Starting phenix.real_space_refine on Mon Mar 25 19:52:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykf_6832/03_2024/5ykf_6832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykf_6832/03_2024/5ykf_6832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykf_6832/03_2024/5ykf_6832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykf_6832/03_2024/5ykf_6832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykf_6832/03_2024/5ykf_6832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5ykf_6832/03_2024/5ykf_6832_updated.pdb" } resolution = 4.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 284 5.16 5 Cl 4 4.86 5 C 33120 2.51 5 N 8652 2.21 5 O 8904 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 534": "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 1111": "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 1498": "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 PHE 217": "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 534": "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 1111": "NH1" <-> "NH2" Residue "D ARG 1145": "NH1" <-> "NH2" Residue "D TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1183": "NH1" <-> "NH2" Residue "D ARG 1218": "NH1" <-> "NH2" Residue "D ARG 1274": "NH1" <-> "NH2" Residue "D ARG 1300": "NH1" <-> "NH2" Residue "D ARG 1353": "NH1" <-> "NH2" Residue "D ARG 1394": "NH1" <-> "NH2" Residue "D ARG 1402": "NH1" <-> "NH2" Residue "D ARG 1421": "NH1" <-> "NH2" Residue "D ARG 1487": "NH1" <-> "NH2" Residue "D ARG 1498": "NH1" <-> "NH2" Residue "D ARG 1531": "NH1" <-> "NH2" Residue "D ARG 1539": "NH1" <-> "NH2" Residue "D ARG 1554": "NH1" <-> "NH2" Residue "E 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 534": "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 1111": "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 1498": "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 534": "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 1111": "NH1" <-> "NH2" Residue "H ARG 1145": "NH1" <-> "NH2" Residue "H TYR 1159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 1183": "NH1" <-> "NH2" Residue "H ARG 1218": "NH1" <-> "NH2" Residue "H ARG 1274": "NH1" <-> "NH2" Residue "H ARG 1300": "NH1" <-> "NH2" Residue "H ARG 1353": "NH1" <-> "NH2" Residue "H ARG 1394": "NH1" <-> "NH2" Residue "H ARG 1402": "NH1" <-> "NH2" Residue "H ARG 1421": "NH1" <-> "NH2" Residue "H ARG 1487": "NH1" <-> "NH2" Residue "H ARG 1498": "NH1" <-> "NH2" Residue "H ARG 1531": "NH1" <-> "NH2" Residue "H ARG 1539": "NH1" <-> "NH2" Residue "H ARG 1554": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 50988 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2463 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "B" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "C" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2463 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "D" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "E" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2463 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "F" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "G" Number of atoms: 2463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2463 Classifications: {'peptide': 325} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 24} Link IDs: {'PTRANS': 13, 'TRANS': 311} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 61 Chain: "H" Number of atoms: 10189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10189 Classifications: {'peptide': 1309} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 45, 'TRANS': 1263} Chain breaks: 11 Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 9, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'AGS': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.98, per 1000 atoms: 0.51 Number of scatterers: 50988 At special positions: 0 Unit cell: (212.055, 212.055, 142.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 284 16.00 P 24 15.00 O 8904 8.00 N 8652 7.00 C 33120 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: 18.84 Conformation dependent library (CDL) restraints added in 9.1 seconds 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 204 helices and 32 sheets defined 58.6% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.16 Creating SS restraints... Processing helix chain 'A' and resid 54 through 57 No H-bonds generated for 'chain 'A' and resid 54 through 57' Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.632A pdb=" N LEU A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 97 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 171 removed outlier: 4.076A pdb=" N ILE A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 266 through 269 removed outlier: 4.360A pdb=" N ASP A 269 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 269' Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'B' and resid 25 through 51 Proline residue: B 35 - end of helix removed outlier: 3.941A pdb=" N PHE B 44 " --> pdb=" O LEU B 40 " (cutoff:3.500A) Proline residue: B 45 - end of helix Processing helix chain 'B' and resid 71 through 95 Processing helix chain 'B' and resid 104 through 129 Proline residue: B 109 - end of helix removed outlier: 3.757A pdb=" N MET B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 159 removed outlier: 3.854A 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: 3.942A 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: 4.081A 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: 4.093A 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: 3.537A pdb=" N TRP B 439 " --> pdb=" O CYS B 435 " (cutoff:3.500A) Proline residue: B 442 - end of helix removed outlier: 8.211A 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: 4.000A 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: 3.652A pdb=" N ILE B 462 " --> pdb=" O VAL B 458 " (cutoff:3.500A) removed outlier: 3.666A 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: 4.018A pdb=" N TYR B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 559 removed outlier: 3.655A 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: 4.074A pdb=" N ALA B 535 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.846A 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: 3.803A pdb=" N ALA B1008 " --> pdb=" O TYR B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.637A 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: 3.821A 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: 3.916A 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: 5.695A 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: 3.724A 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 1278 through 1288 removed outlier: 4.013A pdb=" N GLY B1282 " --> pdb=" O ALA B1278 " (cutoff:3.500A) 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: 4.141A pdb=" N ARG B1314 " --> pdb=" O GLY B1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE B1315 " --> pdb=" O ALA B1311 " (cutoff:3.500A) removed outlier: 3.683A 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: 4.306A 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: 4.372A pdb=" N ASP C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 97 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 171 removed outlier: 4.076A pdb=" N ILE C 154 " --> pdb=" O ILE C 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE C 167 " --> pdb=" O MET C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 180 Processing helix chain 'C' and resid 266 through 269 removed outlier: 4.360A pdb=" N ASP C 269 " --> pdb=" O PRO C 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 269' Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'D' and resid 25 through 51 Proline residue: D 35 - end of helix removed outlier: 3.941A pdb=" N PHE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Proline residue: D 45 - end of helix Processing helix chain 'D' and resid 71 through 95 Processing helix chain 'D' and resid 104 through 129 Proline residue: D 109 - end of helix removed outlier: 3.757A pdb=" N MET D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 159 removed outlier: 3.854A 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: 7.382A 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: 3.630A 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: 3.537A 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: 8.563A pdb=" N SER D 459 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 4.000A 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: 3.652A 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: 4.018A 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: 3.802A pdb=" N LYS D 528 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA D 535 " --> pdb=" O THR D 531 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.803A 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: 4.258A 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: 3.637A 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: 3.821A 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: 3.916A 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: 5.695A 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: 3.724A 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 1278 through 1288 removed outlier: 4.013A pdb=" N GLY D1282 " --> pdb=" O ALA D1278 " (cutoff:3.500A) 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: 4.369A pdb=" N ILE D1315 " --> pdb=" O ALA D1311 " (cutoff:3.500A) removed outlier: 3.683A 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: 4.096A 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: 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: 3.632A pdb=" N LEU E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 97 Processing helix chain 'E' and resid 117 through 128 Processing helix chain 'E' and resid 143 through 171 removed outlier: 4.076A pdb=" N ILE E 154 " --> pdb=" O ILE E 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE E 167 " --> pdb=" O MET E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 180 Processing helix chain 'E' and resid 266 through 269 removed outlier: 4.360A pdb=" N ASP E 269 " --> pdb=" O PRO E 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 266 through 269' Processing helix chain 'E' and resid 346 through 355 Processing helix chain 'F' and resid 25 through 51 Proline residue: F 35 - end of helix removed outlier: 3.941A pdb=" N PHE F 44 " --> pdb=" O LEU F 40 " (cutoff:3.500A) Proline residue: F 45 - end of helix Processing helix chain 'F' and resid 71 through 95 Processing helix chain 'F' and resid 104 through 129 Proline residue: F 109 - end of helix removed outlier: 3.757A pdb=" N MET F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 159 removed outlier: 3.854A 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: 3.942A 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: 4.081A 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: 3.537A 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: 8.563A pdb=" N SER F 459 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 4.000A 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: 3.652A 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: 4.018A 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: 4.074A pdb=" N ALA F 535 " --> pdb=" O THR F 531 " (cutoff:3.500A) removed outlier: 3.612A 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: 3.803A pdb=" N ALA F1008 " --> pdb=" O TYR F1004 " (cutoff:3.500A) Processing helix chain 'F' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER F1014 " --> pdb=" O ILE F1010 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.637A 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: 3.821A 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: 3.916A 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: 3.525A pdb=" N GLY F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR F1212 " --> pdb=" O VAL F1208 " (cutoff:3.500A) removed outlier: 6.124A 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 1278 through 1288 removed outlier: 4.013A pdb=" N GLY F1282 " --> pdb=" O ALA F1278 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F1283 " --> pdb=" O GLY F1279 " (cutoff:3.500A) Processing helix chain 'F' and resid 1291 through 1319 removed outlier: 4.141A pdb=" N ARG F1314 " --> pdb=" O GLY F1310 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE F1315 " --> pdb=" O ALA F1311 " (cutoff:3.500A) removed outlier: 3.683A 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: 4.306A 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: 4.372A pdb=" N ASP G 65 " --> pdb=" O THR G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 97 Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 143 through 171 removed outlier: 4.076A pdb=" N ILE G 154 " --> pdb=" O ILE G 150 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE G 167 " --> pdb=" O MET G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 180 Processing helix chain 'G' and resid 266 through 269 removed outlier: 4.360A pdb=" N ASP G 269 " --> pdb=" O PRO G 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 266 through 269' Processing helix chain 'G' and resid 346 through 355 Processing helix chain 'H' and resid 25 through 51 Proline residue: H 35 - end of helix removed outlier: 3.941A pdb=" N PHE H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Proline residue: H 45 - end of helix Processing helix chain 'H' and resid 71 through 95 Processing helix chain 'H' and resid 104 through 129 Proline residue: H 109 - end of helix removed outlier: 3.757A pdb=" N MET H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 159 removed outlier: 3.854A 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: 3.942A 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: 6.309A pdb=" N ARG H 297 " --> pdb=" O HIS H 293 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG H 298 " --> pdb=" O ALA H 294 " (cutoff:3.500A) removed outlier: 4.081A 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: 3.537A pdb=" N TRP H 439 " --> pdb=" O CYS H 435 " (cutoff:3.500A) Proline residue: H 442 - end of helix removed outlier: 8.211A pdb=" N VAL H 458 " --> pdb=" O TYR H 454 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N SER H 459 " --> pdb=" O ILE H 455 " (cutoff:3.500A) removed outlier: 4.000A 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: 3.652A 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: 3.929A 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: 3.655A 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: 4.074A pdb=" N ALA H 535 " --> pdb=" O THR H 531 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR H 548 " --> pdb=" O ILE H 544 " (cutoff:3.500A) Proline residue: H 551 - end of helix removed outlier: 3.554A 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: 3.803A pdb=" N ALA H1008 " --> pdb=" O TYR H1004 " (cutoff:3.500A) Processing helix chain 'H' and resid 1010 through 1038 removed outlier: 4.195A pdb=" N SER H1014 " --> pdb=" O ILE H1010 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.637A 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: 3.821A 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: 5.695A 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: 3.724A pdb=" N ALA H1237 " --> pdb=" O SER H1233 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR H1242 " --> pdb=" O SER H1238 " (cutoff:3.500A) removed outlier: 3.722A 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 1278 through 1288 removed outlier: 4.013A pdb=" N GLY H1282 " --> pdb=" O ALA H1278 " (cutoff:3.500A) 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: 4.141A pdb=" N ARG H1314 " --> pdb=" O GLY H1310 " (cutoff:3.500A) removed outlier: 4.369A 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: 4.306A 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: 3.640A pdb=" N LEU A 200 " --> pdb=" O ILE A 257 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 214 through 220 removed outlier: 3.662A pdb=" N GLU A 282 " --> pdb=" O VAL A 220 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 313 through 315 Processing sheet with id= D, first strand: chain 'B' and resid 701 through 703 Processing sheet with id= E, first strand: chain 'B' and resid 911 through 913 removed outlier: 3.670A 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: 8.226A pdb=" N ASP B 854 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 7.493A 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: 3.703A pdb=" N GLN B1348 " --> pdb=" O ARG B1402 " (cutoff:3.500A) removed outlier: 3.995A 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: 6.593A pdb=" N SER B1423 " --> pdb=" O ILE B1504 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP B1506 " --> pdb=" O SER B1423 " (cutoff:3.500A) removed outlier: 6.306A 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: 3.781A pdb=" N HIS C 259 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU C 200 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing sheet with id= 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: 8.226A 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: 3.703A pdb=" N GLN D1348 " --> pdb=" O ARG D1402 " (cutoff:3.500A) removed outlier: 3.995A 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: 3.774A 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: 8.255A pdb=" N ILE D1536 " --> pdb=" O PHE D1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET D1505 " --> pdb=" O ILE D1536 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER D1423 " --> pdb=" O ILE D1504 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP D1506 " --> pdb=" O SER D1423 " (cutoff:3.500A) removed outlier: 6.306A 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: 3.640A 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: 3.670A 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: 8.226A 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: 3.703A pdb=" N GLN F1348 " --> pdb=" O ARG F1402 " (cutoff:3.500A) removed outlier: 3.995A 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: 6.551A 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: 6.593A pdb=" N SER F1423 " --> pdb=" O ILE F1504 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP F1506 " --> pdb=" O SER F1423 " (cutoff:3.500A) removed outlier: 6.306A 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: 3.640A 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: 3.602A pdb=" N GLN H1346 " --> pdb=" O ILE H1404 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN H1348 " --> pdb=" O ARG H1402 " (cutoff:3.500A) removed outlier: 3.995A 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: 8.255A pdb=" N ILE H1536 " --> pdb=" O PHE H1503 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N MET H1505 " --> pdb=" O ILE H1536 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N SER H1423 " --> pdb=" O ILE H1504 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ASP H1506 " --> pdb=" O SER H1423 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE H1425 " --> pdb=" O ASP H1506 " (cutoff:3.500A) 2884 hydrogen bonds defined for protein. 8412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.54 Time building geometry restraints manager: 20.36 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: 20304 1.39 - 1.58: 31264 1.58 - 1.76: 40 1.76 - 1.94: 436 1.94 - 2.12: 8 Bond restraints: 52052 Sorted by residual: bond pdb=" PG AGS A 402 " pdb=" S1G AGS A 402 " 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 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 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=" 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=" C4 AGS F2002 " pdb=" C5 AGS F2002 " ideal model delta sigma weight residual 1.386 1.470 -0.084 1.00e-02 1.00e+04 7.10e+01 ... (remaining 52047 not shown) Histogram of bond angle deviations from ideal: 98.80 - 106.22: 1232 106.22 - 113.63: 30696 113.63 - 121.05: 25824 121.05 - 128.46: 12572 128.46 - 135.88: 456 Bond angle restraints: 70780 Sorted by residual: angle pdb=" C5 AGS H2002 " pdb=" C4 AGS H2002 " pdb=" N3 AGS H2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS B2002 " pdb=" C4 AGS B2002 " pdb=" N3 AGS B2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS F2002 " pdb=" C4 AGS F2002 " pdb=" N3 AGS F2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS D2002 " pdb=" C4 AGS D2002 " pdb=" N3 AGS D2002 " ideal model delta sigma weight residual 126.80 118.57 8.23 7.41e-01 1.82e+00 1.23e+02 angle pdb=" C5 AGS C 401 " pdb=" C4 AGS C 401 " pdb=" N3 AGS C 401 " ideal model delta sigma weight residual 126.80 119.14 7.66 7.41e-01 1.82e+00 1.07e+02 ... (remaining 70775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.23: 29948 31.23 - 62.46: 944 62.46 - 93.69: 28 93.69 - 124.92: 8 124.92 - 156.15: 4 Dihedral angle restraints: 30932 sinusoidal: 11952 harmonic: 18980 Sorted by residual: 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 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ASP F 212 " pdb=" C ASP F 212 " pdb=" N LEU F 213 " pdb=" CA LEU F 213 " ideal model delta harmonic sigma weight residual 180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+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 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 30929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 8448 0.157 - 0.313: 76 0.313 - 0.470: 12 0.470 - 0.627: 0 0.627 - 0.783: 4 Chirality restraints: 8540 Sorted by residual: chirality pdb=" PB AGS A 402 " pdb=" O2B AGS A 402 " pdb=" O3A AGS A 402 " pdb=" O3B AGS A 402 " both_signs ideal model delta sigma weight residual True 3.18 -2.40 0.78 2.00e-01 2.50e+01 1.53e+01 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 -2.40 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" PB AGS E 401 " pdb=" O2B AGS E 401 " pdb=" O3A AGS E 401 " pdb=" O3B AGS E 401 " both_signs ideal model delta sigma weight residual True 3.18 -2.40 0.78 2.00e-01 2.50e+01 1.53e+01 ... (remaining 8537 not shown) Planarity restraints: 8660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C25 GBM B2001 " -0.321 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM B2001 " 0.077 2.00e-02 2.50e+03 pdb=" C27 GBM B2001 " -0.172 2.00e-02 2.50e+03 pdb=" N10 GBM B2001 " 0.479 2.00e-02 2.50e+03 pdb=" O6 GBM B2001 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM D2001 " 0.321 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM D2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM D2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM D2001 " -0.479 2.00e-02 2.50e+03 pdb=" O6 GBM D2001 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 GBM F2001 " 0.321 2.00e-02 2.50e+03 2.73e-01 9.30e+02 pdb=" C26 GBM F2001 " -0.077 2.00e-02 2.50e+03 pdb=" C27 GBM F2001 " 0.172 2.00e-02 2.50e+03 pdb=" N10 GBM F2001 " -0.479 2.00e-02 2.50e+03 pdb=" O6 GBM F2001 " 0.062 2.00e-02 2.50e+03 ... (remaining 8657 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 456 2.60 - 3.18: 45916 3.18 - 3.75: 80308 3.75 - 4.33: 103406 4.33 - 4.90: 169080 Nonbonded interactions: 399166 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 H 196 " pdb=" O PHE H 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE F 196 " pdb=" O PHE F 197 " model vdw 2.030 3.040 nonbonded pdb=" O ILE D 196 " pdb=" O PHE D 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 399161 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' and resid 32 through 356) selection = (chain 'C' and resid 32 through 356) selection = (chain 'E' and resid 32 through 356) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 9.780 Check model and map are aligned: 0.800 Set scattering table: 0.510 Process input model: 129.270 Find NCS groups from input model: 3.320 Set up NCS constraints: 0.350 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.173 52052 Z= 0.364 Angle : 0.812 11.984 70780 Z= 0.501 Chirality : 0.051 0.783 8540 Planarity : 0.008 0.273 8660 Dihedral : 14.032 156.155 18576 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.42 % Favored : 95.15 % Rotamer: Outliers : 8.16 % Allowed : 9.19 % Favored : 82.65 % 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: -2.48 (0.09), residues: 6432 helix: -1.04 (0.07), residues: 3948 sheet: -1.58 (0.20), residues: 536 loop : -2.69 (0.12), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D1339 HIS 0.011 0.001 HIS G 175 PHE 0.034 0.002 PHE A 168 TYR 0.014 0.002 TYR D 378 ARG 0.003 0.000 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 444 poor density : 980 time to evaluate : 6.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 81 CYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8782 (t) REVERT: A 152 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8831 (tp-100) REVERT: A 179 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 214 THR cc_start: 0.8880 (t) cc_final: 0.7547 (m) REVERT: A 217 MET cc_start: 0.8485 (ttp) cc_final: 0.8276 (ttp) REVERT: A 273 SER cc_start: 0.9419 (m) cc_final: 0.8973 (p) REVERT: B 112 MET cc_start: 0.9085 (mmm) cc_final: 0.8879 (mmp) REVERT: B 134 LYS cc_start: 0.8821 (mptt) cc_final: 0.7755 (mttt) REVERT: B 248 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8472 (tpt90) REVERT: B 432 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8748 (t80) REVERT: B 456 LEU cc_start: 0.9067 (mp) cc_final: 0.8230 (tt) REVERT: B 583 PHE cc_start: 0.9250 (m-10) cc_final: 0.8983 (m-80) REVERT: B 829 ASN cc_start: 0.4090 (OUTLIER) cc_final: 0.3728 (p0) REVERT: B 892 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6741 (pt0) REVERT: B 1148 LEU cc_start: 0.9342 (mt) cc_final: 0.8837 (tp) REVERT: B 1168 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8022 (tp) REVERT: B 1261 LEU cc_start: 0.9582 (tp) cc_final: 0.9107 (tp) REVERT: B 1289 LEU cc_start: 0.9371 (tp) cc_final: 0.9081 (tt) REVERT: B 1305 MET cc_start: 0.9105 (tpt) cc_final: 0.8586 (tpt) REVERT: B 1432 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4018 (p90) REVERT: B 1448 ASP cc_start: 0.8020 (m-30) cc_final: 0.7802 (t70) REVERT: B 1488 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7553 (tp-100) REVERT: C 81 CYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8782 (t) REVERT: C 152 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8829 (tp-100) REVERT: C 179 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8201 (mt-10) REVERT: C 214 THR cc_start: 0.8883 (t) cc_final: 0.7548 (m) REVERT: C 217 MET cc_start: 0.8484 (ttp) cc_final: 0.8276 (ttp) REVERT: C 273 SER cc_start: 0.9421 (m) cc_final: 0.8976 (p) REVERT: D 112 MET cc_start: 0.9086 (mmm) cc_final: 0.8881 (mmp) REVERT: D 134 LYS cc_start: 0.8819 (mptt) cc_final: 0.7752 (mttt) REVERT: D 248 ARG cc_start: 0.8821 (mtp-110) cc_final: 0.8470 (tpt90) REVERT: D 432 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8747 (t80) REVERT: D 456 LEU cc_start: 0.9068 (mp) cc_final: 0.8226 (tt) REVERT: D 583 PHE cc_start: 0.9246 (m-10) cc_final: 0.8981 (m-80) REVERT: D 829 ASN cc_start: 0.4090 (OUTLIER) cc_final: 0.3731 (p0) REVERT: D 892 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6743 (pt0) REVERT: D 1148 LEU cc_start: 0.9344 (mt) cc_final: 0.8842 (tp) REVERT: D 1168 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8020 (tp) REVERT: D 1261 LEU cc_start: 0.9582 (tp) cc_final: 0.9106 (tp) REVERT: D 1289 LEU cc_start: 0.9372 (tp) cc_final: 0.9082 (tt) REVERT: D 1305 MET cc_start: 0.9105 (tpt) cc_final: 0.8581 (tpt) REVERT: D 1432 PHE cc_start: 0.5636 (OUTLIER) cc_final: 0.4022 (p90) REVERT: D 1448 ASP cc_start: 0.8016 (m-30) cc_final: 0.7800 (t70) REVERT: D 1488 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7554 (tp-100) REVERT: E 81 CYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8782 (t) REVERT: E 152 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8827 (tp-100) REVERT: E 179 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8200 (mt-10) REVERT: E 214 THR cc_start: 0.8882 (t) cc_final: 0.7546 (m) REVERT: E 217 MET cc_start: 0.8483 (ttp) cc_final: 0.8275 (ttp) REVERT: E 273 SER cc_start: 0.9420 (m) cc_final: 0.8975 (p) REVERT: F 112 MET cc_start: 0.9086 (mmm) cc_final: 0.8880 (mmp) REVERT: F 134 LYS cc_start: 0.8816 (mptt) cc_final: 0.7752 (mttt) REVERT: F 248 ARG cc_start: 0.8821 (mtp-110) cc_final: 0.8470 (tpt90) REVERT: F 432 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8745 (t80) REVERT: F 456 LEU cc_start: 0.9072 (mp) cc_final: 0.8234 (tt) REVERT: F 583 PHE cc_start: 0.9246 (m-10) cc_final: 0.8978 (m-80) REVERT: F 829 ASN cc_start: 0.4091 (OUTLIER) cc_final: 0.3732 (p0) REVERT: F 892 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6752 (pt0) REVERT: F 1148 LEU cc_start: 0.9345 (mt) cc_final: 0.8842 (tp) REVERT: F 1168 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8024 (tp) REVERT: F 1261 LEU cc_start: 0.9582 (tp) cc_final: 0.9108 (tp) REVERT: F 1289 LEU cc_start: 0.9373 (tp) cc_final: 0.9085 (tt) REVERT: F 1305 MET cc_start: 0.9103 (tpt) cc_final: 0.8582 (tpt) REVERT: F 1432 PHE cc_start: 0.5637 (OUTLIER) cc_final: 0.4023 (p90) REVERT: F 1448 ASP cc_start: 0.8012 (m-30) cc_final: 0.7797 (t70) REVERT: F 1488 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7556 (tp-100) REVERT: G 81 CYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8780 (t) REVERT: G 152 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8831 (tp-100) REVERT: G 179 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8203 (mt-10) REVERT: G 214 THR cc_start: 0.8881 (t) cc_final: 0.7545 (m) REVERT: G 217 MET cc_start: 0.8483 (ttp) cc_final: 0.8274 (ttp) REVERT: G 273 SER cc_start: 0.9418 (m) cc_final: 0.8972 (p) REVERT: H 112 MET cc_start: 0.9085 (mmm) cc_final: 0.8878 (mmp) REVERT: H 134 LYS cc_start: 0.8821 (mptt) cc_final: 0.7755 (mttt) REVERT: H 248 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8470 (tpt90) REVERT: H 432 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8745 (t80) REVERT: H 456 LEU cc_start: 0.9069 (mp) cc_final: 0.8231 (tt) REVERT: H 583 PHE cc_start: 0.9248 (m-10) cc_final: 0.8983 (m-80) REVERT: H 829 ASN cc_start: 0.4091 (OUTLIER) cc_final: 0.3733 (p0) REVERT: H 892 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6747 (pt0) REVERT: H 1148 LEU cc_start: 0.9344 (mt) cc_final: 0.8839 (tp) REVERT: H 1168 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8022 (tp) REVERT: H 1261 LEU cc_start: 0.9582 (tp) cc_final: 0.9107 (tp) REVERT: H 1289 LEU cc_start: 0.9372 (tp) cc_final: 0.9085 (tt) REVERT: H 1305 MET cc_start: 0.9104 (tpt) cc_final: 0.8583 (tpt) REVERT: H 1432 PHE cc_start: 0.5640 (OUTLIER) cc_final: 0.4025 (p90) REVERT: H 1448 ASP cc_start: 0.8016 (m-30) cc_final: 0.7799 (t70) REVERT: H 1488 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7555 (tp-100) outliers start: 444 outliers final: 108 residues processed: 1364 average time/residue: 0.5910 time to fit residues: 1355.6534 Evaluate side-chains 640 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 500 time to evaluate : 5.886 ------------------------------------------------------------------------------- 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: 8.9990 chunk 491 optimal weight: 0.8980 chunk 272 optimal weight: 8.9990 chunk 167 optimal weight: 1.9990 chunk 331 optimal weight: 0.0970 chunk 262 optimal weight: 0.1980 chunk 507 optimal weight: 2.9990 chunk 196 optimal weight: 0.1980 chunk 308 optimal weight: 0.7980 chunk 378 optimal weight: 8.9990 chunk 588 optimal weight: 8.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 70 HIS ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 GLN A 259 HIS A 348 GLN B 326 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN B 485 GLN ** B 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS C 48 ASN C 70 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 259 HIS C 348 GLN D 326 HIS ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN D 485 GLN ** D 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 909 GLN ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 HIS E 48 ASN E 70 HIS ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN E 259 HIS E 348 GLN F 326 HIS ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 ASN F 485 GLN ** F 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 46 HIS G 48 ASN G 70 HIS ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN G 259 HIS G 348 GLN H 326 HIS ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 ASN H 485 GLN ** H 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 52052 Z= 0.212 Angle : 0.695 9.769 70780 Z= 0.351 Chirality : 0.044 0.186 8540 Planarity : 0.005 0.048 8660 Dihedral : 9.327 163.791 7180 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.86 % Favored : 96.08 % Rotamer: Outliers : 0.24 % Allowed : 3.38 % Favored : 96.38 % 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: -0.99 (0.10), residues: 6432 helix: 0.22 (0.08), residues: 3972 sheet: -1.18 (0.21), residues: 520 loop : -2.23 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 439 HIS 0.006 0.001 HIS A 216 PHE 0.029 0.002 PHE H 44 TYR 0.039 0.002 TYR B1254 ARG 0.009 0.001 ARG F1498 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 760 time to evaluate : 5.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 TRP cc_start: 0.9077 (m-10) cc_final: 0.8694 (m-90) REVERT: A 137 MET cc_start: 0.8311 (tpt) cc_final: 0.7955 (tpp) REVERT: A 179 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 273 SER cc_start: 0.9294 (m) cc_final: 0.8944 (p) REVERT: B 104 LEU cc_start: 0.8571 (mp) cc_final: 0.8291 (mm) REVERT: B 112 MET cc_start: 0.9187 (mmm) cc_final: 0.8935 (mmp) REVERT: B 134 LYS cc_start: 0.8487 (mptt) cc_final: 0.7657 (mttt) REVERT: B 157 PHE cc_start: 0.9239 (m-80) cc_final: 0.8676 (m-10) REVERT: B 181 MET cc_start: 0.9061 (mmm) cc_final: 0.8752 (mmm) REVERT: B 184 LEU cc_start: 0.9354 (mt) cc_final: 0.9108 (mt) REVERT: B 257 MET cc_start: 0.9085 (pmm) cc_final: 0.8775 (pmm) REVERT: B 423 ILE cc_start: 0.9008 (pt) cc_final: 0.8558 (mm) REVERT: B 456 LEU cc_start: 0.9086 (mp) cc_final: 0.8604 (tp) REVERT: B 506 MET cc_start: 0.7400 (mtm) cc_final: 0.7148 (mtm) REVERT: B 583 PHE cc_start: 0.9155 (m-10) cc_final: 0.8953 (m-80) REVERT: B 584 HIS cc_start: 0.8577 (m90) cc_final: 0.8221 (m170) REVERT: B 1110 MET cc_start: 0.7329 (tpp) cc_final: 0.6890 (tpp) REVERT: B 1148 LEU cc_start: 0.9327 (mt) cc_final: 0.8858 (tp) REVERT: B 1305 MET cc_start: 0.9056 (tpt) cc_final: 0.8519 (tpt) REVERT: C 48 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7931 (t0) REVERT: C 83 TRP cc_start: 0.9082 (m-10) cc_final: 0.8702 (m-90) REVERT: C 137 MET cc_start: 0.8308 (tpt) cc_final: 0.7955 (tpp) REVERT: C 179 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8276 (mt-10) REVERT: C 273 SER cc_start: 0.9294 (m) cc_final: 0.8943 (p) REVERT: D 104 LEU cc_start: 0.8574 (mp) cc_final: 0.8294 (mm) REVERT: D 112 MET cc_start: 0.9187 (mmm) cc_final: 0.8935 (mmp) REVERT: D 134 LYS cc_start: 0.8484 (mptt) cc_final: 0.7655 (mttt) REVERT: D 157 PHE cc_start: 0.9241 (m-80) cc_final: 0.8678 (m-10) REVERT: D 181 MET cc_start: 0.9060 (mmm) cc_final: 0.8751 (mmm) REVERT: D 184 LEU cc_start: 0.9354 (mt) cc_final: 0.9106 (mt) REVERT: D 257 MET cc_start: 0.9088 (pmm) cc_final: 0.8777 (pmm) REVERT: D 423 ILE cc_start: 0.9004 (pt) cc_final: 0.8558 (mm) REVERT: D 456 LEU cc_start: 0.9086 (mp) cc_final: 0.8601 (tp) REVERT: D 506 MET cc_start: 0.7399 (mtm) cc_final: 0.7147 (mtm) REVERT: D 583 PHE cc_start: 0.9154 (m-10) cc_final: 0.8953 (m-80) REVERT: D 584 HIS cc_start: 0.8574 (m90) cc_final: 0.8219 (m170) REVERT: D 1110 MET cc_start: 0.7323 (tpp) cc_final: 0.6890 (tpp) REVERT: D 1148 LEU cc_start: 0.9329 (mt) cc_final: 0.8861 (tp) REVERT: D 1305 MET cc_start: 0.9051 (tpt) cc_final: 0.8512 (tpt) REVERT: E 83 TRP cc_start: 0.9081 (m-10) cc_final: 0.8698 (m-90) REVERT: E 137 MET cc_start: 0.8309 (tpt) cc_final: 0.7957 (tpp) REVERT: E 179 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8278 (mt-10) REVERT: E 273 SER cc_start: 0.9295 (m) cc_final: 0.8945 (p) REVERT: F 104 LEU cc_start: 0.8573 (mp) cc_final: 0.8294 (mm) REVERT: F 112 MET cc_start: 0.9188 (mmm) cc_final: 0.8935 (mmp) REVERT: F 134 LYS cc_start: 0.8484 (mptt) cc_final: 0.7654 (mttt) REVERT: F 157 PHE cc_start: 0.9241 (m-80) cc_final: 0.8679 (m-10) REVERT: F 181 MET cc_start: 0.9058 (mmm) cc_final: 0.8749 (mmm) REVERT: F 184 LEU cc_start: 0.9353 (mt) cc_final: 0.9106 (mt) REVERT: F 257 MET cc_start: 0.9086 (pmm) cc_final: 0.8775 (pmm) REVERT: F 423 ILE cc_start: 0.9006 (pt) cc_final: 0.8559 (mm) REVERT: F 456 LEU cc_start: 0.9087 (mp) cc_final: 0.8607 (tp) REVERT: F 506 MET cc_start: 0.7399 (mtm) cc_final: 0.7144 (mtm) REVERT: F 584 HIS cc_start: 0.8578 (m90) cc_final: 0.8221 (m170) REVERT: F 1110 MET cc_start: 0.7326 (tpp) cc_final: 0.6888 (tpp) REVERT: F 1148 LEU cc_start: 0.9330 (mt) cc_final: 0.8862 (tp) REVERT: F 1305 MET cc_start: 0.9048 (tpt) cc_final: 0.8510 (tpt) REVERT: G 83 TRP cc_start: 0.9080 (m-10) cc_final: 0.8697 (m-90) REVERT: G 137 MET cc_start: 0.8305 (tpt) cc_final: 0.7952 (tpp) REVERT: G 179 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8277 (mt-10) REVERT: G 273 SER cc_start: 0.9292 (m) cc_final: 0.8940 (p) REVERT: H 104 LEU cc_start: 0.8572 (mp) cc_final: 0.8294 (mm) REVERT: H 112 MET cc_start: 0.9188 (mmm) cc_final: 0.8937 (mmp) REVERT: H 134 LYS cc_start: 0.8485 (mptt) cc_final: 0.7655 (mttt) REVERT: H 157 PHE cc_start: 0.9241 (m-80) cc_final: 0.8677 (m-10) REVERT: H 181 MET cc_start: 0.9061 (mmm) cc_final: 0.8753 (mmm) REVERT: H 184 LEU cc_start: 0.9354 (mt) cc_final: 0.9107 (mt) REVERT: H 257 MET cc_start: 0.9084 (pmm) cc_final: 0.8768 (pmm) REVERT: H 423 ILE cc_start: 0.9008 (pt) cc_final: 0.8557 (mm) REVERT: H 456 LEU cc_start: 0.9087 (mp) cc_final: 0.8608 (tp) REVERT: H 506 MET cc_start: 0.7407 (mtm) cc_final: 0.7152 (mtm) REVERT: H 584 HIS cc_start: 0.8576 (m90) cc_final: 0.8223 (m170) REVERT: H 1110 MET cc_start: 0.7328 (tpp) cc_final: 0.6887 (tpp) REVERT: H 1148 LEU cc_start: 0.9328 (mt) cc_final: 0.8857 (tp) REVERT: H 1305 MET cc_start: 0.9053 (tpt) cc_final: 0.8516 (tpt) outliers start: 13 outliers final: 0 residues processed: 773 average time/residue: 0.5697 time to fit residues: 759.8792 Evaluate side-chains 453 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 452 time to evaluate : 5.763 ------------------------------------------------------------------------------- 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: 10.0000 chunk 489 optimal weight: 1.9990 chunk 400 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 589 optimal weight: 8.9990 chunk 636 optimal weight: 40.0000 chunk 525 optimal weight: 6.9990 chunk 584 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 472 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS ** B 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 500 ASN B 822 GLN ** B 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 HIS ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 ASN D 822 GLN ** D 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1135 HIS ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 326 HIS ** F 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 ASN F 822 GLN ** F 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 HIS ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 326 HIS ** H 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 500 ASN H 822 GLN ** H 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1135 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 52052 Z= 0.403 Angle : 0.770 8.993 70780 Z= 0.400 Chirality : 0.045 0.191 8540 Planarity : 0.005 0.045 8660 Dihedral : 9.351 152.889 7180 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 17.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.79 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % 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: -0.54 (0.10), residues: 6432 helix: 0.48 (0.08), residues: 3972 sheet: -0.67 (0.21), residues: 504 loop : -1.93 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1088 HIS 0.013 0.002 HIS A 259 PHE 0.029 0.002 PHE C 168 TYR 0.019 0.002 TYR H 512 ARG 0.007 0.001 ARG F 798 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 502 time to evaluate : 5.705 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 75 PHE cc_start: 0.8219 (m-80) cc_final: 0.8019 (m-80) REVERT: A 123 PHE cc_start: 0.9355 (t80) cc_final: 0.8251 (t80) REVERT: A 179 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8587 (mt-10) REVERT: A 273 SER cc_start: 0.9334 (m) cc_final: 0.8999 (p) REVERT: B 112 MET cc_start: 0.9249 (mmm) cc_final: 0.9020 (mmp) REVERT: B 134 LYS cc_start: 0.8786 (mptt) cc_final: 0.8576 (mmtt) REVERT: B 157 PHE cc_start: 0.9333 (m-80) cc_final: 0.8765 (m-10) REVERT: B 181 MET cc_start: 0.9227 (mmm) cc_final: 0.8953 (mmm) REVERT: B 257 MET cc_start: 0.9148 (pmm) cc_final: 0.8822 (pmm) REVERT: B 429 MET cc_start: 0.8646 (tmm) cc_final: 0.8433 (tmm) REVERT: B 456 LEU cc_start: 0.9290 (mp) cc_final: 0.8557 (tp) REVERT: B 583 PHE cc_start: 0.9214 (m-10) cc_final: 0.8994 (m-80) REVERT: B 1025 MET cc_start: 0.8883 (mmm) cc_final: 0.8588 (mmm) REVERT: B 1252 MET cc_start: 0.9338 (ppp) cc_final: 0.9017 (ppp) REVERT: B 1298 MET cc_start: 0.8947 (ttt) cc_final: 0.8564 (ttt) REVERT: B 1305 MET cc_start: 0.9082 (tpt) cc_final: 0.8528 (tpt) REVERT: C 75 PHE cc_start: 0.8223 (m-80) cc_final: 0.8020 (m-80) REVERT: C 123 PHE cc_start: 0.9356 (t80) cc_final: 0.8253 (t80) REVERT: C 179 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8589 (mt-10) REVERT: C 273 SER cc_start: 0.9338 (m) cc_final: 0.9003 (p) REVERT: D 112 MET cc_start: 0.9250 (mmm) cc_final: 0.9022 (mmp) REVERT: D 134 LYS cc_start: 0.8785 (mptt) cc_final: 0.8576 (mmtt) REVERT: D 157 PHE cc_start: 0.9332 (m-80) cc_final: 0.8765 (m-10) REVERT: D 181 MET cc_start: 0.9225 (mmm) cc_final: 0.8948 (mmm) REVERT: D 257 MET cc_start: 0.9155 (pmm) cc_final: 0.8833 (pmm) REVERT: D 429 MET cc_start: 0.8643 (tmm) cc_final: 0.8432 (tmm) REVERT: D 456 LEU cc_start: 0.9290 (mp) cc_final: 0.8557 (tp) REVERT: D 583 PHE cc_start: 0.9213 (m-10) cc_final: 0.8994 (m-80) REVERT: D 1025 MET cc_start: 0.8885 (mmm) cc_final: 0.8590 (mmm) REVERT: D 1252 MET cc_start: 0.9343 (ppp) cc_final: 0.9025 (ppp) REVERT: D 1298 MET cc_start: 0.8949 (ttt) cc_final: 0.8563 (ttt) REVERT: D 1305 MET cc_start: 0.9080 (tpt) cc_final: 0.8525 (tpt) REVERT: E 123 PHE cc_start: 0.9357 (t80) cc_final: 0.8257 (t80) REVERT: E 179 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8590 (mt-10) REVERT: E 273 SER cc_start: 0.9335 (m) cc_final: 0.9000 (p) REVERT: F 112 MET cc_start: 0.9248 (mmm) cc_final: 0.9019 (mmp) REVERT: F 134 LYS cc_start: 0.8785 (mptt) cc_final: 0.8575 (mmtt) REVERT: F 157 PHE cc_start: 0.9333 (m-80) cc_final: 0.8766 (m-10) REVERT: F 181 MET cc_start: 0.9226 (mmm) cc_final: 0.8951 (mmm) REVERT: F 257 MET cc_start: 0.9148 (pmm) cc_final: 0.8823 (pmm) REVERT: F 429 MET cc_start: 0.8647 (tmm) cc_final: 0.8433 (tmm) REVERT: F 456 LEU cc_start: 0.9288 (mp) cc_final: 0.8571 (tp) REVERT: F 1025 MET cc_start: 0.8886 (mmm) cc_final: 0.8591 (mmm) REVERT: F 1252 MET cc_start: 0.9342 (ppp) cc_final: 0.9021 (ppp) REVERT: F 1298 MET cc_start: 0.8951 (ttt) cc_final: 0.8565 (ttt) REVERT: F 1305 MET cc_start: 0.9080 (tpt) cc_final: 0.8524 (tpt) REVERT: G 123 PHE cc_start: 0.9354 (t80) cc_final: 0.8252 (t80) REVERT: G 179 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8584 (mt-10) REVERT: G 273 SER cc_start: 0.9334 (m) cc_final: 0.8999 (p) REVERT: H 112 MET cc_start: 0.9249 (mmm) cc_final: 0.9022 (mmp) REVERT: H 134 LYS cc_start: 0.8787 (mptt) cc_final: 0.8576 (mmtt) REVERT: H 157 PHE cc_start: 0.9334 (m-80) cc_final: 0.8767 (m-10) REVERT: H 181 MET cc_start: 0.9226 (mmm) cc_final: 0.8952 (mmm) REVERT: H 257 MET cc_start: 0.9146 (pmm) cc_final: 0.8815 (pmm) REVERT: H 429 MET cc_start: 0.8649 (tmm) cc_final: 0.8432 (tmm) REVERT: H 456 LEU cc_start: 0.9288 (mp) cc_final: 0.8572 (tp) REVERT: H 1025 MET cc_start: 0.8882 (mmm) cc_final: 0.8586 (mmm) REVERT: H 1252 MET cc_start: 0.9343 (ppp) cc_final: 0.9022 (ppp) REVERT: H 1298 MET cc_start: 0.8949 (ttt) cc_final: 0.8565 (ttt) REVERT: H 1305 MET cc_start: 0.9080 (tpt) cc_final: 0.8525 (tpt) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.5666 time to fit residues: 496.7606 Evaluate side-chains 350 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 5.593 ------------------------------------------------------------------------------- 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: 0.9990 chunk 443 optimal weight: 3.9990 chunk 305 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 281 optimal weight: 5.9990 chunk 395 optimal weight: 5.9990 chunk 591 optimal weight: 9.9990 chunk 626 optimal weight: 10.0000 chunk 309 optimal weight: 40.0000 chunk 560 optimal weight: 20.0000 chunk 168 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN A 299 GLN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN C 299 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 GLN ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN E 299 GLN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 GLN ** F 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN G 299 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 GLN ** H 846 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 52052 Z= 0.245 Angle : 0.646 8.845 70780 Z= 0.335 Chirality : 0.042 0.204 8540 Planarity : 0.004 0.088 8660 Dihedral : 8.999 148.410 7180 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.98 % Favored : 95.96 % Rotamer: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.88 % 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: -0.09 (0.10), residues: 6432 helix: 0.86 (0.08), residues: 3984 sheet: -0.66 (0.21), residues: 508 loop : -1.77 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 83 HIS 0.007 0.001 HIS G 259 PHE 0.033 0.002 PHE E 75 TYR 0.014 0.001 TYR C 304 ARG 0.005 0.000 ARG D1222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 509 time to evaluate : 5.988 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: A 137 MET cc_start: 0.8097 (tpp) cc_final: 0.7695 (tpp) REVERT: A 179 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8533 (mt-10) REVERT: A 273 SER cc_start: 0.9328 (m) cc_final: 0.8999 (p) REVERT: A 288 GLU cc_start: 0.8024 (pm20) cc_final: 0.7658 (pm20) REVERT: A 292 GLU cc_start: 0.8634 (pm20) cc_final: 0.7988 (pm20) REVERT: B 157 PHE cc_start: 0.9302 (m-80) cc_final: 0.8706 (m-10) REVERT: B 184 LEU cc_start: 0.9387 (mt) cc_final: 0.9083 (tp) REVERT: B 257 MET cc_start: 0.9114 (pmm) cc_final: 0.8843 (pmm) REVERT: B 429 MET cc_start: 0.8810 (tmm) cc_final: 0.8550 (tmm) REVERT: B 441 MET cc_start: 0.8754 (mmm) cc_final: 0.8255 (mmm) REVERT: B 456 LEU cc_start: 0.9356 (mp) cc_final: 0.8472 (tt) REVERT: B 583 PHE cc_start: 0.9206 (m-10) cc_final: 0.8970 (m-80) REVERT: B 1025 MET cc_start: 0.8887 (mmm) cc_final: 0.8589 (mmm) REVERT: B 1252 MET cc_start: 0.9245 (ppp) cc_final: 0.8988 (ppp) REVERT: B 1298 MET cc_start: 0.8895 (ttt) cc_final: 0.8476 (ttt) REVERT: B 1305 MET cc_start: 0.9045 (tpt) cc_final: 0.8501 (tpt) REVERT: C 137 MET cc_start: 0.8086 (tpp) cc_final: 0.7689 (tpp) REVERT: C 179 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8537 (mt-10) REVERT: C 273 SER cc_start: 0.9331 (m) cc_final: 0.9004 (p) REVERT: C 288 GLU cc_start: 0.8024 (pm20) cc_final: 0.7654 (pm20) REVERT: C 292 GLU cc_start: 0.8629 (pm20) cc_final: 0.7960 (pm20) REVERT: D 157 PHE cc_start: 0.9302 (m-80) cc_final: 0.8709 (m-10) REVERT: D 184 LEU cc_start: 0.9387 (mt) cc_final: 0.9082 (tp) REVERT: D 257 MET cc_start: 0.9120 (pmm) cc_final: 0.8847 (pmm) REVERT: D 429 MET cc_start: 0.8805 (tmm) cc_final: 0.8554 (tmm) REVERT: D 441 MET cc_start: 0.8749 (mmm) cc_final: 0.8252 (mmm) REVERT: D 456 LEU cc_start: 0.9354 (mp) cc_final: 0.8469 (tt) REVERT: D 583 PHE cc_start: 0.9203 (m-10) cc_final: 0.8968 (m-80) REVERT: D 1025 MET cc_start: 0.8891 (mmm) cc_final: 0.8593 (mmm) REVERT: D 1252 MET cc_start: 0.9247 (ppp) cc_final: 0.8991 (ppp) REVERT: D 1298 MET cc_start: 0.8898 (ttt) cc_final: 0.8477 (ttt) REVERT: D 1305 MET cc_start: 0.9041 (tpt) cc_final: 0.8496 (tpt) REVERT: E 137 MET cc_start: 0.8090 (tpp) cc_final: 0.7686 (tpp) REVERT: E 179 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8537 (mt-10) REVERT: E 273 SER cc_start: 0.9328 (m) cc_final: 0.9000 (p) REVERT: E 288 GLU cc_start: 0.8031 (pm20) cc_final: 0.7663 (pm20) REVERT: E 292 GLU cc_start: 0.8629 (pm20) cc_final: 0.7988 (pm20) REVERT: F 157 PHE cc_start: 0.9301 (m-80) cc_final: 0.8706 (m-10) REVERT: F 184 LEU cc_start: 0.9388 (mt) cc_final: 0.9083 (tp) REVERT: F 257 MET cc_start: 0.9118 (pmm) cc_final: 0.8842 (pmm) REVERT: F 429 MET cc_start: 0.8807 (tmm) cc_final: 0.8551 (tmm) REVERT: F 441 MET cc_start: 0.8750 (mmm) cc_final: 0.8252 (mmm) REVERT: F 456 LEU cc_start: 0.9366 (mp) cc_final: 0.8503 (tt) REVERT: F 583 PHE cc_start: 0.9114 (m-80) cc_final: 0.8851 (m-80) REVERT: F 1025 MET cc_start: 0.8891 (mmm) cc_final: 0.8592 (mmm) REVERT: F 1252 MET cc_start: 0.9248 (ppp) cc_final: 0.8991 (ppp) REVERT: F 1298 MET cc_start: 0.8897 (ttt) cc_final: 0.8479 (ttt) REVERT: F 1305 MET cc_start: 0.9038 (tpt) cc_final: 0.8493 (tpt) REVERT: G 137 MET cc_start: 0.8085 (tpp) cc_final: 0.7686 (tpp) REVERT: G 179 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8536 (mt-10) REVERT: G 273 SER cc_start: 0.9327 (m) cc_final: 0.8998 (p) REVERT: G 288 GLU cc_start: 0.8039 (pm20) cc_final: 0.7665 (pm20) REVERT: G 292 GLU cc_start: 0.8632 (pm20) cc_final: 0.7964 (pm20) REVERT: H 157 PHE cc_start: 0.9302 (m-80) cc_final: 0.8705 (m-10) REVERT: H 184 LEU cc_start: 0.9385 (mt) cc_final: 0.9084 (tp) REVERT: H 257 MET cc_start: 0.9115 (pmm) cc_final: 0.8840 (pmm) REVERT: H 429 MET cc_start: 0.8807 (tmm) cc_final: 0.8549 (tmm) REVERT: H 441 MET cc_start: 0.8754 (mmm) cc_final: 0.8253 (mmm) REVERT: H 456 LEU cc_start: 0.9367 (mp) cc_final: 0.8502 (tt) REVERT: H 583 PHE cc_start: 0.9118 (m-80) cc_final: 0.8853 (m-80) REVERT: H 1025 MET cc_start: 0.8889 (mmm) cc_final: 0.8589 (mmm) REVERT: H 1252 MET cc_start: 0.9246 (ppp) cc_final: 0.8988 (ppp) REVERT: H 1298 MET cc_start: 0.8898 (ttt) cc_final: 0.8479 (ttt) REVERT: H 1305 MET cc_start: 0.9042 (tpt) cc_final: 0.8497 (tpt) outliers start: 4 outliers final: 4 residues processed: 513 average time/residue: 0.6155 time to fit residues: 553.9921 Evaluate side-chains 373 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 369 time to evaluate : 5.915 ------------------------------------------------------------------------------- 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: 3.9990 chunk 355 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 466 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 chunk 534 optimal weight: 20.0000 chunk 432 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 319 optimal weight: 3.9990 chunk 562 optimal weight: 20.0000 chunk 158 optimal weight: 50.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 909 GLN C 48 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 909 GLN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 909 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 52052 Z= 0.231 Angle : 0.638 8.749 70780 Z= 0.328 Chirality : 0.042 0.192 8540 Planarity : 0.004 0.077 8660 Dihedral : 8.779 143.454 7180 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.90 % Favored : 96.04 % Rotamer: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.63 % 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: 0.20 (0.10), residues: 6432 helix: 1.05 (0.08), residues: 3972 sheet: -0.34 (0.22), residues: 480 loop : -1.61 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 83 HIS 0.005 0.001 HIS G 259 PHE 0.032 0.002 PHE G 168 TYR 0.025 0.001 TYR H 512 ARG 0.007 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 508 time to evaluate : 6.027 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 137 MET cc_start: 0.8251 (tpp) cc_final: 0.7820 (tpp) REVERT: A 179 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8384 (mt-10) REVERT: A 273 SER cc_start: 0.9317 (m) cc_final: 0.8970 (p) REVERT: A 288 GLU cc_start: 0.8015 (pm20) cc_final: 0.7747 (pm20) REVERT: B 157 PHE cc_start: 0.9287 (m-80) cc_final: 0.8982 (m-80) REVERT: B 181 MET cc_start: 0.9172 (mmm) cc_final: 0.8890 (mmm) REVERT: B 257 MET cc_start: 0.9111 (pmm) cc_final: 0.8781 (pmm) REVERT: B 429 MET cc_start: 0.8803 (tmm) cc_final: 0.8559 (tmm) REVERT: B 441 MET cc_start: 0.8728 (mmm) cc_final: 0.8342 (mmm) REVERT: B 456 LEU cc_start: 0.9369 (mp) cc_final: 0.8473 (tt) REVERT: B 583 PHE cc_start: 0.9172 (m-10) cc_final: 0.8944 (m-80) REVERT: B 1025 MET cc_start: 0.8882 (mmm) cc_final: 0.8584 (mmm) REVERT: B 1252 MET cc_start: 0.9352 (ppp) cc_final: 0.9025 (ppp) REVERT: B 1298 MET cc_start: 0.8904 (ttt) cc_final: 0.8476 (ttt) REVERT: B 1305 MET cc_start: 0.9068 (tpt) cc_final: 0.8487 (tpt) REVERT: C 137 MET cc_start: 0.8254 (tpp) cc_final: 0.7818 (tpp) REVERT: C 179 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8380 (mt-10) REVERT: C 273 SER cc_start: 0.9320 (m) cc_final: 0.8974 (p) REVERT: C 288 GLU cc_start: 0.8015 (pm20) cc_final: 0.7745 (pm20) REVERT: D 157 PHE cc_start: 0.9287 (m-80) cc_final: 0.8982 (m-80) REVERT: D 181 MET cc_start: 0.9171 (mmm) cc_final: 0.8889 (mmm) REVERT: D 257 MET cc_start: 0.9115 (pmm) cc_final: 0.8787 (pmm) REVERT: D 429 MET cc_start: 0.8799 (tmm) cc_final: 0.8562 (tmm) REVERT: D 441 MET cc_start: 0.8722 (mmm) cc_final: 0.8339 (mmm) REVERT: D 456 LEU cc_start: 0.9369 (mp) cc_final: 0.8472 (tt) REVERT: D 583 PHE cc_start: 0.9168 (m-10) cc_final: 0.8943 (m-80) REVERT: D 1025 MET cc_start: 0.8884 (mmm) cc_final: 0.8586 (mmm) REVERT: D 1252 MET cc_start: 0.9352 (ppp) cc_final: 0.9030 (ppp) REVERT: D 1298 MET cc_start: 0.8905 (ttt) cc_final: 0.8478 (ttt) REVERT: D 1305 MET cc_start: 0.9066 (tpt) cc_final: 0.8484 (tpt) REVERT: E 137 MET cc_start: 0.8259 (tpp) cc_final: 0.7820 (tpp) REVERT: E 179 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8387 (mt-10) REVERT: E 273 SER cc_start: 0.9318 (m) cc_final: 0.8969 (p) REVERT: E 288 GLU cc_start: 0.8020 (pm20) cc_final: 0.7751 (pm20) REVERT: F 157 PHE cc_start: 0.9288 (m-80) cc_final: 0.8982 (m-80) REVERT: F 181 MET cc_start: 0.9171 (mmm) cc_final: 0.8889 (mmm) REVERT: F 257 MET cc_start: 0.9113 (pmm) cc_final: 0.8782 (pmm) REVERT: F 429 MET cc_start: 0.8800 (tmm) cc_final: 0.8563 (tmm) REVERT: F 441 MET cc_start: 0.8725 (mmm) cc_final: 0.8340 (mmm) REVERT: F 456 LEU cc_start: 0.9372 (mp) cc_final: 0.8487 (tt) REVERT: F 583 PHE cc_start: 0.9105 (m-80) cc_final: 0.8809 (m-80) REVERT: F 1025 MET cc_start: 0.8883 (mmm) cc_final: 0.8584 (mmm) REVERT: F 1252 MET cc_start: 0.9350 (ppp) cc_final: 0.9025 (ppp) REVERT: F 1298 MET cc_start: 0.8906 (ttt) cc_final: 0.8478 (ttt) REVERT: F 1305 MET cc_start: 0.9063 (tpt) cc_final: 0.8478 (tpt) REVERT: G 137 MET cc_start: 0.8255 (tpp) cc_final: 0.7818 (tpp) REVERT: G 179 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8379 (mt-10) REVERT: G 273 SER cc_start: 0.9317 (m) cc_final: 0.8971 (p) REVERT: G 288 GLU cc_start: 0.8026 (pm20) cc_final: 0.7756 (pm20) REVERT: H 157 PHE cc_start: 0.9287 (m-80) cc_final: 0.8981 (m-80) REVERT: H 181 MET cc_start: 0.9170 (mmm) cc_final: 0.8888 (mmm) REVERT: H 257 MET cc_start: 0.9111 (pmm) cc_final: 0.8782 (pmm) REVERT: H 429 MET cc_start: 0.8801 (tmm) cc_final: 0.8560 (tmm) REVERT: H 441 MET cc_start: 0.8728 (mmm) cc_final: 0.8341 (mmm) REVERT: H 456 LEU cc_start: 0.9375 (mp) cc_final: 0.8490 (tt) REVERT: H 583 PHE cc_start: 0.9107 (m-80) cc_final: 0.8810 (m-80) REVERT: H 1025 MET cc_start: 0.8881 (mmm) cc_final: 0.8580 (mmm) REVERT: H 1252 MET cc_start: 0.9353 (ppp) cc_final: 0.9027 (ppp) REVERT: H 1298 MET cc_start: 0.8905 (ttt) cc_final: 0.8479 (ttt) REVERT: H 1305 MET cc_start: 0.9067 (tpt) cc_final: 0.8485 (tpt) outliers start: 3 outliers final: 0 residues processed: 511 average time/residue: 0.5448 time to fit residues: 495.2774 Evaluate side-chains 357 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 5.880 ------------------------------------------------------------------------------- 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: 5.9990 chunk 564 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 367 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 520 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 207 optimal weight: 0.7980 chunk 329 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1296 ASN C 48 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1296 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1296 ASN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 52052 Z= 0.236 Angle : 0.634 9.008 70780 Z= 0.325 Chirality : 0.042 0.186 8540 Planarity : 0.004 0.072 8660 Dihedral : 8.534 137.100 7180 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 6432 helix: 1.14 (0.08), residues: 4008 sheet: -0.22 (0.23), residues: 480 loop : -1.52 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 90 HIS 0.004 0.001 HIS A 259 PHE 0.029 0.002 PHE C 168 TYR 0.019 0.001 TYR H 512 ARG 0.007 0.000 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 494 time to evaluate : 5.812 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 137 MET cc_start: 0.8297 (tpp) cc_final: 0.7875 (tpp) REVERT: A 179 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8388 (mt-10) REVERT: A 273 SER cc_start: 0.9315 (m) cc_final: 0.8945 (p) REVERT: B 112 MET cc_start: 0.9130 (mmp) cc_final: 0.8916 (mmp) REVERT: B 157 PHE cc_start: 0.9291 (m-80) cc_final: 0.8957 (m-80) REVERT: B 181 MET cc_start: 0.9172 (mmm) cc_final: 0.8887 (mmm) REVERT: B 184 LEU cc_start: 0.9378 (mt) cc_final: 0.9168 (mt) REVERT: B 257 MET cc_start: 0.9049 (pmm) cc_final: 0.8717 (pmm) REVERT: B 456 LEU cc_start: 0.9343 (mp) cc_final: 0.8429 (tt) REVERT: B 506 MET cc_start: 0.7482 (mpp) cc_final: 0.7180 (mpp) REVERT: B 583 PHE cc_start: 0.9157 (m-10) cc_final: 0.8904 (m-80) REVERT: B 1252 MET cc_start: 0.9274 (ppp) cc_final: 0.9055 (ppp) REVERT: B 1298 MET cc_start: 0.8926 (ttt) cc_final: 0.8502 (ttt) REVERT: B 1305 MET cc_start: 0.9042 (tpt) cc_final: 0.8495 (tpt) REVERT: C 137 MET cc_start: 0.8291 (tpp) cc_final: 0.7863 (tpp) REVERT: C 179 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8390 (mt-10) REVERT: C 273 SER cc_start: 0.9317 (m) cc_final: 0.8946 (p) REVERT: D 112 MET cc_start: 0.9130 (mmp) cc_final: 0.8916 (mmp) REVERT: D 157 PHE cc_start: 0.9293 (m-80) cc_final: 0.8956 (m-80) REVERT: D 181 MET cc_start: 0.9173 (mmm) cc_final: 0.8896 (mmm) REVERT: D 184 LEU cc_start: 0.9377 (mt) cc_final: 0.9170 (mt) REVERT: D 257 MET cc_start: 0.9047 (pmm) cc_final: 0.8717 (pmm) REVERT: D 456 LEU cc_start: 0.9343 (mp) cc_final: 0.8426 (tt) REVERT: D 506 MET cc_start: 0.7484 (mpp) cc_final: 0.7182 (mpp) REVERT: D 583 PHE cc_start: 0.9156 (m-10) cc_final: 0.8903 (m-80) REVERT: D 1252 MET cc_start: 0.9277 (ppp) cc_final: 0.9055 (ppp) REVERT: D 1298 MET cc_start: 0.8928 (ttt) cc_final: 0.8507 (ttt) REVERT: D 1305 MET cc_start: 0.9039 (tpt) cc_final: 0.8493 (tpt) REVERT: E 137 MET cc_start: 0.8290 (tpp) cc_final: 0.7867 (tpp) REVERT: E 179 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8393 (mt-10) REVERT: E 273 SER cc_start: 0.9316 (m) cc_final: 0.8944 (p) REVERT: F 112 MET cc_start: 0.9130 (mmp) cc_final: 0.8915 (mmp) REVERT: F 157 PHE cc_start: 0.9292 (m-80) cc_final: 0.8954 (m-80) REVERT: F 181 MET cc_start: 0.9172 (mmm) cc_final: 0.8895 (mmm) REVERT: F 184 LEU cc_start: 0.9377 (mt) cc_final: 0.9170 (mt) REVERT: F 257 MET cc_start: 0.9049 (pmm) cc_final: 0.8719 (pmm) REVERT: F 456 LEU cc_start: 0.9336 (mp) cc_final: 0.8416 (tt) REVERT: F 506 MET cc_start: 0.7480 (mpp) cc_final: 0.7178 (mpp) REVERT: F 583 PHE cc_start: 0.9115 (m-80) cc_final: 0.8754 (m-80) REVERT: F 1252 MET cc_start: 0.9269 (ppp) cc_final: 0.9050 (ppp) REVERT: F 1298 MET cc_start: 0.8931 (ttt) cc_final: 0.8507 (ttt) REVERT: F 1305 MET cc_start: 0.9036 (tpt) cc_final: 0.8489 (tpt) REVERT: G 137 MET cc_start: 0.8287 (tpp) cc_final: 0.7863 (tpp) REVERT: G 179 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8390 (mt-10) REVERT: G 273 SER cc_start: 0.9315 (m) cc_final: 0.8943 (p) REVERT: H 112 MET cc_start: 0.9132 (mmp) cc_final: 0.8918 (mmp) REVERT: H 157 PHE cc_start: 0.9292 (m-80) cc_final: 0.8954 (m-80) REVERT: H 181 MET cc_start: 0.9172 (mmm) cc_final: 0.8884 (mmm) REVERT: H 184 LEU cc_start: 0.9375 (mt) cc_final: 0.9166 (mt) REVERT: H 257 MET cc_start: 0.9049 (pmm) cc_final: 0.8717 (pmm) REVERT: H 456 LEU cc_start: 0.9338 (mp) cc_final: 0.8419 (tt) REVERT: H 506 MET cc_start: 0.7485 (mpp) cc_final: 0.7183 (mpp) REVERT: H 583 PHE cc_start: 0.9116 (m-80) cc_final: 0.8756 (m-80) REVERT: H 1252 MET cc_start: 0.9272 (ppp) cc_final: 0.9055 (ppp) REVERT: H 1298 MET cc_start: 0.8928 (ttt) cc_final: 0.8507 (ttt) REVERT: H 1305 MET cc_start: 0.9040 (tpt) cc_final: 0.8493 (tpt) outliers start: 4 outliers final: 4 residues processed: 498 average time/residue: 0.5415 time to fit residues: 480.5017 Evaluate side-chains 347 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 343 time to evaluate : 5.698 ------------------------------------------------------------------------------- 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: 9.9990 chunk 70 optimal weight: 5.9990 chunk 357 optimal weight: 0.1980 chunk 457 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 527 optimal weight: 2.9990 chunk 350 optimal weight: 8.9990 chunk 624 optimal weight: 0.3980 chunk 390 optimal weight: 20.0000 chunk 380 optimal weight: 10.0000 chunk 288 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 52052 Z= 0.252 Angle : 0.652 9.514 70780 Z= 0.333 Chirality : 0.042 0.187 8540 Planarity : 0.004 0.069 8660 Dihedral : 8.429 133.502 7180 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.43 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 0.43 (0.11), residues: 6432 helix: 1.22 (0.08), residues: 4004 sheet: -0.21 (0.23), residues: 496 loop : -1.55 (0.14), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP G 83 HIS 0.004 0.001 HIS C 259 PHE 0.027 0.002 PHE G 75 TYR 0.014 0.001 TYR F 512 ARG 0.005 0.000 ARG E 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 485 time to evaluate : 5.825 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 123 PHE cc_start: 0.9250 (t80) cc_final: 0.8989 (t80) REVERT: A 137 MET cc_start: 0.8367 (tpp) cc_final: 0.7945 (tpp) REVERT: A 179 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8436 (mt-10) REVERT: A 273 SER cc_start: 0.9288 (m) cc_final: 0.8930 (p) REVERT: A 288 GLU cc_start: 0.7866 (pm20) cc_final: 0.7482 (pm20) REVERT: B 112 MET cc_start: 0.9122 (mmp) cc_final: 0.8897 (mmp) REVERT: B 157 PHE cc_start: 0.9288 (m-80) cc_final: 0.8965 (m-80) REVERT: B 184 LEU cc_start: 0.9379 (mt) cc_final: 0.9145 (tp) REVERT: B 257 MET cc_start: 0.9019 (pmm) cc_final: 0.8691 (pmm) REVERT: B 441 MET cc_start: 0.8725 (mmm) cc_final: 0.8185 (mmm) REVERT: B 456 LEU cc_start: 0.9357 (mp) cc_final: 0.8431 (tt) REVERT: B 506 MET cc_start: 0.7397 (mpp) cc_final: 0.7123 (mpp) REVERT: B 583 PHE cc_start: 0.9149 (m-10) cc_final: 0.8890 (m-80) REVERT: B 1025 MET cc_start: 0.8764 (mmm) cc_final: 0.8503 (mmm) REVERT: B 1298 MET cc_start: 0.8829 (ttt) cc_final: 0.8396 (ttt) REVERT: B 1305 MET cc_start: 0.9041 (tpt) cc_final: 0.8497 (tpt) REVERT: C 123 PHE cc_start: 0.9249 (t80) cc_final: 0.8987 (t80) REVERT: C 137 MET cc_start: 0.8355 (tpp) cc_final: 0.7931 (tpp) REVERT: C 179 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8436 (mt-10) REVERT: C 273 SER cc_start: 0.9291 (m) cc_final: 0.8933 (p) REVERT: C 288 GLU cc_start: 0.7864 (pm20) cc_final: 0.7479 (pm20) REVERT: D 112 MET cc_start: 0.9121 (mmp) cc_final: 0.8896 (mmp) REVERT: D 157 PHE cc_start: 0.9290 (m-80) cc_final: 0.8967 (m-80) REVERT: D 184 LEU cc_start: 0.9377 (mt) cc_final: 0.9145 (tp) REVERT: D 257 MET cc_start: 0.9019 (pmm) cc_final: 0.8691 (pmm) REVERT: D 441 MET cc_start: 0.8719 (mmm) cc_final: 0.8178 (mmm) REVERT: D 456 LEU cc_start: 0.9359 (mp) cc_final: 0.8433 (tt) REVERT: D 506 MET cc_start: 0.7403 (mpp) cc_final: 0.7128 (mpp) REVERT: D 583 PHE cc_start: 0.9149 (m-10) cc_final: 0.8891 (m-80) REVERT: D 1025 MET cc_start: 0.8767 (mmm) cc_final: 0.8508 (mmm) REVERT: D 1298 MET cc_start: 0.8832 (ttt) cc_final: 0.8397 (ttt) REVERT: D 1305 MET cc_start: 0.9041 (tpt) cc_final: 0.8498 (tpt) REVERT: E 123 PHE cc_start: 0.9255 (t80) cc_final: 0.8992 (t80) REVERT: E 137 MET cc_start: 0.8358 (tpp) cc_final: 0.7935 (tpp) REVERT: E 179 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8442 (mt-10) REVERT: E 273 SER cc_start: 0.9288 (m) cc_final: 0.8929 (p) REVERT: E 288 GLU cc_start: 0.7865 (pm20) cc_final: 0.7482 (pm20) REVERT: F 112 MET cc_start: 0.9121 (mmp) cc_final: 0.8896 (mmp) REVERT: F 157 PHE cc_start: 0.9289 (m-80) cc_final: 0.8963 (m-80) REVERT: F 184 LEU cc_start: 0.9379 (mt) cc_final: 0.9146 (tp) REVERT: F 257 MET cc_start: 0.9018 (pmm) cc_final: 0.8692 (pmm) REVERT: F 441 MET cc_start: 0.8723 (mmm) cc_final: 0.8182 (mmm) REVERT: F 456 LEU cc_start: 0.9348 (mp) cc_final: 0.8428 (tt) REVERT: F 506 MET cc_start: 0.7394 (mpp) cc_final: 0.7121 (mpp) REVERT: F 583 PHE cc_start: 0.9094 (m-80) cc_final: 0.8709 (m-80) REVERT: F 730 MET cc_start: 0.3137 (tpt) cc_final: 0.2935 (tpt) REVERT: F 1025 MET cc_start: 0.8765 (mmm) cc_final: 0.8505 (mmm) REVERT: F 1298 MET cc_start: 0.8832 (ttt) cc_final: 0.8397 (ttt) REVERT: F 1305 MET cc_start: 0.9037 (tpt) cc_final: 0.8493 (tpt) REVERT: G 123 PHE cc_start: 0.9252 (t80) cc_final: 0.8989 (t80) REVERT: G 137 MET cc_start: 0.8355 (tpp) cc_final: 0.7929 (tpp) REVERT: G 179 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8434 (mt-10) REVERT: G 273 SER cc_start: 0.9288 (m) cc_final: 0.8929 (p) REVERT: G 288 GLU cc_start: 0.7868 (pm20) cc_final: 0.7483 (pm20) REVERT: H 112 MET cc_start: 0.9125 (mmp) cc_final: 0.8899 (mmp) REVERT: H 157 PHE cc_start: 0.9290 (m-80) cc_final: 0.8965 (m-80) REVERT: H 184 LEU cc_start: 0.9375 (mt) cc_final: 0.9146 (tp) REVERT: H 257 MET cc_start: 0.9018 (pmm) cc_final: 0.8693 (pmm) REVERT: H 441 MET cc_start: 0.8720 (mmm) cc_final: 0.8179 (mmm) REVERT: H 456 LEU cc_start: 0.9351 (mp) cc_final: 0.8429 (tt) REVERT: H 506 MET cc_start: 0.7400 (mpp) cc_final: 0.7126 (mpp) REVERT: H 583 PHE cc_start: 0.9096 (m-80) cc_final: 0.8710 (m-80) REVERT: H 1025 MET cc_start: 0.8762 (mmm) cc_final: 0.8500 (mmm) REVERT: H 1298 MET cc_start: 0.8832 (ttt) cc_final: 0.8398 (ttt) REVERT: H 1305 MET cc_start: 0.9040 (tpt) cc_final: 0.8497 (tpt) outliers start: 0 outliers final: 0 residues processed: 485 average time/residue: 0.5331 time to fit residues: 460.7097 Evaluate side-chains 356 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 5.748 ------------------------------------------------------------------------------- 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: 8.9990 chunk 249 optimal weight: 6.9990 chunk 373 optimal weight: 10.0000 chunk 188 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 397 optimal weight: 20.0000 chunk 425 optimal weight: 8.9990 chunk 308 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 490 optimal weight: 0.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 ASN ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 153 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 909 GLN E 153 ASN ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 52052 Z= 0.288 Angle : 0.691 8.794 70780 Z= 0.356 Chirality : 0.043 0.194 8540 Planarity : 0.004 0.068 8660 Dihedral : 8.403 130.439 7180 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.59 % Favored : 95.35 % Rotamer: Outliers : 0.02 % Allowed : 1.12 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.11), residues: 6432 helix: 1.20 (0.08), residues: 3992 sheet: -0.17 (0.23), residues: 496 loop : -1.53 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.003 TRP G 83 HIS 0.005 0.001 HIS A 259 PHE 0.040 0.002 PHE E 168 TYR 0.019 0.002 TYR D 454 ARG 0.005 0.000 ARG G 34 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 6.071 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 137 MET cc_start: 0.8439 (tpp) cc_final: 0.7972 (tpp) REVERT: A 179 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8480 (mt-10) REVERT: A 273 SER cc_start: 0.9241 (m) cc_final: 0.8879 (p) REVERT: A 288 GLU cc_start: 0.7899 (pm20) cc_final: 0.7640 (pm20) REVERT: B 157 PHE cc_start: 0.9285 (m-80) cc_final: 0.8960 (m-80) REVERT: B 257 MET cc_start: 0.9037 (pmm) cc_final: 0.8719 (pmm) REVERT: B 441 MET cc_start: 0.8759 (mmm) cc_final: 0.8150 (mmm) REVERT: B 456 LEU cc_start: 0.9375 (mp) cc_final: 0.8454 (tt) REVERT: B 506 MET cc_start: 0.7453 (mpp) cc_final: 0.7166 (mpp) REVERT: B 583 PHE cc_start: 0.9158 (m-10) cc_final: 0.8896 (m-80) REVERT: B 1025 MET cc_start: 0.8768 (mmm) cc_final: 0.8493 (mmm) REVERT: B 1252 MET cc_start: 0.8936 (ppp) cc_final: 0.8704 (ppp) REVERT: B 1298 MET cc_start: 0.8864 (ttt) cc_final: 0.8487 (ttt) REVERT: B 1305 MET cc_start: 0.9060 (tpt) cc_final: 0.8513 (tpt) REVERT: C 137 MET cc_start: 0.8434 (tpp) cc_final: 0.7967 (tpp) REVERT: C 179 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8479 (mt-10) REVERT: C 273 SER cc_start: 0.9242 (m) cc_final: 0.8879 (p) REVERT: C 288 GLU cc_start: 0.7909 (pm20) cc_final: 0.7646 (pm20) REVERT: D 157 PHE cc_start: 0.9285 (m-80) cc_final: 0.8959 (m-80) REVERT: D 257 MET cc_start: 0.9033 (pmm) cc_final: 0.8716 (pmm) REVERT: D 441 MET cc_start: 0.8757 (mmm) cc_final: 0.8149 (mmm) REVERT: D 456 LEU cc_start: 0.9374 (mp) cc_final: 0.8453 (tt) REVERT: D 506 MET cc_start: 0.7454 (mpp) cc_final: 0.7167 (mpp) REVERT: D 583 PHE cc_start: 0.9158 (m-10) cc_final: 0.8896 (m-80) REVERT: D 1025 MET cc_start: 0.8769 (mmm) cc_final: 0.8495 (mmm) REVERT: D 1252 MET cc_start: 0.8935 (ppp) cc_final: 0.8699 (ppp) REVERT: D 1298 MET cc_start: 0.8865 (ttt) cc_final: 0.8488 (ttt) REVERT: D 1305 MET cc_start: 0.9060 (tpt) cc_final: 0.8513 (tpt) REVERT: E 137 MET cc_start: 0.8435 (tpp) cc_final: 0.7967 (tpp) REVERT: E 179 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8487 (mt-10) REVERT: E 273 SER cc_start: 0.9241 (m) cc_final: 0.8877 (p) REVERT: E 288 GLU cc_start: 0.7906 (pm20) cc_final: 0.7646 (pm20) REVERT: F 157 PHE cc_start: 0.9284 (m-80) cc_final: 0.8958 (m-80) REVERT: F 257 MET cc_start: 0.9034 (pmm) cc_final: 0.8721 (pmm) REVERT: F 441 MET cc_start: 0.8757 (mmm) cc_final: 0.8154 (mmm) REVERT: F 456 LEU cc_start: 0.9376 (mp) cc_final: 0.8475 (tt) REVERT: F 506 MET cc_start: 0.7450 (mpp) cc_final: 0.7163 (mpp) REVERT: F 583 PHE cc_start: 0.9109 (m-80) cc_final: 0.8694 (m-80) REVERT: F 1025 MET cc_start: 0.8768 (mmm) cc_final: 0.8493 (mmm) REVERT: F 1252 MET cc_start: 0.8932 (ppp) cc_final: 0.8699 (ppp) REVERT: F 1298 MET cc_start: 0.8866 (ttt) cc_final: 0.8490 (ttt) REVERT: F 1305 MET cc_start: 0.9053 (tpt) cc_final: 0.8507 (tpt) REVERT: G 137 MET cc_start: 0.8434 (tpp) cc_final: 0.7968 (tpp) REVERT: G 179 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8476 (mt-10) REVERT: G 273 SER cc_start: 0.9239 (m) cc_final: 0.8875 (p) REVERT: G 288 GLU cc_start: 0.7906 (pm20) cc_final: 0.7644 (pm20) REVERT: H 157 PHE cc_start: 0.9286 (m-80) cc_final: 0.8959 (m-80) REVERT: H 257 MET cc_start: 0.9035 (pmm) cc_final: 0.8721 (pmm) REVERT: H 441 MET cc_start: 0.8755 (mmm) cc_final: 0.8148 (mmm) REVERT: H 456 LEU cc_start: 0.9379 (mp) cc_final: 0.8475 (tt) REVERT: H 506 MET cc_start: 0.7454 (mpp) cc_final: 0.7167 (mpp) REVERT: H 583 PHE cc_start: 0.9110 (m-80) cc_final: 0.8694 (m-80) REVERT: H 1025 MET cc_start: 0.8766 (mmm) cc_final: 0.8491 (mmm) REVERT: H 1252 MET cc_start: 0.8938 (ppp) cc_final: 0.8702 (ppp) REVERT: H 1298 MET cc_start: 0.8863 (ttt) cc_final: 0.8486 (ttt) REVERT: H 1305 MET cc_start: 0.9057 (tpt) cc_final: 0.8510 (tpt) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.5350 time to fit residues: 447.4911 Evaluate side-chains 356 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 5.545 ------------------------------------------------------------------------------- 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: 5.9990 chunk 598 optimal weight: 20.0000 chunk 545 optimal weight: 5.9990 chunk 582 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 457 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 chunk 525 optimal weight: 4.9990 chunk 550 optimal weight: 0.9990 chunk 579 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 52052 Z= 0.201 Angle : 0.637 8.468 70780 Z= 0.325 Chirality : 0.042 0.177 8540 Planarity : 0.004 0.064 8660 Dihedral : 8.235 127.469 7180 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.52 (0.11), residues: 6432 helix: 1.31 (0.08), residues: 3972 sheet: -0.08 (0.23), residues: 480 loop : -1.53 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP C 83 HIS 0.009 0.001 HIS B 326 PHE 0.024 0.002 PHE G 75 TYR 0.042 0.002 TYR F 512 ARG 0.004 0.000 ARG C 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 5.455 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 60 PHE cc_start: 0.8891 (p90) cc_final: 0.8666 (p90) REVERT: A 137 MET cc_start: 0.8390 (tpp) cc_final: 0.7609 (tpp) REVERT: A 179 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 273 SER cc_start: 0.9200 (m) cc_final: 0.8853 (t) REVERT: B 37 VAL cc_start: 0.9443 (t) cc_final: 0.9168 (t) REVERT: B 181 MET cc_start: 0.9338 (mmm) cc_final: 0.9067 (mmm) REVERT: B 184 LEU cc_start: 0.9351 (mt) cc_final: 0.9150 (tp) REVERT: B 441 MET cc_start: 0.8658 (mmm) cc_final: 0.8124 (mmm) REVERT: B 456 LEU cc_start: 0.9345 (mp) cc_final: 0.8438 (tt) REVERT: B 506 MET cc_start: 0.7303 (mpp) cc_final: 0.7006 (mpp) REVERT: B 584 HIS cc_start: 0.8436 (m90) cc_final: 0.8008 (m170) REVERT: B 1025 MET cc_start: 0.8793 (mmm) cc_final: 0.8518 (mmm) REVERT: B 1252 MET cc_start: 0.8788 (ppp) cc_final: 0.8546 (ppp) REVERT: B 1298 MET cc_start: 0.8877 (ttt) cc_final: 0.8502 (ttt) REVERT: B 1305 MET cc_start: 0.9082 (tpt) cc_final: 0.8593 (tpt) REVERT: C 60 PHE cc_start: 0.8891 (p90) cc_final: 0.8650 (p90) REVERT: C 137 MET cc_start: 0.8392 (tpp) cc_final: 0.7595 (tpp) REVERT: C 179 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8426 (mt-10) REVERT: C 273 SER cc_start: 0.9202 (m) cc_final: 0.8854 (t) REVERT: D 37 VAL cc_start: 0.9448 (t) cc_final: 0.9173 (t) REVERT: D 181 MET cc_start: 0.9337 (mmm) cc_final: 0.9066 (mmm) REVERT: D 441 MET cc_start: 0.8656 (mmm) cc_final: 0.8122 (mmm) REVERT: D 456 LEU cc_start: 0.9345 (mp) cc_final: 0.8437 (tt) REVERT: D 506 MET cc_start: 0.7306 (mpp) cc_final: 0.7007 (mpp) REVERT: D 584 HIS cc_start: 0.8436 (m90) cc_final: 0.8009 (m170) REVERT: D 1025 MET cc_start: 0.8797 (mmm) cc_final: 0.8524 (mmm) REVERT: D 1252 MET cc_start: 0.8791 (ppp) cc_final: 0.8544 (ppp) REVERT: D 1298 MET cc_start: 0.8879 (ttt) cc_final: 0.8503 (ttt) REVERT: D 1305 MET cc_start: 0.9080 (tpt) cc_final: 0.8593 (tpt) REVERT: E 60 PHE cc_start: 0.8887 (p90) cc_final: 0.8655 (p90) REVERT: E 137 MET cc_start: 0.8383 (tpp) cc_final: 0.7602 (tpp) REVERT: E 179 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8434 (mt-10) REVERT: E 273 SER cc_start: 0.9201 (m) cc_final: 0.8851 (t) REVERT: F 37 VAL cc_start: 0.9447 (t) cc_final: 0.9175 (t) REVERT: F 181 MET cc_start: 0.9338 (mmm) cc_final: 0.9066 (mmm) REVERT: F 184 LEU cc_start: 0.9351 (mt) cc_final: 0.9149 (tp) REVERT: F 441 MET cc_start: 0.8653 (mmm) cc_final: 0.8120 (mmm) REVERT: F 456 LEU cc_start: 0.9347 (mp) cc_final: 0.8457 (tt) REVERT: F 506 MET cc_start: 0.7304 (mpp) cc_final: 0.7008 (mpp) REVERT: F 583 PHE cc_start: 0.9091 (m-80) cc_final: 0.8690 (m-80) REVERT: F 1025 MET cc_start: 0.8797 (mmm) cc_final: 0.8521 (mmm) REVERT: F 1252 MET cc_start: 0.8782 (ppp) cc_final: 0.8537 (ppp) REVERT: F 1298 MET cc_start: 0.8879 (ttt) cc_final: 0.8499 (ttt) REVERT: F 1305 MET cc_start: 0.9077 (tpt) cc_final: 0.8586 (tpt) REVERT: G 60 PHE cc_start: 0.8886 (p90) cc_final: 0.8648 (p90) REVERT: G 137 MET cc_start: 0.8394 (tpp) cc_final: 0.7592 (tpp) REVERT: G 179 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8426 (mt-10) REVERT: G 273 SER cc_start: 0.9199 (m) cc_final: 0.8851 (t) REVERT: H 37 VAL cc_start: 0.9448 (t) cc_final: 0.9174 (t) REVERT: H 181 MET cc_start: 0.9338 (mmm) cc_final: 0.9066 (mmm) REVERT: H 441 MET cc_start: 0.8654 (mmm) cc_final: 0.8119 (mmm) REVERT: H 456 LEU cc_start: 0.9349 (mp) cc_final: 0.8458 (tt) REVERT: H 506 MET cc_start: 0.7301 (mpp) cc_final: 0.7006 (mpp) REVERT: H 583 PHE cc_start: 0.9092 (m-80) cc_final: 0.8693 (m-80) REVERT: H 1025 MET cc_start: 0.8795 (mmm) cc_final: 0.8519 (mmm) REVERT: H 1252 MET cc_start: 0.8790 (ppp) cc_final: 0.8549 (ppp) REVERT: H 1298 MET cc_start: 0.8878 (ttt) cc_final: 0.8498 (ttt) REVERT: H 1305 MET cc_start: 0.9079 (tpt) cc_final: 0.8589 (tpt) outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.5543 time to fit residues: 470.0095 Evaluate side-chains 377 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 377 time to evaluate : 6.315 ------------------------------------------------------------------------------- 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: 6.9990 chunk 615 optimal weight: 4.9990 chunk 375 optimal weight: 5.9990 chunk 291 optimal weight: 2.9990 chunk 427 optimal weight: 8.9990 chunk 645 optimal weight: 20.0000 chunk 594 optimal weight: 9.9990 chunk 514 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 397 optimal weight: 20.0000 chunk 315 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN C 153 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 326 HIS ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 153 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 52052 Z= 0.294 Angle : 0.687 8.573 70780 Z= 0.355 Chirality : 0.043 0.193 8540 Planarity : 0.004 0.066 8660 Dihedral : 8.211 125.454 7180 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 0.02 % Allowed : 0.42 % Favored : 99.56 % 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: 0.48 (0.11), residues: 6432 helix: 1.25 (0.08), residues: 3972 sheet: -0.10 (0.23), residues: 496 loop : -1.47 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.003 TRP C 83 HIS 0.005 0.001 HIS D 584 PHE 0.032 0.002 PHE D 583 TYR 0.039 0.002 TYR B 123 ARG 0.005 0.000 ARG C 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 464 time to evaluate : 5.877 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 60 PHE cc_start: 0.9009 (p90) cc_final: 0.8750 (p90) REVERT: A 137 MET cc_start: 0.8454 (tpp) cc_final: 0.7999 (tpp) REVERT: A 179 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8466 (mt-10) REVERT: A 273 SER cc_start: 0.9210 (m) cc_final: 0.8897 (t) REVERT: B 157 PHE cc_start: 0.9393 (m-10) cc_final: 0.9157 (m-80) REVERT: B 181 MET cc_start: 0.9366 (mmm) cc_final: 0.9153 (mmm) REVERT: B 441 MET cc_start: 0.8623 (mmm) cc_final: 0.8066 (mmm) REVERT: B 456 LEU cc_start: 0.9358 (mp) cc_final: 0.8457 (tt) REVERT: B 506 MET cc_start: 0.7432 (mpp) cc_final: 0.6937 (mpp) REVERT: B 583 PHE cc_start: 0.9032 (m-80) cc_final: 0.8758 (m-80) REVERT: B 1252 MET cc_start: 0.8805 (ppp) cc_final: 0.8540 (ppp) REVERT: B 1290 MET cc_start: 0.8613 (mtm) cc_final: 0.7752 (mtt) REVERT: B 1298 MET cc_start: 0.8816 (ttt) cc_final: 0.8476 (ttt) REVERT: B 1305 MET cc_start: 0.9078 (tpt) cc_final: 0.8529 (tpt) REVERT: C 60 PHE cc_start: 0.8979 (p90) cc_final: 0.8773 (p90) REVERT: C 137 MET cc_start: 0.8447 (tpp) cc_final: 0.7999 (tpp) REVERT: C 179 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8464 (mt-10) REVERT: C 273 SER cc_start: 0.9215 (m) cc_final: 0.8900 (t) REVERT: D 157 PHE cc_start: 0.9391 (m-10) cc_final: 0.9156 (m-80) REVERT: D 181 MET cc_start: 0.9384 (mmm) cc_final: 0.9150 (mmm) REVERT: D 441 MET cc_start: 0.8616 (mmm) cc_final: 0.8062 (mmm) REVERT: D 456 LEU cc_start: 0.9360 (mp) cc_final: 0.8458 (tt) REVERT: D 506 MET cc_start: 0.7430 (mpp) cc_final: 0.6934 (mpp) REVERT: D 583 PHE cc_start: 0.9031 (m-80) cc_final: 0.8755 (m-80) REVERT: D 1252 MET cc_start: 0.8805 (ppp) cc_final: 0.8578 (ppp) REVERT: D 1290 MET cc_start: 0.8611 (mtm) cc_final: 0.7750 (mtt) REVERT: D 1298 MET cc_start: 0.8818 (ttt) cc_final: 0.8475 (ttt) REVERT: D 1305 MET cc_start: 0.9075 (tpt) cc_final: 0.8525 (tpt) REVERT: E 60 PHE cc_start: 0.9001 (p90) cc_final: 0.8747 (p90) REVERT: E 137 MET cc_start: 0.8450 (tpp) cc_final: 0.7994 (tpp) REVERT: E 179 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8471 (mt-10) REVERT: E 273 SER cc_start: 0.9210 (m) cc_final: 0.8896 (t) REVERT: F 157 PHE cc_start: 0.9391 (m-10) cc_final: 0.9154 (m-80) REVERT: F 181 MET cc_start: 0.9364 (mmm) cc_final: 0.9151 (mmm) REVERT: F 441 MET cc_start: 0.8626 (mmm) cc_final: 0.8078 (mmm) REVERT: F 456 LEU cc_start: 0.9373 (mp) cc_final: 0.8464 (tt) REVERT: F 506 MET cc_start: 0.7431 (mpp) cc_final: 0.6934 (mpp) REVERT: F 583 PHE cc_start: 0.9152 (m-80) cc_final: 0.8731 (m-80) REVERT: F 1252 MET cc_start: 0.8799 (ppp) cc_final: 0.8548 (ppp) REVERT: F 1298 MET cc_start: 0.8822 (ttt) cc_final: 0.8481 (ttt) REVERT: F 1305 MET cc_start: 0.9071 (tpt) cc_final: 0.8523 (tpt) REVERT: G 60 PHE cc_start: 0.8975 (p90) cc_final: 0.8770 (p90) REVERT: G 137 MET cc_start: 0.8445 (tpp) cc_final: 0.7999 (tpp) REVERT: G 179 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8465 (mt-10) REVERT: G 273 SER cc_start: 0.9209 (m) cc_final: 0.8894 (t) REVERT: H 157 PHE cc_start: 0.9393 (m-10) cc_final: 0.9156 (m-80) REVERT: H 181 MET cc_start: 0.9383 (mmm) cc_final: 0.9148 (mmm) REVERT: H 441 MET cc_start: 0.8623 (mmm) cc_final: 0.8076 (mmm) REVERT: H 456 LEU cc_start: 0.9375 (mp) cc_final: 0.8461 (tt) REVERT: H 506 MET cc_start: 0.7432 (mpp) cc_final: 0.6937 (mpp) REVERT: H 583 PHE cc_start: 0.9153 (m-80) cc_final: 0.8731 (m-80) REVERT: H 1252 MET cc_start: 0.8801 (ppp) cc_final: 0.8551 (ppp) REVERT: H 1298 MET cc_start: 0.8820 (ttt) cc_final: 0.8479 (ttt) REVERT: H 1305 MET cc_start: 0.9074 (tpt) cc_final: 0.8525 (tpt) outliers start: 1 outliers final: 0 residues processed: 465 average time/residue: 0.5389 time to fit residues: 445.1924 Evaluate side-chains 351 residues out of total 5688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 5.415 ------------------------------------------------------------------------------- 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: 10.0000 chunk 547 optimal weight: 3.9990 chunk 157 optimal weight: 20.0000 chunk 474 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 514 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 528 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 67 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 48 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 67 HIS ** F 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 HIS ** H 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 909 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1098 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.072963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054380 restraints weight = 299703.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055849 restraints weight = 176435.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056129 restraints weight = 110450.872| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.5810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 52052 Z= 0.300 Angle : 0.689 8.540 70780 Z= 0.356 Chirality : 0.044 0.332 8540 Planarity : 0.004 0.065 8660 Dihedral : 8.136 126.112 7180 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.62 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.11), residues: 6432 helix: 1.16 (0.08), residues: 3980 sheet: -0.09 (0.23), residues: 492 loop : -1.46 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.003 TRP C 83 HIS 0.009 0.001 HIS D 584 PHE 0.049 0.002 PHE H 432 TYR 0.035 0.002 TYR F 512 ARG 0.006 0.000 ARG B 388 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10496.58 seconds wall clock time: 191 minutes 20.84 seconds (11480.84 seconds total)