562 (tpp) REVERT: G 81 CYS cc_start: 0.8722 (t) cc_final: 0.7502 (t) REVERT: G 83 TRP cc_start: 0.8475 (m-10) cc_final: 0.8208 (m-10) REVERT: G 88 MET cc_start: 0.9059 (tmm) cc_final: 0.8840 (tmm) REVERT: G 95 PHE cc_start: 0.9144 (t80) cc_final: 0.8783 (t80) REVERT: G 332 LYS cc_start: 0.8665 (mtmt) cc_final: 0.8076 (mtmm) REVERT: H 233 MET cc_start: 0.9553 (mmm) cc_final: 0.9015 (mmm) REVERT: H 319 CYS cc_start: 0.8849 (m) cc_final: 0.8539 (m) REVERT: H 502 MET cc_start: 0.8289 (mtt) cc_final: 0.8009 (mmm) REVERT: H 903 MET cc_start: 0.6733 (mmp) cc_final: 0.5681 (tmm) REVERT: H 1025 MET cc_start: 0.7832 (mmm) cc_final: 0.7527 (mmm) REVERT: H 1031 ASP cc_start: 0.8695 (m-30) cc_final: 0.7556 (t0) REVERT: H 1066 MET cc_start: 0.7759 (mtm) cc_final: 0.6943 (mmm) REVERT: H 1103 ASN cc_start: 0.7671 (m-40) cc_final: 0.7389 (m-40) REVERT: H 1142 CYS cc_start: 0.9191 (t) cc_final: 0.8856 (m) REVERT: H 1283 LEU cc_start: 0.9153 (mp) cc_final: 0.8857 (mp) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.5444 time to fit residues: 523.5377 Evaluate side-chains 398 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 6.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 1.9990 chunk 249 optimal weight: 9.9990 chunk 373 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 397 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 308 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 490 optimal weight: 0.9980 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN E 48 ASN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 51576 Z= 0.251 Angle : 0.674 13.929 70172 Z= 0.340 Chirality : 0.043 0.210 8516 Planarity : 0.004 0.059 8588 Dihedral : 7.958 152.629 7064 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.58 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.51 (0.11), residues: 6408 helix: 1.29 (0.08), residues: 3924 sheet: -0.56 (0.21), residues: 552 loop : -1.32 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP D1452 HIS 0.005 0.001 HIS C 259 PHE 0.048 0.002 PHE E 75 TYR 0.015 0.002 TYR F 124 ARG 0.015 0.001 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 5.897 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: A 73 LEU cc_start: 0.9105 (tt) cc_final: 0.8881 (pp) REVERT: A 81 CYS cc_start: 0.8552 (t) cc_final: 0.7699 (t) REVERT: A 88 MET cc_start: 0.9074 (tmm) cc_final: 0.8751 (tmm) REVERT: A 164 LEU cc_start: 0.9441 (tt) cc_final: 0.9097 (tt) REVERT: A 332 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8016 (mtmm) REVERT: B 233 MET cc_start: 0.9560 (mmm) cc_final: 0.9009 (mmm) REVERT: B 319 CYS cc_start: 0.8899 (m) cc_final: 0.8603 (m) REVERT: B 710 MET cc_start: 0.5605 (mmp) cc_final: 0.4460 (tpt) REVERT: B 903 MET cc_start: 0.6825 (mmp) cc_final: 0.6616 (mmp) REVERT: B 1025 MET cc_start: 0.7899 (mmm) cc_final: 0.7564 (mmm) REVERT: B 1031 ASP cc_start: 0.8775 (m-30) cc_final: 0.7665 (t0) REVERT: B 1066 MET cc_start: 0.7846 (mtm) cc_final: 0.7055 (mmm) REVERT: B 1142 CYS cc_start: 0.9146 (t) cc_final: 0.8751 (m) REVERT: B 1252 MET cc_start: 0.8951 (tpp) cc_final: 0.8595 (tpp) REVERT: B 1283 LEU cc_start: 0.9118 (mp) cc_final: 0.8652 (mp) REVERT: C 81 CYS cc_start: 0.8385 (t) cc_final: 0.7339 (t) REVERT: C 88 MET cc_start: 0.9065 (tmm) cc_final: 0.8822 (tmm) REVERT: C 95 PHE cc_start: 0.9144 (t80) cc_final: 0.8782 (t80) REVERT: C 164 LEU cc_start: 0.9423 (tt) cc_final: 0.9079 (tt) REVERT: C 199 MET cc_start: 0.7323 (mmp) cc_final: 0.7068 (mmp) REVERT: C 256 ILE cc_start: 0.8880 (mp) cc_final: 0.8540 (tt) REVERT: C 332 LYS cc_start: 0.8466 (mtmt) cc_final: 0.8018 (mtmm) REVERT: D 233 MET cc_start: 0.9558 (mmm) cc_final: 0.9017 (mmm) REVERT: D 319 CYS cc_start: 0.8854 (m) cc_final: 0.8563 (m) REVERT: D 801 MET cc_start: 0.8909 (ptt) cc_final: 0.8515 (tmm) REVERT: D 1025 MET cc_start: 0.7910 (mmm) cc_final: 0.7572 (mmm) REVERT: D 1031 ASP cc_start: 0.8774 (m-30) cc_final: 0.7669 (t0) REVERT: D 1066 MET cc_start: 0.7768 (mtm) cc_final: 0.6988 (mmm) REVERT: D 1142 CYS cc_start: 0.9148 (t) cc_final: 0.8766 (m) REVERT: D 1283 LEU cc_start: 0.9121 (mp) cc_final: 0.8665 (mp) REVERT: E 73 LEU cc_start: 0.9155 (tt) cc_final: 0.8876 (pp) REVERT: E 81 CYS cc_start: 0.8670 (t) cc_final: 0.7458 (t) REVERT: E 83 TRP cc_start: 0.8618 (m-10) cc_final: 0.8319 (m-10) REVERT: E 88 MET cc_start: 0.9058 (tmm) cc_final: 0.8755 (tmm) REVERT: E 332 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8255 (mtpp) REVERT: F 233 MET cc_start: 0.9557 (mmm) cc_final: 0.9025 (mmm) REVERT: F 319 CYS cc_start: 0.8901 (m) cc_final: 0.8611 (m) REVERT: F 801 MET cc_start: 0.8871 (ptt) cc_final: 0.8464 (tmm) REVERT: F 1025 MET cc_start: 0.7917 (mmm) cc_final: 0.7578 (mmm) REVERT: F 1031 ASP cc_start: 0.8772 (m-30) cc_final: 0.7674 (t0) REVERT: F 1066 MET cc_start: 0.7772 (mtm) cc_final: 0.6988 (mmm) REVERT: F 1142 CYS cc_start: 0.9160 (t) cc_final: 0.8762 (m) REVERT: F 1252 MET cc_start: 0.9015 (tpp) cc_final: 0.8753 (tpp) REVERT: F 1283 LEU cc_start: 0.9161 (mp) cc_final: 0.8673 (mp) REVERT: G 73 LEU cc_start: 0.9152 (tt) cc_final: 0.8875 (pp) REVERT: G 77 MET cc_start: 0.8921 (tpt) cc_final: 0.8538 (tpp) REVERT: G 81 CYS cc_start: 0.8583 (t) cc_final: 0.7406 (t) REVERT: G 83 TRP cc_start: 0.8503 (m-10) cc_final: 0.8221 (m-10) REVERT: G 88 MET cc_start: 0.9052 (tmm) cc_final: 0.8794 (tmm) REVERT: G 95 PHE cc_start: 0.9141 (t80) cc_final: 0.8785 (t80) REVERT: G 148 ILE cc_start: 0.9499 (tp) cc_final: 0.9272 (tt) REVERT: G 332 LYS cc_start: 0.8330 (mtmt) cc_final: 0.7733 (mtmm) REVERT: H 233 MET cc_start: 0.9558 (mmm) cc_final: 0.9007 (mmm) REVERT: H 319 CYS cc_start: 0.8904 (m) cc_final: 0.8610 (m) REVERT: H 429 MET cc_start: 0.8658 (ppp) cc_final: 0.8360 (ppp) REVERT: H 903 MET cc_start: 0.6337 (mmp) cc_final: 0.5507 (mmm) REVERT: H 1025 MET cc_start: 0.7911 (mmm) cc_final: 0.7573 (mmm) REVERT: H 1031 ASP cc_start: 0.8771 (m-30) cc_final: 0.7677 (t0) REVERT: H 1066 MET cc_start: 0.7774 (mtm) cc_final: 0.6987 (mmm) REVERT: H 1103 ASN cc_start: 0.7684 (m-40) cc_final: 0.7402 (m-40) REVERT: H 1142 CYS cc_start: 0.9125 (t) cc_final: 0.8737 (m) REVERT: H 1252 MET cc_start: 0.8829 (tpp) cc_final: 0.8494 (tpp) REVERT: H 1283 LEU cc_start: 0.9165 (mp) cc_final: 0.8668 (mp) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.5377 time to fit residues: 519.1291 Evaluate side-chains 408 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 5.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 0.9990 chunk 598 optimal weight: 20.0000 chunk 545 optimal weight: 6.9990 chunk 582 optimal weight: 8.9990 chunk 350 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 457 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 525 optimal weight: 1.9990 chunk 550 optimal weight: 9.9990 chunk 579 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 48 ASN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 48 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN E 48 ASN ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN G 48 ASN ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1293 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 51576 Z= 0.204 Angle : 0.639 11.617 70172 Z= 0.320 Chirality : 0.042 0.243 8516 Planarity : 0.004 0.060 8588 Dihedral : 7.804 155.567 7064 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.17 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.60 (0.11), residues: 6408 helix: 1.39 (0.08), residues: 3936 sheet: -0.54 (0.21), residues: 520 loop : -1.35 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B1452 HIS 0.005 0.001 HIS F 71 PHE 0.040 0.001 PHE E 75 TYR 0.028 0.001 TYR F 124 ARG 0.013 0.000 ARG E 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 557 time to evaluate : 6.120 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: A 73 LEU cc_start: 0.9120 (tt) cc_final: 0.8908 (pp) REVERT: A 77 MET cc_start: 0.8877 (tpt) cc_final: 0.8545 (tpp) REVERT: A 81 CYS cc_start: 0.8607 (t) cc_final: 0.7661 (t) REVERT: A 88 MET cc_start: 0.9044 (tmm) cc_final: 0.8802 (tmm) REVERT: A 164 LEU cc_start: 0.9234 (tt) cc_final: 0.8776 (tt) REVERT: A 332 LYS cc_start: 0.8448 (mtmt) cc_final: 0.7976 (mtmm) REVERT: B 233 MET cc_start: 0.9545 (mmm) cc_final: 0.8991 (mmm) REVERT: B 271 ASP cc_start: 0.9070 (t0) cc_final: 0.8798 (t0) REVERT: B 319 CYS cc_start: 0.8824 (m) cc_final: 0.8536 (m) REVERT: B 502 MET cc_start: 0.8531 (mtt) cc_final: 0.8045 (mmt) REVERT: B 710 MET cc_start: 0.5537 (mmp) cc_final: 0.4437 (tpt) REVERT: B 903 MET cc_start: 0.6412 (mmp) cc_final: 0.5552 (mmm) REVERT: B 1025 MET cc_start: 0.7858 (mmm) cc_final: 0.7548 (mmm) REVERT: B 1031 ASP cc_start: 0.8596 (m-30) cc_final: 0.7641 (t0) REVERT: B 1066 MET cc_start: 0.7809 (mtm) cc_final: 0.7058 (mmm) REVERT: B 1142 CYS cc_start: 0.9096 (t) cc_final: 0.8672 (m) REVERT: B 1248 LEU cc_start: 0.9229 (tp) cc_final: 0.8748 (tp) REVERT: B 1283 LEU cc_start: 0.9099 (mp) cc_final: 0.8670 (mp) REVERT: B 1550 MET cc_start: 0.5402 (ptm) cc_final: 0.5046 (ppp) REVERT: C 77 MET cc_start: 0.8852 (tpt) cc_final: 0.8554 (tpp) REVERT: C 81 CYS cc_start: 0.8388 (t) cc_final: 0.7375 (t) REVERT: C 88 MET cc_start: 0.9060 (tmm) cc_final: 0.8814 (tmm) REVERT: C 164 LEU cc_start: 0.9382 (tt) cc_final: 0.9041 (tt) REVERT: C 166 CYS cc_start: 0.9011 (p) cc_final: 0.8804 (p) REVERT: C 199 MET cc_start: 0.7263 (mmp) cc_final: 0.6940 (mmp) REVERT: C 256 ILE cc_start: 0.8869 (mp) cc_final: 0.8596 (tt) REVERT: C 332 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7971 (mtmm) REVERT: D 233 MET cc_start: 0.9549 (mmm) cc_final: 0.9007 (mmm) REVERT: D 271 ASP cc_start: 0.9068 (t0) cc_final: 0.8797 (t0) REVERT: D 319 CYS cc_start: 0.8826 (m) cc_final: 0.8541 (m) REVERT: D 710 MET cc_start: 0.6037 (mmp) cc_final: 0.4334 (tpt) REVERT: D 801 MET cc_start: 0.8900 (ptt) cc_final: 0.8504 (tmm) REVERT: D 1025 MET cc_start: 0.7870 (mmm) cc_final: 0.7552 (mmm) REVERT: D 1031 ASP cc_start: 0.8598 (m-30) cc_final: 0.7647 (t0) REVERT: D 1066 MET cc_start: 0.7800 (mtm) cc_final: 0.7049 (mmm) REVERT: D 1142 CYS cc_start: 0.9084 (t) cc_final: 0.8628 (m) REVERT: D 1252 MET cc_start: 0.8833 (tpp) cc_final: 0.8551 (tpp) REVERT: D 1283 LEU cc_start: 0.9102 (mp) cc_final: 0.8673 (mp) REVERT: D 1550 MET cc_start: 0.5439 (ptm) cc_final: 0.5074 (ppp) REVERT: E 73 LEU cc_start: 0.9100 (tt) cc_final: 0.8836 (pp) REVERT: E 77 MET cc_start: 0.8877 (tpt) cc_final: 0.8509 (tpp) REVERT: E 81 CYS cc_start: 0.8623 (t) cc_final: 0.7466 (t) REVERT: E 88 MET cc_start: 0.9056 (tmm) cc_final: 0.8826 (tmm) REVERT: E 164 LEU cc_start: 0.9408 (tt) cc_final: 0.9185 (tt) REVERT: E 166 CYS cc_start: 0.8902 (p) cc_final: 0.8668 (p) REVERT: E 332 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8319 (mtpp) REVERT: F 233 MET cc_start: 0.9545 (mmm) cc_final: 0.9013 (mmm) REVERT: F 271 ASP cc_start: 0.9078 (t0) cc_final: 0.8808 (t0) REVERT: F 319 CYS cc_start: 0.8883 (m) cc_final: 0.8591 (m) REVERT: F 710 MET cc_start: 0.6024 (mmp) cc_final: 0.4308 (tpt) REVERT: F 801 MET cc_start: 0.8904 (ptt) cc_final: 0.8507 (tmm) REVERT: F 1025 MET cc_start: 0.7875 (mmm) cc_final: 0.7559 (mmm) REVERT: F 1031 ASP cc_start: 0.8596 (m-30) cc_final: 0.7641 (t0) REVERT: F 1066 MET cc_start: 0.7808 (mtm) cc_final: 0.7053 (mmm) REVERT: F 1142 CYS cc_start: 0.9088 (t) cc_final: 0.8622 (m) REVERT: F 1252 MET cc_start: 0.8991 (tpp) cc_final: 0.8706 (tpp) REVERT: F 1283 LEU cc_start: 0.9154 (mp) cc_final: 0.8688 (mp) REVERT: G 73 LEU cc_start: 0.9086 (tt) cc_final: 0.8823 (pp) REVERT: G 77 MET cc_start: 0.8953 (tpt) cc_final: 0.8577 (tpp) REVERT: G 81 CYS cc_start: 0.8606 (t) cc_final: 0.7449 (t) REVERT: G 88 MET cc_start: 0.9054 (tmm) cc_final: 0.8786 (tmm) REVERT: G 332 LYS cc_start: 0.8326 (mtmt) cc_final: 0.7833 (mtmm) REVERT: H 233 MET cc_start: 0.9541 (mmm) cc_final: 0.8991 (mmm) REVERT: H 319 CYS cc_start: 0.8881 (m) cc_final: 0.8590 (m) REVERT: H 429 MET cc_start: 0.8625 (ppp) cc_final: 0.8301 (ppp) REVERT: H 710 MET cc_start: 0.6004 (mmp) cc_final: 0.4311 (tpt) REVERT: H 903 MET cc_start: 0.6297 (mmp) cc_final: 0.5494 (mmm) REVERT: H 1025 MET cc_start: 0.7866 (mmm) cc_final: 0.7556 (mmm) REVERT: H 1031 ASP cc_start: 0.8612 (m-30) cc_final: 0.7680 (t0) REVERT: H 1066 MET cc_start: 0.7809 (mtm) cc_final: 0.7057 (mmm) REVERT: H 1103 ASN cc_start: 0.7633 (m-40) cc_final: 0.7358 (m-40) REVERT: H 1142 CYS cc_start: 0.9081 (t) cc_final: 0.8663 (m) REVERT: H 1248 LEU cc_start: 0.9234 (tp) cc_final: 0.8753 (tp) REVERT: H 1283 LEU cc_start: 0.9144 (mp) cc_final: 0.8676 (mp) REVERT: H 1550 MET cc_start: 0.5406 (ptm) cc_final: 0.5036 (ppp) outliers start: 0 outliers final: 0 residues processed: 557 average time/residue: 0.5526 time to fit residues: 542.5120 Evaluate side-chains 435 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 5.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 5.9990 chunk 615 optimal weight: 5.9990 chunk 375 optimal weight: 0.0060 chunk 291 optimal weight: 2.9990 chunk 427 optimal weight: 30.0000 chunk 645 optimal weight: 7.9990 chunk 594 optimal weight: 10.0000 chunk 514 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 397 optimal weight: 20.0000 chunk 315 optimal weight: 8.9990 overall best weight: 4.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 698 ASN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN E 48 ASN E 216 HIS ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN ** F1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1518 ASN G 41 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 51576 Z= 0.246 Angle : 0.670 12.905 70172 Z= 0.336 Chirality : 0.043 0.287 8516 Planarity : 0.004 0.063 8588 Dihedral : 7.825 157.717 7064 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.46 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.51 (0.11), residues: 6408 helix: 1.30 (0.08), residues: 3944 sheet: -0.47 (0.22), residues: 520 loop : -1.38 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP E 83 HIS 0.005 0.001 HIS G 259 PHE 0.055 0.002 PHE F 433 TYR 0.035 0.002 TYR B 124 ARG 0.014 0.001 ARG A 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 5.994 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: A 81 CYS cc_start: 0.8691 (t) cc_final: 0.7721 (t) REVERT: A 83 TRP cc_start: 0.8730 (m-10) cc_final: 0.7719 (m-90) REVERT: A 88 MET cc_start: 0.9035 (tmm) cc_final: 0.8747 (tmm) REVERT: A 164 LEU cc_start: 0.9318 (tt) cc_final: 0.9117 (tt) REVERT: A 199 MET cc_start: 0.7768 (mmm) cc_final: 0.7482 (mmm) REVERT: A 332 LYS cc_start: 0.8427 (mtmt) cc_final: 0.7963 (mtmm) REVERT: B 233 MET cc_start: 0.9552 (mmm) cc_final: 0.9000 (mmm) REVERT: B 271 ASP cc_start: 0.9104 (t0) cc_final: 0.8863 (t0) REVERT: B 319 CYS cc_start: 0.8821 (m) cc_final: 0.8526 (m) REVERT: B 502 MET cc_start: 0.8489 (mtt) cc_final: 0.8046 (mmt) REVERT: B 903 MET cc_start: 0.6490 (mmp) cc_final: 0.5606 (mmm) REVERT: B 1025 MET cc_start: 0.7856 (mmm) cc_final: 0.7541 (mmm) REVERT: B 1031 ASP cc_start: 0.8762 (m-30) cc_final: 0.7671 (t0) REVERT: B 1066 MET cc_start: 0.7809 (mtm) cc_final: 0.7055 (mmm) REVERT: B 1142 CYS cc_start: 0.9167 (t) cc_final: 0.8705 (m) REVERT: B 1283 LEU cc_start: 0.9115 (mp) cc_final: 0.8646 (mp) REVERT: C 81 CYS cc_start: 0.8423 (t) cc_final: 0.7473 (t) REVERT: C 88 MET cc_start: 0.9060 (tmm) cc_final: 0.8783 (tmm) REVERT: C 164 LEU cc_start: 0.9357 (tt) cc_final: 0.9144 (tt) REVERT: C 199 MET cc_start: 0.7219 (mmp) cc_final: 0.6953 (mmp) REVERT: C 332 LYS cc_start: 0.8431 (mtmt) cc_final: 0.7966 (mtmm) REVERT: D 233 MET cc_start: 0.9556 (mmm) cc_final: 0.9028 (mmm) REVERT: D 271 ASP cc_start: 0.9102 (t0) cc_final: 0.8860 (t0) REVERT: D 319 CYS cc_start: 0.8829 (m) cc_final: 0.8533 (m) REVERT: D 502 MET cc_start: 0.8047 (mtt) cc_final: 0.7692 (mmm) REVERT: D 710 MET cc_start: 0.6155 (mmp) cc_final: 0.4296 (tpt) REVERT: D 801 MET cc_start: 0.8864 (ptt) cc_final: 0.8454 (tmm) REVERT: D 1025 MET cc_start: 0.7801 (mmm) cc_final: 0.7487 (mmm) REVERT: D 1031 ASP cc_start: 0.8773 (m-30) cc_final: 0.7727 (t0) REVERT: D 1066 MET cc_start: 0.7838 (mtm) cc_final: 0.7072 (mmm) REVERT: D 1142 CYS cc_start: 0.9120 (t) cc_final: 0.8649 (m) REVERT: D 1252 MET cc_start: 0.8814 (tpp) cc_final: 0.8607 (tpp) REVERT: D 1283 LEU cc_start: 0.9118 (mp) cc_final: 0.8657 (mp) REVERT: D 1550 MET cc_start: 0.5435 (ptm) cc_final: 0.5080 (ppp) REVERT: E 73 LEU cc_start: 0.9113 (tt) cc_final: 0.8860 (pp) REVERT: E 81 CYS cc_start: 0.8569 (t) cc_final: 0.7504 (t) REVERT: E 88 MET cc_start: 0.9046 (tmm) cc_final: 0.8778 (tmm) REVERT: E 329 ASP cc_start: 0.7761 (p0) cc_final: 0.6996 (p0) REVERT: E 332 LYS cc_start: 0.8720 (mtpt) cc_final: 0.8094 (mtmm) REVERT: F 233 MET cc_start: 0.9548 (mmm) cc_final: 0.9044 (mmm) REVERT: F 271 ASP cc_start: 0.9105 (t0) cc_final: 0.8860 (t0) REVERT: F 275 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8127 (ttp-110) REVERT: F 319 CYS cc_start: 0.8835 (m) cc_final: 0.8541 (m) REVERT: F 502 MET cc_start: 0.7612 (mmm) cc_final: 0.7162 (mmm) REVERT: F 710 MET cc_start: 0.6142 (mmp) cc_final: 0.4279 (tpt) REVERT: F 801 MET cc_start: 0.8873 (ptt) cc_final: 0.8362 (tmm) REVERT: F 1025 MET cc_start: 0.7866 (mmm) cc_final: 0.7553 (mmm) REVERT: F 1031 ASP cc_start: 0.8756 (m-30) cc_final: 0.7682 (t0) REVERT: F 1066 MET cc_start: 0.7776 (mtm) cc_final: 0.7014 (mmm) REVERT: F 1142 CYS cc_start: 0.9104 (t) cc_final: 0.8598 (m) REVERT: F 1252 MET cc_start: 0.8988 (tpp) cc_final: 0.8688 (tpp) REVERT: F 1283 LEU cc_start: 0.9141 (mp) cc_final: 0.8690 (mp) REVERT: F 1550 MET cc_start: 0.5434 (ptm) cc_final: 0.5085 (ppp) REVERT: G 73 LEU cc_start: 0.9115 (tt) cc_final: 0.8892 (pp) REVERT: G 77 MET cc_start: 0.8921 (tpt) cc_final: 0.8540 (tpp) REVERT: G 88 MET cc_start: 0.9127 (tmm) cc_final: 0.8733 (tmm) REVERT: G 90 TRP cc_start: 0.8412 (m100) cc_final: 0.8107 (m100) REVERT: G 332 LYS cc_start: 0.8397 (mtmt) cc_final: 0.7872 (mtmm) REVERT: H 233 MET cc_start: 0.9550 (mmm) cc_final: 0.9015 (mmm) REVERT: H 319 CYS cc_start: 0.8838 (m) cc_final: 0.8539 (m) REVERT: H 429 MET cc_start: 0.8628 (ppp) cc_final: 0.8301 (ppp) REVERT: H 502 MET cc_start: 0.7699 (mmm) cc_final: 0.7306 (mmm) REVERT: H 710 MET cc_start: 0.6114 (mmp) cc_final: 0.4277 (tpt) REVERT: H 903 MET cc_start: 0.6373 (mmp) cc_final: 0.5667 (mmm) REVERT: H 1025 MET cc_start: 0.7857 (mmm) cc_final: 0.7545 (mmm) REVERT: H 1031 ASP cc_start: 0.8716 (m-30) cc_final: 0.7662 (t0) REVERT: H 1066 MET cc_start: 0.7809 (mtm) cc_final: 0.7055 (mmm) REVERT: H 1103 ASN cc_start: 0.7723 (m-40) cc_final: 0.7449 (m110) REVERT: H 1142 CYS cc_start: 0.9141 (t) cc_final: 0.8725 (m) REVERT: H 1283 LEU cc_start: 0.9149 (mp) cc_final: 0.8679 (mp) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.5455 time to fit residues: 511.4984 Evaluate side-chains 418 residues out of total 5672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 5.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 5.9990 chunk 547 optimal weight: 9.9990 chunk 157 optimal weight: 5.9990 chunk 474 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 chunk 142 optimal weight: 30.0000 chunk 514 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 528 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN ** A 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 HIS ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1518 ASN C 41 ASN C 48 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 698 ASN ** D1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 ASN E 48 ASN ** E 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 ASN ** F 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN F 698 ASN ** F1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN ** G 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 216 HIS ** G 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 ASN ** H 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN H 698 ASN ** H1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.083495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.065381 restraints weight = 299541.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.064310 restraints weight = 188954.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064617 restraints weight = 149201.556| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.6705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 51576 Z= 0.261 Angle : 0.680 13.354 70172 Z= 0.342 Chirality : 0.044 0.294 8516 Planarity : 0.004 0.065 8588 Dihedral : 7.918 160.477 7064 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.11), residues: 6408 helix: 1.30 (0.08), residues: 3916 sheet: -0.48 (0.22), residues: 528 loop : -1.41 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP E 83 HIS 0.005 0.001 HIS G 259 PHE 0.039 0.002 PHE A 75 TYR 0.022 0.002 TYR B 124 ARG 0.013 0.001 ARG E 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11343.69 seconds wall clock time: 207 minutes 23.56 seconds (12443.56 seconds total)