Starting phenix.real_space_refine on Mon Feb 19 13:13:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/02_2024/6ef0_9042_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/02_2024/6ef0_9042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/02_2024/6ef0_9042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/02_2024/6ef0_9042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/02_2024/6ef0_9042_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/02_2024/6ef0_9042_updated.pdb" } resolution = 4.43 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 88 5.16 5 C 15565 2.51 5 N 4292 2.21 5 O 4788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 4": "NH1" <-> "NH2" Residue "B TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 143": "NH1" <-> "NH2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 166": "NH1" <-> "NH2" Residue "E ARG 10": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 202": "NH1" <-> "NH2" Residue "H ARG 222": "NH1" <-> "NH2" Residue "I ARG 262": "NH1" <-> "NH2" Residue "J ARG 228": "NH1" <-> "NH2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "J ARG 306": "NH1" <-> "NH2" Residue "K TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 209": "NH1" <-> "NH2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M ARG 299": "NH1" <-> "NH2" Residue "M ARG 342": "NH1" <-> "NH2" Residue "M ARG 366": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24748 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1864 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1859 Classifications: {'peptide': 250} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 12, 'TRANS': 237} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 1834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1834 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 238} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "D" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1856 Classifications: {'peptide': 242} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 231} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1885 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 244} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "F" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1783 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 227} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1868 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 236} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "H" Number of atoms: 1831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1831 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 13, 'TRANS': 243} Unresolved non-hydrogen bonds: 175 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 12, 'GLN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 122 Chain: "I" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1913 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 11, 'TRANS': 259} Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 108 Chain: "J" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2005 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 258} Chain breaks: 1 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 64 Chain: "K" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2016 Classifications: {'peptide': 272} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 259} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 78 Chain: "L" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2057 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 257} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 55 Chain: "M" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1737 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 68} Link IDs: {'PTRANS': 9, 'TRANS': 248} Unresolved non-hydrogen bonds: 268 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 228 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'TRP:plan': 1, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 175 Chain: "s" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 66 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 13.53, per 1000 atoms: 0.55 Number of scatterers: 24748 At special positions: 0 Unit cell: (136.99, 139.05, 129.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 15 15.00 O 4788 8.00 N 4292 7.00 C 15565 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.69 Conformation dependent library (CDL) restraints added in 4.8 seconds 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 125 helices and 20 sheets defined 34.2% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 27 through 36 removed outlier: 4.125A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASN A 36 " --> pdb=" O PHE A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 108 removed outlier: 4.125A pdb=" N ASN A 92 " --> pdb=" O PRO A 88 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N TYR A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 123 through 129 removed outlier: 3.526A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 186 No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.528A pdb=" N PHE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N MET A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.513A pdb=" N GLU A 243 " --> pdb=" O ASN A 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 244 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 30 removed outlier: 3.881A pdb=" N THR B 26 " --> pdb=" O ASP B 22 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA B 27 " --> pdb=" O TYR B 23 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 removed outlier: 4.111A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 88 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 101 No H-bonds generated for 'chain 'B' and resid 98 through 101' Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.731A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 178 removed outlier: 4.202A pdb=" N GLU B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 178 " --> pdb=" O PHE B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 199 removed outlier: 4.255A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'C' and resid 21 through 31 removed outlier: 4.576A pdb=" N SER C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 87 through 102 removed outlier: 4.195A pdb=" N ILE C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS C 94 " --> pdb=" O THR C 90 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 100 " --> pdb=" O GLN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 122 removed outlier: 5.052A pdb=" N ASP C 117 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE C 118 " --> pdb=" O ARG C 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C 121 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 removed outlier: 3.774A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 199 removed outlier: 4.518A pdb=" N LYS C 199 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 232 through 241 removed outlier: 4.118A pdb=" N ILE C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 removed outlier: 4.291A pdb=" N LYS D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ARG D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 3.580A pdb=" N ARG D 90 " --> pdb=" O ILE D 86 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLU D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 119 removed outlier: 4.305A pdb=" N GLN D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLN D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 removed outlier: 3.523A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.713A pdb=" N LEU D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLU D 201 " --> pdb=" O ARG D 197 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL D 202 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 226 through 240 removed outlier: 3.690A pdb=" N TYR D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLN D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU D 237 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS D 240 " --> pdb=" O ILE D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 29 Processing helix chain 'E' and resid 86 through 102 removed outlier: 4.419A pdb=" N THR E 94 " --> pdb=" O GLU E 90 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 95 " --> pdb=" O HIS E 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA E 96 " --> pdb=" O ALA E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 117 removed outlier: 4.104A pdb=" N GLN E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N SER E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 121 No H-bonds generated for 'chain 'E' and resid 119 through 121' Processing helix chain 'E' and resid 177 through 184 removed outlier: 3.639A pdb=" N ALA E 181 " --> pdb=" O GLU E 177 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N GLU E 182 " --> pdb=" O GLY E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 removed outlier: 3.928A pdb=" N LEU E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E 202 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 216 No H-bonds generated for 'chain 'E' and resid 214 through 216' Processing helix chain 'E' and resid 233 through 239 Processing helix chain 'E' and resid 244 through 247 Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.820A pdb=" N ALA F 28 " --> pdb=" O TYR F 24 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 96 removed outlier: 4.473A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN F 91 " --> pdb=" O TYR F 87 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS F 92 " --> pdb=" O LEU F 88 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER F 96 " --> pdb=" O CYS F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 120 removed outlier: 3.574A pdb=" N GLY F 109 " --> pdb=" O VAL F 105 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASP F 114 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS F 118 " --> pdb=" O ASP F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 174 Processing helix chain 'F' and resid 186 through 195 removed outlier: 3.668A pdb=" N ILE F 190 " --> pdb=" O PRO F 186 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 231 through 233 No H-bonds generated for 'chain 'F' and resid 231 through 233' Processing helix chain 'G' and resid 22 through 25 No H-bonds generated for 'chain 'G' and resid 22 through 25' Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 82 through 103 removed outlier: 3.688A pdb=" N LEU G 88 " --> pdb=" O ASP G 84 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 119 removed outlier: 4.582A pdb=" N GLN G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 123 No H-bonds generated for 'chain 'G' and resid 121 through 123' Processing helix chain 'G' and resid 169 through 182 removed outlier: 3.575A pdb=" N ALA G 174 " --> pdb=" O GLN G 170 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP G 181 " --> pdb=" O GLU G 177 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N HIS G 182 " --> pdb=" O LYS G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 189 through 207 removed outlier: 3.523A pdb=" N VAL G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE G 199 " --> pdb=" O GLN G 195 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N GLU G 205 " --> pdb=" O TYR G 201 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ASN G 207 " --> pdb=" O ALA G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 224 No H-bonds generated for 'chain 'G' and resid 221 through 224' Processing helix chain 'G' and resid 234 through 247 removed outlier: 3.662A pdb=" N ASP G 241 " --> pdb=" O GLN G 237 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE G 242 " --> pdb=" O GLU G 238 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE G 247 " --> pdb=" O ALA G 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.804A pdb=" N LYS H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU H 223 " --> pdb=" O GLU H 219 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL H 224 " --> pdb=" O LYS H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 236 No H-bonds generated for 'chain 'H' and resid 233 through 236' Processing helix chain 'H' and resid 256 through 264 removed outlier: 4.054A pdb=" N ALA H 260 " --> pdb=" O LYS H 256 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL H 263 " --> pdb=" O CYS H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 268 No H-bonds generated for 'chain 'H' and resid 266 through 268' Processing helix chain 'H' and resid 276 through 279 No H-bonds generated for 'chain 'H' and resid 276 through 279' Processing helix chain 'H' and resid 287 through 298 Processing helix chain 'H' and resid 312 through 315 No H-bonds generated for 'chain 'H' and resid 312 through 315' Processing helix chain 'H' and resid 319 through 321 No H-bonds generated for 'chain 'H' and resid 319 through 321' Processing helix chain 'H' and resid 328 through 340 Processing helix chain 'H' and resid 406 through 409 No H-bonds generated for 'chain 'H' and resid 406 through 409' Processing helix chain 'H' and resid 419 through 426 Processing helix chain 'H' and resid 429 through 432 No H-bonds generated for 'chain 'H' and resid 429 through 432' Processing helix chain 'H' and resid 441 through 449 removed outlier: 3.670A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 197 removed outlier: 4.334A pdb=" N LYS I 195 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 203 Processing helix chain 'I' and resid 206 through 211 Processing helix chain 'I' and resid 231 through 239 removed outlier: 3.637A pdb=" N ALA I 237 " --> pdb=" O ALA I 233 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ASN I 238 " --> pdb=" O LYS I 234 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN I 239 " --> pdb=" O ALA I 235 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 252 Processing helix chain 'I' and resid 261 through 273 removed outlier: 3.811A pdb=" N ARG I 265 " --> pdb=" O PRO I 261 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE I 268 " --> pdb=" O CYS I 264 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LYS I 269 " --> pdb=" O ARG I 265 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL I 270 " --> pdb=" O GLN I 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 286 No H-bonds generated for 'chain 'I' and resid 284 through 286' Processing helix chain 'I' and resid 298 through 315 removed outlier: 3.542A pdb=" N ILE I 302 " --> pdb=" O GLY I 298 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU I 308 " --> pdb=" O ARG I 304 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU I 309 " --> pdb=" O THR I 305 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP I 314 " --> pdb=" O LEU I 310 " (cutoff:3.500A) Processing helix chain 'I' and resid 355 through 360 removed outlier: 3.509A pdb=" N LYS I 360 " --> pdb=" O SER I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 363 through 368 removed outlier: 4.195A pdb=" N LYS I 368 " --> pdb=" O ILE I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 377 through 379 No H-bonds generated for 'chain 'I' and resid 377 through 379' Processing helix chain 'I' and resid 392 through 404 removed outlier: 4.248A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 413 through 426 removed outlier: 3.650A pdb=" N ASN I 426 " --> pdb=" O ARG I 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 138 removed outlier: 4.195A pdb=" N MET J 138 " --> pdb=" O SER J 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 135 through 138' Processing helix chain 'J' and resid 154 through 165 removed outlier: 4.495A pdb=" N ILE J 164 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 177 No H-bonds generated for 'chain 'J' and resid 174 through 177' Processing helix chain 'J' and resid 196 through 205 removed outlier: 4.339A pdb=" N ALA J 203 " --> pdb=" O ALA J 199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS J 204 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS J 205 " --> pdb=" O ALA J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 240 removed outlier: 3.541A pdb=" N ARG J 231 " --> pdb=" O ARG J 228 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU J 232 " --> pdb=" O MET J 229 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE J 234 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL J 235 " --> pdb=" O GLU J 232 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET J 236 " --> pdb=" O LEU J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 275 removed outlier: 3.541A pdb=" N MET J 272 " --> pdb=" O VAL J 268 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU J 274 " --> pdb=" O ARG J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 305 No H-bonds generated for 'chain 'J' and resid 302 through 305' Processing helix chain 'J' and resid 321 through 330 removed outlier: 3.569A pdb=" N ALA J 325 " --> pdb=" O VAL J 321 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 348 No H-bonds generated for 'chain 'J' and resid 345 through 348' Processing helix chain 'J' and resid 358 through 372 removed outlier: 3.707A pdb=" N ALA J 365 " --> pdb=" O VAL J 361 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY J 366 " --> pdb=" O CYS J 362 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU J 372 " --> pdb=" O TYR J 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 389 removed outlier: 4.010A pdb=" N GLY J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL J 389 " --> pdb=" O ALA J 385 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 188 removed outlier: 3.546A pdb=" N ILE K 184 " --> pdb=" O GLN K 180 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ARG K 185 " --> pdb=" O LYS K 181 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA K 187 " --> pdb=" O GLU K 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL K 188 " --> pdb=" O ILE K 184 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 193 No H-bonds generated for 'chain 'K' and resid 190 through 193' Processing helix chain 'K' and resid 196 through 199 No H-bonds generated for 'chain 'K' and resid 196 through 199' Processing helix chain 'K' and resid 222 through 228 removed outlier: 3.776A pdb=" N VAL K 226 " --> pdb=" O LEU K 222 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 264 removed outlier: 4.347A pdb=" N ASP K 256 " --> pdb=" O ARG K 252 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL K 257 " --> pdb=" O MET K 253 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N PHE K 258 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG K 259 " --> pdb=" O ARG K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 277 No H-bonds generated for 'chain 'K' and resid 275 through 277' Processing helix chain 'K' and resid 291 through 304 removed outlier: 3.771A pdb=" N ILE K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU K 299 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 358 removed outlier: 4.040A pdb=" N ARG K 350 " --> pdb=" O ARG K 346 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY K 354 " --> pdb=" O ARG K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 397 removed outlier: 4.734A pdb=" N GLY K 391 " --> pdb=" O MET K 387 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU K 392 " --> pdb=" O GLN K 388 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA K 394 " --> pdb=" O ALA K 390 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ARG K 396 " --> pdb=" O LEU K 392 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LYS K 397 " --> pdb=" O ARG K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 404 through 414 removed outlier: 3.946A pdb=" N GLU K 408 " --> pdb=" O GLN K 404 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA K 412 " --> pdb=" O GLU K 408 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR K 413 " --> pdb=" O GLU K 409 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN K 414 " --> pdb=" O ALA K 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 170 No H-bonds generated for 'chain 'L' and resid 167 through 170' Processing helix chain 'L' and resid 180 through 182 No H-bonds generated for 'chain 'L' and resid 180 through 182' Processing helix chain 'L' and resid 196 through 202 Proline residue: L 200 - end of helix No H-bonds generated for 'chain 'L' and resid 196 through 202' Processing helix chain 'L' and resid 204 through 210 removed outlier: 3.806A pdb=" N VAL L 210 " --> pdb=" O PHE L 207 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 239 removed outlier: 3.550A pdb=" N VAL L 235 " --> pdb=" O LEU L 231 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ALA L 236 " --> pdb=" O ALA L 232 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA L 237 " --> pdb=" O LYS L 233 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR L 238 " --> pdb=" O ALA L 234 " (cutoff:3.500A) Processing helix chain 'L' and resid 258 through 271 removed outlier: 3.826A pdb=" N ILE L 262 " --> pdb=" O GLU L 258 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE L 263 " --> pdb=" O SER L 259 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG L 264 " --> pdb=" O ALA L 260 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA L 268 " --> pdb=" O ARG L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 283 through 286 Processing helix chain 'L' and resid 298 through 311 removed outlier: 3.802A pdb=" N GLN L 302 " --> pdb=" O ASP L 298 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU L 307 " --> pdb=" O ARG L 303 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU L 308 " --> pdb=" O THR L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 338 No H-bonds generated for 'chain 'L' and resid 335 through 338' Processing helix chain 'L' and resid 356 through 365 removed outlier: 4.356A pdb=" N ILE L 360 " --> pdb=" O GLY L 356 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE L 361 " --> pdb=" O ARG L 357 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N HIS L 364 " --> pdb=" O ILE L 360 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR L 365 " --> pdb=" O PHE L 361 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 384 removed outlier: 4.204A pdb=" N ASP L 384 " --> pdb=" O LYS L 381 " (cutoff:3.500A) Processing helix chain 'L' and resid 390 through 402 removed outlier: 3.958A pdb=" N GLY L 399 " --> pdb=" O ALA L 395 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 429 removed outlier: 3.947A pdb=" N ALA L 423 " --> pdb=" O VAL L 419 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU L 424 " --> pdb=" O ARG L 420 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL L 425 " --> pdb=" O LYS L 421 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU L 429 " --> pdb=" O VAL L 425 " (cutoff:3.500A) Processing helix chain 'M' and resid 187 through 201 removed outlier: 4.743A pdb=" N GLU M 195 " --> pdb=" O GLU M 191 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA M 196 " --> pdb=" O GLU M 192 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE M 197 " --> pdb=" O LEU M 193 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU M 199 " --> pdb=" O GLU M 195 " (cutoff:3.500A) Proline residue: M 200 - end of helix Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 228 through 237 removed outlier: 3.588A pdb=" N ALA M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 250 No H-bonds generated for 'chain 'M' and resid 248 through 250' Processing helix chain 'M' and resid 258 through 270 removed outlier: 3.746A pdb=" N ARG M 264 " --> pdb=" O ALA M 260 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE M 267 " --> pdb=" O VAL M 263 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ALA M 268 " --> pdb=" O ARG M 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 286 No H-bonds generated for 'chain 'M' and resid 284 through 286' Processing helix chain 'M' and resid 299 through 310 removed outlier: 3.510A pdb=" N ARG M 303 " --> pdb=" O ARG M 299 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N LEU M 306 " --> pdb=" O GLN M 302 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU M 307 " --> pdb=" O ARG M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 365 removed outlier: 3.619A pdb=" N ALA M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLN M 359 " --> pdb=" O ASP M 355 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE M 360 " --> pdb=" O SER M 356 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE M 363 " --> pdb=" O GLN M 359 " (cutoff:3.500A) Processing helix chain 'M' and resid 376 through 381 removed outlier: 4.560A pdb=" N ARG M 381 " --> pdb=" O GLN M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 388 through 405 removed outlier: 3.765A pdb=" N LYS M 392 " --> pdb=" O GLY M 388 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL M 394 " --> pdb=" O GLN M 390 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR M 395 " --> pdb=" O LEU M 391 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N VAL M 396 " --> pdb=" O LYS M 392 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N GLU M 397 " --> pdb=" O ALA M 393 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET M 400 " --> pdb=" O VAL M 396 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA M 402 " --> pdb=" O ALA M 398 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU M 403 " --> pdb=" O GLY M 399 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN M 405 " --> pdb=" O ILE M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 422 removed outlier: 4.251A pdb=" N SER M 420 " --> pdb=" O VAL M 416 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU M 421 " --> pdb=" O GLU M 417 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL M 422 " --> pdb=" O GLY M 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 416 through 422' Processing sheet with id= A, first strand: chain 'A' and resid 42 through 45 removed outlier: 3.535A pdb=" N LEU A 43 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 52 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 141 through 146 removed outlier: 3.711A pdb=" N TYR A 155 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 154 " --> pdb=" O TYR A 166 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.711A pdb=" N PHE A 234 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 161 through 164 removed outlier: 3.525A pdb=" N VAL B 44 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 47 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU B 210 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 213 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 236 " --> pdb=" O ILE B 213 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 149 removed outlier: 6.578A pdb=" N ALA B 73 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU B 66 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 44 through 49 removed outlier: 4.403A pdb=" N VAL C 45 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 38 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA C 35 " --> pdb=" O VAL C 165 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 74 through 79 removed outlier: 3.647A pdb=" N ALA C 76 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 161 through 164 removed outlier: 3.549A pdb=" N GLN D 162 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 164 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU D 44 " --> pdb=" O THR D 213 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR D 213 " --> pdb=" O LEU D 44 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 71 through 74 removed outlier: 3.648A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 169 through 171 removed outlier: 3.605A pdb=" N GLY E 39 " --> pdb=" O LYS E 170 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL E 47 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL E 46 " --> pdb=" O ILE E 222 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN E 218 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS E 229 " --> pdb=" O CYS E 221 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.785A pdb=" N LEU E 143 " --> pdb=" O ALA E 77 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 35 through 39 removed outlier: 3.739A pdb=" N LEU F 38 " --> pdb=" O VAL F 45 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA F 214 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 48 " --> pdb=" O SER F 212 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR F 223 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 63 through 65 removed outlier: 4.030A pdb=" N GLY F 71 " --> pdb=" O ILE F 135 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU F 133 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY F 136 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N HIS F 143 " --> pdb=" O GLY F 136 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 37 through 40 removed outlier: 3.520A pdb=" N ILE G 38 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 49 " --> pdb=" O ILE G 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL G 50 " --> pdb=" O GLU G 215 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'G' and resid 67 through 69 removed outlier: 3.589A pdb=" N GLN G 68 " --> pdb=" O CYS G 76 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS G 76 " --> pdb=" O GLN G 68 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'G' and resid 137 through 142 Processing sheet with id= Q, first strand: chain 'H' and resid 246 through 248 removed outlier: 6.239A pdb=" N ARG H 373 " --> pdb=" O LEU H 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'I' and resid 246 through 248 removed outlier: 6.030A pdb=" N PHE I 280 " --> pdb=" O ILE I 247 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'J' and resid 186 through 189 removed outlier: 3.693A pdb=" N ILE J 314 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR J 188 " --> pdb=" O ILE J 314 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 277 through 280 removed outlier: 6.678A pdb=" N LYS L 322 " --> pdb=" O ILE L 278 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N MET L 280 " --> pdb=" O LYS L 322 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE L 324 " --> pdb=" O MET L 280 " (cutoff:3.500A) No H-bonds generated for sheet with id= T 548 hydrogen bonds defined for protein. 1533 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: 6.85 Time building geometry restraints manager: 11.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8160 1.34 - 1.45: 4299 1.45 - 1.57: 12509 1.57 - 1.69: 26 1.69 - 1.81: 147 Bond restraints: 25141 Sorted by residual: bond pdb=" C4 ATP I 501 " pdb=" C5 ATP I 501 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C4 ATP J 501 " pdb=" C5 ATP J 501 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.72e+01 bond pdb=" C4 ATP K 501 " pdb=" C5 ATP K 501 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.59e+01 bond pdb=" C5 ATP K 501 " pdb=" C6 ATP K 501 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.29e+01 bond pdb=" C5 ATP I 501 " pdb=" N7 ATP I 501 " ideal model delta sigma weight residual 1.387 1.331 0.056 1.00e-02 1.00e+04 3.12e+01 ... (remaining 25136 not shown) Histogram of bond angle deviations from ideal: 97.70 - 105.47: 519 105.47 - 113.24: 13736 113.24 - 121.01: 11851 121.01 - 128.79: 7859 128.79 - 136.56: 147 Bond angle restraints: 34112 Sorted by residual: angle pdb=" PB ATP J 501 " pdb=" O3B ATP J 501 " pdb=" PG ATP J 501 " ideal model delta sigma weight residual 139.87 116.11 23.76 1.00e+00 1.00e+00 5.65e+02 angle pdb=" PB ATP K 501 " pdb=" O3B ATP K 501 " pdb=" PG ATP K 501 " ideal model delta sigma weight residual 139.87 118.79 21.08 1.00e+00 1.00e+00 4.44e+02 angle pdb=" PB ATP I 501 " pdb=" O3B ATP I 501 " pdb=" PG ATP I 501 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PA ATP I 501 " pdb=" O3A ATP I 501 " pdb=" PB ATP I 501 " ideal model delta sigma weight residual 136.83 117.43 19.40 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PA ATP J 501 " pdb=" O3A ATP J 501 " pdb=" PB ATP J 501 " ideal model delta sigma weight residual 136.83 117.48 19.35 1.00e+00 1.00e+00 3.74e+02 ... (remaining 34107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 15139 35.73 - 71.45: 153 71.45 - 107.18: 11 107.18 - 142.90: 2 142.90 - 178.63: 2 Dihedral angle restraints: 15307 sinusoidal: 5786 harmonic: 9521 Sorted by residual: dihedral pdb=" C5' ADP L 501 " pdb=" O5' ADP L 501 " pdb=" PA ADP L 501 " pdb=" O2A ADP L 501 " ideal model delta sinusoidal sigma weight residual 300.00 121.38 178.63 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP L 501 " pdb=" O3A ADP L 501 " pdb=" PA ADP L 501 " pdb=" PB ADP L 501 " ideal model delta sinusoidal sigma weight residual -60.00 115.03 -175.03 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" CA ILE I 361 " pdb=" C ILE I 361 " pdb=" N LEU I 362 " pdb=" CA LEU I 362 " ideal model delta harmonic sigma weight residual -180.00 -145.56 -34.44 0 5.00e+00 4.00e-02 4.75e+01 ... (remaining 15304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3389 0.081 - 0.161: 556 0.161 - 0.242: 30 0.242 - 0.322: 0 0.322 - 0.403: 1 Chirality restraints: 3976 Sorted by residual: chirality pdb=" CB ILE H 431 " pdb=" CA ILE H 431 " pdb=" CG1 ILE H 431 " pdb=" CG2 ILE H 431 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.05e+00 chirality pdb=" CB VAL D 116 " pdb=" CA VAL D 116 " pdb=" CG1 VAL D 116 " pdb=" CG2 VAL D 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CB VAL C 75 " pdb=" CA VAL C 75 " pdb=" CG1 VAL C 75 " pdb=" CG2 VAL C 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3973 not shown) Planarity restraints: 4421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 173 " 0.018 2.00e-02 2.50e+03 3.53e-02 1.25e+01 pdb=" C LEU J 173 " -0.061 2.00e-02 2.50e+03 pdb=" O LEU J 173 " 0.023 2.00e-02 2.50e+03 pdb=" N PHE J 174 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP H 362 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO H 363 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO H 363 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 363 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 130 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO G 131 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO G 131 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO G 131 " -0.032 5.00e-02 4.00e+02 ... (remaining 4418 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 777 2.65 - 3.21: 27282 3.21 - 3.78: 37276 3.78 - 4.34: 50300 4.34 - 4.90: 76456 Nonbonded interactions: 192091 Sorted by model distance: nonbonded pdb=" OG1 THR K 220 " pdb=" O3B ATP K 501 " model vdw 2.089 2.440 nonbonded pdb=" OG1 THR I 230 " pdb=" O1B ATP I 501 " model vdw 2.099 2.440 nonbonded pdb=" OG1 THR M 370 " pdb=" O VAL M 410 " model vdw 2.147 2.440 nonbonded pdb=" O ALA H 430 " pdb=" N ARG H 435 " model vdw 2.172 2.520 nonbonded pdb=" O PHE H 295 " pdb=" N ARG H 299 " model vdw 2.177 2.520 ... (remaining 192086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 2.100 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: 0.020 Extract box with map and model: 9.160 Check model and map are aligned: 0.350 Set scattering table: 0.230 Process input model: 65.790 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.011 0.117 25141 Z= 0.706 Angle : 1.074 23.763 34112 Z= 0.630 Chirality : 0.057 0.403 3976 Planarity : 0.006 0.060 4421 Dihedral : 13.016 178.628 9189 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.76 % Favored : 83.24 % Rotamer: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.12), residues: 3288 helix: -3.88 (0.10), residues: 979 sheet: -4.35 (0.18), residues: 363 loop : -3.19 (0.14), residues: 1946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 159 HIS 0.018 0.003 HIS L 273 PHE 0.032 0.003 PHE D 11 TYR 0.027 0.003 TYR A 162 ARG 0.017 0.002 ARG D 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 641 time to evaluate : 3.122 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: A 26 TYR cc_start: 0.7442 (m-10) cc_final: 0.7174 (m-10) REVERT: A 49 ASP cc_start: 0.8616 (t70) cc_final: 0.8163 (t0) REVERT: A 89 ASP cc_start: 0.8463 (p0) cc_final: 0.7453 (t0) REVERT: A 106 TYR cc_start: 0.7791 (t80) cc_final: 0.6624 (m-10) REVERT: B 97 TYR cc_start: 0.6933 (t80) cc_final: 0.6508 (t80) REVERT: B 99 ARG cc_start: 0.8282 (mtt90) cc_final: 0.7897 (mtt90) REVERT: B 111 VAL cc_start: 0.9021 (p) cc_final: 0.8761 (t) REVERT: B 241 GLN cc_start: 0.7637 (pm20) cc_final: 0.7279 (pm20) REVERT: C 1 MET cc_start: 0.5345 (ptm) cc_final: 0.4811 (ptt) REVERT: C 27 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7874 (tm-30) REVERT: C 129 ARG cc_start: 0.8664 (ptt-90) cc_final: 0.8446 (ptt90) REVERT: C 213 PHE cc_start: 0.8274 (p90) cc_final: 0.7761 (p90) REVERT: C 235 ILE cc_start: 0.8816 (mt) cc_final: 0.8563 (mt) REVERT: D 149 GLN cc_start: 0.7091 (tm130) cc_final: 0.6544 (tm-30) REVERT: E 90 GLU cc_start: 0.8517 (tt0) cc_final: 0.7850 (tp30) REVERT: E 182 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7581 (tm-30) REVERT: F 24 TYR cc_start: 0.8846 (m-80) cc_final: 0.8412 (m-80) REVERT: F 173 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8185 (mt-10) REVERT: G 86 ARG cc_start: 0.7723 (tpp-160) cc_final: 0.7322 (tpt170) REVERT: G 132 PHE cc_start: 0.7681 (m-10) cc_final: 0.7475 (m-10) REVERT: G 212 PHE cc_start: 0.8622 (p90) cc_final: 0.8216 (p90) REVERT: G 225 ASN cc_start: 0.7292 (t0) cc_final: 0.7089 (t0) REVERT: G 242 PHE cc_start: 0.7279 (t80) cc_final: 0.6937 (t80) REVERT: H 376 GLU cc_start: 0.7089 (tm-30) cc_final: 0.6605 (tm-30) REVERT: H 392 HIS cc_start: 0.8050 (m-70) cc_final: 0.7539 (m90) REVERT: I 222 TYR cc_start: 0.6680 (m-80) cc_final: 0.6414 (m-80) REVERT: I 306 MET cc_start: 0.8760 (tmm) cc_final: 0.8513 (tmm) REVERT: I 348 ILE cc_start: 0.8812 (mp) cc_final: 0.8521 (mp) REVERT: I 398 GLU cc_start: 0.8492 (tp30) cc_final: 0.8260 (tp30) REVERT: J 137 MET cc_start: 0.8779 (pmm) cc_final: 0.8492 (pmm) REVERT: J 156 GLN cc_start: 0.8940 (mp10) cc_final: 0.8275 (mp10) REVERT: J 227 SER cc_start: 0.9206 (m) cc_final: 0.8697 (t) REVERT: J 247 MET cc_start: 0.8762 (mtt) cc_final: 0.8276 (mtt) REVERT: J 292 MET cc_start: 0.8458 (ttm) cc_final: 0.8223 (mtm) REVERT: J 327 ILE cc_start: 0.9415 (mm) cc_final: 0.9185 (mm) REVERT: J 368 TYR cc_start: 0.7698 (t80) cc_final: 0.6931 (t80) REVERT: K 164 ASN cc_start: 0.8762 (p0) cc_final: 0.8549 (p0) REVERT: K 196 ASP cc_start: 0.9037 (p0) cc_final: 0.8778 (p0) REVERT: K 238 ASN cc_start: 0.9102 (p0) cc_final: 0.8893 (p0) REVERT: K 289 ASP cc_start: 0.8695 (p0) cc_final: 0.8384 (p0) REVERT: K 322 ASP cc_start: 0.8251 (p0) cc_final: 0.8042 (p0) REVERT: K 346 ARG cc_start: 0.8294 (mtm-85) cc_final: 0.7594 (ppt170) REVERT: L 221 TYR cc_start: 0.8390 (p90) cc_final: 0.8136 (p90) REVERT: L 279 PHE cc_start: 0.8592 (t80) cc_final: 0.7744 (t80) REVERT: L 328 ASN cc_start: 0.8898 (m110) cc_final: 0.8471 (m-40) REVERT: L 359 GLU cc_start: 0.9302 (mp0) cc_final: 0.8994 (mp0) outliers start: 0 outliers final: 0 residues processed: 641 average time/residue: 0.4158 time to fit residues: 396.1485 Evaluate side-chains 422 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 275 optimal weight: 0.3980 chunk 247 optimal weight: 0.1980 chunk 137 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 296 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 GLN A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 21 GLN C 103 ASN C 177 GLN C 233 GLN D 16 HIS D 19 GLN E 216 ASN F 90 GLN F 210 ASN H 392 HIS I 238 ASN I 418 GLN K 244 HIS L 311 GLN L 328 ASN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25141 Z= 0.197 Angle : 0.737 8.772 34112 Z= 0.372 Chirality : 0.047 0.173 3976 Planarity : 0.005 0.048 4421 Dihedral : 9.574 156.687 3694 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.85 % Favored : 91.15 % Rotamer: Outliers : 0.20 % Allowed : 5.00 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -4.18 (0.13), residues: 3288 helix: -2.69 (0.12), residues: 1113 sheet: -3.32 (0.22), residues: 381 loop : -2.73 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 218 HIS 0.006 0.001 HIS M 364 PHE 0.023 0.002 PHE A 205 TYR 0.021 0.002 TYR H 249 ARG 0.007 0.001 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 619 time to evaluate : 2.633 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: A 49 ASP cc_start: 0.8362 (t70) cc_final: 0.8093 (t0) REVERT: A 89 ASP cc_start: 0.8406 (p0) cc_final: 0.7663 (t0) REVERT: A 92 ASN cc_start: 0.7988 (p0) cc_final: 0.7372 (t0) REVERT: A 106 TYR cc_start: 0.7880 (t80) cc_final: 0.6821 (m-10) REVERT: A 162 TYR cc_start: 0.6822 (p90) cc_final: 0.6512 (p90) REVERT: A 231 ASP cc_start: 0.7395 (t70) cc_final: 0.7036 (t70) REVERT: B 117 ILE cc_start: 0.8920 (mm) cc_final: 0.8562 (mm) REVERT: B 241 GLN cc_start: 0.7811 (pm20) cc_final: 0.7363 (pm20) REVERT: C 1 MET cc_start: 0.4980 (ptm) cc_final: 0.4494 (ptt) REVERT: C 114 ARG cc_start: 0.8789 (tpm170) cc_final: 0.8501 (tpp-160) REVERT: C 120 GLN cc_start: 0.8351 (tm-30) cc_final: 0.7984 (tm-30) REVERT: C 213 PHE cc_start: 0.8112 (p90) cc_final: 0.7793 (p90) REVERT: D 56 ASP cc_start: 0.7196 (t70) cc_final: 0.6896 (m-30) REVERT: D 120 TYR cc_start: 0.8137 (m-80) cc_final: 0.7545 (m-80) REVERT: D 149 GLN cc_start: 0.7298 (tm-30) cc_final: 0.6987 (tm-30) REVERT: D 163 THR cc_start: 0.9466 (p) cc_final: 0.9170 (t) REVERT: E 84 ASP cc_start: 0.8664 (p0) cc_final: 0.8364 (p0) REVERT: E 90 GLU cc_start: 0.8463 (tt0) cc_final: 0.7705 (tp30) REVERT: F 24 TYR cc_start: 0.8726 (m-80) cc_final: 0.8357 (m-80) REVERT: F 128 TYR cc_start: 0.8140 (m-10) cc_final: 0.7926 (m-10) REVERT: F 144 LEU cc_start: 0.8966 (tp) cc_final: 0.8646 (tp) REVERT: F 145 LEU cc_start: 0.8579 (mt) cc_final: 0.8335 (mt) REVERT: F 147 PHE cc_start: 0.8563 (t80) cc_final: 0.8080 (t80) REVERT: F 228 GLU cc_start: 0.8425 (mp0) cc_final: 0.8190 (mm-30) REVERT: G 18 ASP cc_start: 0.8924 (p0) cc_final: 0.8692 (p0) REVERT: G 53 LEU cc_start: 0.8596 (tt) cc_final: 0.8084 (pp) REVERT: G 212 PHE cc_start: 0.8716 (p90) cc_final: 0.8437 (p90) REVERT: G 225 ASN cc_start: 0.6923 (t0) cc_final: 0.6674 (t0) REVERT: H 392 HIS cc_start: 0.7901 (m90) cc_final: 0.7338 (m90) REVERT: H 448 ASP cc_start: 0.8999 (t0) cc_final: 0.8719 (t0) REVERT: I 219 VAL cc_start: 0.7482 (p) cc_final: 0.6987 (m) REVERT: I 222 TYR cc_start: 0.7006 (m-80) cc_final: 0.6728 (m-80) REVERT: I 306 MET cc_start: 0.8421 (tmm) cc_final: 0.8207 (tmm) REVERT: I 326 MET cc_start: 0.8112 (pmm) cc_final: 0.7892 (pmm) REVERT: I 355 LEU cc_start: 0.8786 (tt) cc_final: 0.8387 (mt) REVERT: I 417 LYS cc_start: 0.9064 (tttm) cc_final: 0.8723 (tptt) REVERT: J 236 MET cc_start: 0.8921 (ppp) cc_final: 0.8167 (ppp) REVERT: J 327 ILE cc_start: 0.9385 (mm) cc_final: 0.9076 (mm) REVERT: J 328 LEU cc_start: 0.9436 (tt) cc_final: 0.9221 (pp) REVERT: J 359 LYS cc_start: 0.9122 (ptmt) cc_final: 0.8806 (ttpt) REVERT: K 161 MET cc_start: 0.7611 (ppp) cc_final: 0.7162 (ppp) REVERT: K 273 GLU cc_start: 0.7541 (tt0) cc_final: 0.7341 (tt0) REVERT: K 285 GLN cc_start: 0.9234 (mm-40) cc_final: 0.8953 (mm-40) REVERT: K 298 GLU cc_start: 0.8480 (pp20) cc_final: 0.8254 (pp20) REVERT: K 322 ASP cc_start: 0.8135 (p0) cc_final: 0.7910 (p0) REVERT: K 339 GLU cc_start: 0.8672 (pm20) cc_final: 0.8419 (pm20) REVERT: K 346 ARG cc_start: 0.8157 (mtm-85) cc_final: 0.7628 (ptt90) REVERT: L 221 TYR cc_start: 0.8559 (p90) cc_final: 0.8323 (p90) REVERT: L 306 MET cc_start: 0.8524 (mtt) cc_final: 0.8164 (mtt) REVERT: L 328 ASN cc_start: 0.8629 (m-40) cc_final: 0.8211 (m-40) REVERT: L 349 ILE cc_start: 0.9032 (pt) cc_final: 0.8507 (pt) REVERT: M 265 ASP cc_start: 0.8540 (p0) cc_final: 0.8228 (m-30) outliers start: 5 outliers final: 1 residues processed: 622 average time/residue: 0.3779 time to fit residues: 357.5974 Evaluate side-chains 448 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 447 time to evaluate : 2.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 164 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 246 optimal weight: 0.0670 chunk 201 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 296 optimal weight: 9.9990 chunk 320 optimal weight: 3.9990 chunk 264 optimal weight: 9.9990 chunk 294 optimal weight: 0.3980 chunk 101 optimal weight: 0.3980 chunk 237 optimal weight: 4.9990 overall best weight: 1.7722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN B 123 GLN B 218 ASN C 103 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN I 238 ASN M 310 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25141 Z= 0.210 Angle : 0.678 8.367 34112 Z= 0.343 Chirality : 0.045 0.166 3976 Planarity : 0.004 0.094 4421 Dihedral : 8.589 124.036 3694 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.12 % Allowed : 5.48 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -3.46 (0.14), residues: 3288 helix: -2.08 (0.14), residues: 1121 sheet: -2.81 (0.23), residues: 420 loop : -2.30 (0.15), residues: 1747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 218 HIS 0.004 0.001 HIS M 364 PHE 0.015 0.001 PHE A 205 TYR 0.015 0.001 TYR L 221 ARG 0.007 0.001 ARG G 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 561 time to evaluate : 3.082 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: A 41 ASN cc_start: 0.8528 (m110) cc_final: 0.8151 (m-40) REVERT: A 49 ASP cc_start: 0.8317 (t70) cc_final: 0.7856 (t0) REVERT: A 89 ASP cc_start: 0.8459 (p0) cc_final: 0.7623 (t0) REVERT: A 92 ASN cc_start: 0.8116 (p0) cc_final: 0.7870 (p0) REVERT: A 162 TYR cc_start: 0.7032 (p90) cc_final: 0.6747 (p90) REVERT: A 231 ASP cc_start: 0.7445 (t70) cc_final: 0.7113 (t70) REVERT: B 117 ILE cc_start: 0.8892 (mm) cc_final: 0.8569 (mm) REVERT: B 119 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7656 (tp-100) REVERT: B 241 GLN cc_start: 0.7675 (pm20) cc_final: 0.7328 (pm20) REVERT: C 1 MET cc_start: 0.4912 (ptm) cc_final: 0.4598 (ptt) REVERT: C 114 ARG cc_start: 0.8932 (tpm170) cc_final: 0.8617 (tpp-160) REVERT: C 120 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8080 (tm-30) REVERT: C 134 SER cc_start: 0.9409 (t) cc_final: 0.9038 (m) REVERT: D 16 HIS cc_start: 0.8717 (m90) cc_final: 0.8334 (m90) REVERT: D 120 TYR cc_start: 0.8262 (m-80) cc_final: 0.7652 (m-80) REVERT: D 149 GLN cc_start: 0.7368 (tm-30) cc_final: 0.6943 (tm-30) REVERT: D 163 THR cc_start: 0.9585 (p) cc_final: 0.9331 (t) REVERT: E 84 ASP cc_start: 0.8629 (p0) cc_final: 0.8379 (p0) REVERT: E 90 GLU cc_start: 0.8387 (tt0) cc_final: 0.8166 (mt-10) REVERT: E 121 LEU cc_start: 0.7775 (mt) cc_final: 0.7510 (tp) REVERT: F 87 TYR cc_start: 0.8954 (t80) cc_final: 0.8555 (t80) REVERT: F 90 GLN cc_start: 0.8377 (mp-120) cc_final: 0.7706 (mp10) REVERT: F 147 PHE cc_start: 0.8315 (t80) cc_final: 0.8030 (t80) REVERT: G 18 ASP cc_start: 0.8893 (p0) cc_final: 0.8666 (p0) REVERT: G 33 ASN cc_start: 0.8766 (m110) cc_final: 0.8526 (m-40) REVERT: G 53 LEU cc_start: 0.8662 (tt) cc_final: 0.8247 (pt) REVERT: G 110 PRO cc_start: 0.9072 (Cg_exo) cc_final: 0.8796 (Cg_endo) REVERT: G 225 ASN cc_start: 0.6880 (t0) cc_final: 0.6573 (t0) REVERT: H 392 HIS cc_start: 0.7747 (m90) cc_final: 0.7220 (m90) REVERT: H 448 ASP cc_start: 0.9241 (t0) cc_final: 0.8902 (t0) REVERT: I 193 GLU cc_start: 0.8926 (mp0) cc_final: 0.8623 (mp0) REVERT: I 219 VAL cc_start: 0.7600 (p) cc_final: 0.7013 (m) REVERT: I 222 TYR cc_start: 0.7053 (m-80) cc_final: 0.6782 (m-80) REVERT: I 289 THR cc_start: 0.8562 (p) cc_final: 0.8330 (p) REVERT: I 326 MET cc_start: 0.8117 (pmm) cc_final: 0.7800 (pmm) REVERT: I 343 ARG cc_start: 0.7082 (mtt90) cc_final: 0.6768 (mtt90) REVERT: I 355 LEU cc_start: 0.8847 (tt) cc_final: 0.8476 (mt) REVERT: I 417 LYS cc_start: 0.9049 (tttm) cc_final: 0.8622 (tptt) REVERT: J 161 LYS cc_start: 0.8571 (mtmm) cc_final: 0.8128 (tptt) REVERT: J 236 MET cc_start: 0.8940 (ppp) cc_final: 0.8351 (ppp) REVERT: J 240 HIS cc_start: 0.8184 (m90) cc_final: 0.7892 (m90) REVERT: J 269 GLN cc_start: 0.9032 (tt0) cc_final: 0.8381 (tm-30) REVERT: J 327 ILE cc_start: 0.9375 (mm) cc_final: 0.9108 (mm) REVERT: J 359 LYS cc_start: 0.9175 (ptmt) cc_final: 0.8974 (ttpt) REVERT: J 368 TYR cc_start: 0.7910 (t80) cc_final: 0.7493 (t80) REVERT: K 161 MET cc_start: 0.7887 (ppp) cc_final: 0.7497 (ppp) REVERT: K 221 MET cc_start: 0.8442 (ppp) cc_final: 0.8203 (ppp) REVERT: K 260 LEU cc_start: 0.9293 (tp) cc_final: 0.9091 (tp) REVERT: K 285 GLN cc_start: 0.9283 (mm-40) cc_final: 0.9032 (mm-40) REVERT: K 292 VAL cc_start: 0.8864 (m) cc_final: 0.8553 (p) REVERT: K 298 GLU cc_start: 0.8533 (pp20) cc_final: 0.8315 (pp20) REVERT: K 322 ASP cc_start: 0.8246 (p0) cc_final: 0.8011 (p0) REVERT: K 325 ASP cc_start: 0.9012 (p0) cc_final: 0.8759 (p0) REVERT: K 346 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7572 (ppt170) REVERT: L 328 ASN cc_start: 0.8603 (m-40) cc_final: 0.8195 (m-40) REVERT: L 386 PHE cc_start: 0.8415 (m-80) cc_final: 0.7507 (m-80) REVERT: M 322 LYS cc_start: 0.3695 (mmmt) cc_final: 0.3355 (mttt) outliers start: 3 outliers final: 0 residues processed: 564 average time/residue: 0.3993 time to fit residues: 348.5522 Evaluate side-chains 430 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 3.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 293 optimal weight: 10.0000 chunk 222 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 297 optimal weight: 5.9990 chunk 315 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 282 optimal weight: 0.0050 chunk 84 optimal weight: 4.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN B 218 ASN C 103 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25141 Z= 0.201 Angle : 0.658 8.355 34112 Z= 0.331 Chirality : 0.045 0.198 3976 Planarity : 0.004 0.056 4421 Dihedral : 8.046 91.979 3694 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -3.09 (0.14), residues: 3288 helix: -1.72 (0.14), residues: 1139 sheet: -2.41 (0.23), residues: 437 loop : -2.16 (0.15), residues: 1712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 160 HIS 0.020 0.001 HIS G 204 PHE 0.020 0.001 PHE C 213 TYR 0.030 0.001 TYR F 24 ARG 0.006 0.001 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 542 time to evaluate : 3.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8322 (t70) cc_final: 0.7810 (t0) REVERT: A 89 ASP cc_start: 0.8497 (p0) cc_final: 0.7597 (t0) REVERT: A 92 ASN cc_start: 0.8115 (p0) cc_final: 0.7866 (p0) REVERT: A 162 TYR cc_start: 0.6955 (p90) cc_final: 0.6710 (p90) REVERT: A 231 ASP cc_start: 0.7625 (t70) cc_final: 0.7228 (t70) REVERT: B 117 ILE cc_start: 0.8903 (mm) cc_final: 0.8596 (mm) REVERT: B 241 GLN cc_start: 0.7564 (pm20) cc_final: 0.7260 (pm20) REVERT: C 1 MET cc_start: 0.4799 (ptm) cc_final: 0.4498 (ptt) REVERT: C 114 ARG cc_start: 0.8913 (tpm170) cc_final: 0.8633 (tpp-160) REVERT: C 120 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 134 SER cc_start: 0.9316 (t) cc_final: 0.9035 (m) REVERT: D 16 HIS cc_start: 0.8733 (m90) cc_final: 0.8332 (m90) REVERT: D 149 GLN cc_start: 0.7564 (tm-30) cc_final: 0.6992 (tm-30) REVERT: D 168 SER cc_start: 0.9284 (p) cc_final: 0.9073 (p) REVERT: D 176 GLU cc_start: 0.7511 (mp0) cc_final: 0.6756 (mt-10) REVERT: E 84 ASP cc_start: 0.8609 (p0) cc_final: 0.8390 (p0) REVERT: E 90 GLU cc_start: 0.8367 (tt0) cc_final: 0.8154 (mt-10) REVERT: E 121 LEU cc_start: 0.8288 (mt) cc_final: 0.8072 (tp) REVERT: F 102 LYS cc_start: 0.8263 (mmmt) cc_final: 0.7440 (mtmt) REVERT: G 18 ASP cc_start: 0.8844 (p0) cc_final: 0.8602 (p0) REVERT: G 33 ASN cc_start: 0.8793 (m110) cc_final: 0.8588 (m-40) REVERT: G 53 LEU cc_start: 0.8630 (tt) cc_final: 0.8333 (pp) REVERT: G 110 PRO cc_start: 0.9116 (Cg_exo) cc_final: 0.8832 (Cg_endo) REVERT: G 206 ASP cc_start: 0.9028 (p0) cc_final: 0.8726 (p0) REVERT: G 212 PHE cc_start: 0.8990 (p90) cc_final: 0.8505 (p90) REVERT: G 225 ASN cc_start: 0.6928 (t0) cc_final: 0.6653 (t0) REVERT: H 383 GLU cc_start: 0.8551 (tp30) cc_final: 0.8285 (tp30) REVERT: H 448 ASP cc_start: 0.9282 (t0) cc_final: 0.9000 (t0) REVERT: I 193 GLU cc_start: 0.9050 (mp0) cc_final: 0.8698 (mp0) REVERT: I 222 TYR cc_start: 0.7207 (m-80) cc_final: 0.6872 (m-80) REVERT: I 343 ARG cc_start: 0.7055 (mtt90) cc_final: 0.6648 (mtm-85) REVERT: I 355 LEU cc_start: 0.8844 (tt) cc_final: 0.8504 (mt) REVERT: I 395 MET cc_start: 0.9037 (tpp) cc_final: 0.8743 (tpp) REVERT: I 417 LYS cc_start: 0.9057 (tttm) cc_final: 0.8630 (tptt) REVERT: J 236 MET cc_start: 0.8915 (ppp) cc_final: 0.8519 (ppp) REVERT: J 249 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7588 (mm-30) REVERT: J 269 GLN cc_start: 0.9140 (tt0) cc_final: 0.8322 (tm-30) REVERT: J 327 ILE cc_start: 0.9355 (mm) cc_final: 0.9103 (mm) REVERT: J 328 LEU cc_start: 0.9522 (tt) cc_final: 0.9272 (pp) REVERT: J 359 LYS cc_start: 0.9197 (ptmt) cc_final: 0.8986 (ttpt) REVERT: K 161 MET cc_start: 0.8049 (ppp) cc_final: 0.7637 (ppp) REVERT: K 221 MET cc_start: 0.8567 (ppp) cc_final: 0.8296 (ppp) REVERT: K 285 GLN cc_start: 0.9290 (mm-40) cc_final: 0.9069 (mm-40) REVERT: K 292 VAL cc_start: 0.8745 (m) cc_final: 0.8408 (p) REVERT: K 298 GLU cc_start: 0.8581 (pp20) cc_final: 0.8331 (pp20) REVERT: K 325 ASP cc_start: 0.8990 (p0) cc_final: 0.8661 (p0) REVERT: K 334 LEU cc_start: 0.8780 (mt) cc_final: 0.8181 (mt) REVERT: K 346 ARG cc_start: 0.8182 (mtm-85) cc_final: 0.7567 (ppt170) REVERT: L 281 ASP cc_start: 0.8202 (p0) cc_final: 0.6660 (p0) REVERT: L 328 ASN cc_start: 0.8558 (m-40) cc_final: 0.8113 (m-40) REVERT: L 382 MET cc_start: 0.8441 (ppp) cc_final: 0.7858 (ppp) REVERT: L 386 PHE cc_start: 0.8227 (m-80) cc_final: 0.8016 (m-80) outliers start: 2 outliers final: 0 residues processed: 543 average time/residue: 0.3388 time to fit residues: 290.1745 Evaluate side-chains 434 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 262 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 chunk 4 optimal weight: 6.9990 chunk 234 optimal weight: 0.4980 chunk 130 optimal weight: 10.0000 chunk 268 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 282 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN C 103 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 25141 Z= 0.430 Angle : 0.811 10.133 34112 Z= 0.418 Chirality : 0.049 0.209 3976 Planarity : 0.005 0.062 4421 Dihedral : 8.702 91.485 3694 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 0.08 % Allowed : 5.65 % Favored : 94.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -3.12 (0.14), residues: 3288 helix: -1.76 (0.14), residues: 1148 sheet: -2.33 (0.23), residues: 446 loop : -2.18 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 179 HIS 0.008 0.002 HIS L 273 PHE 0.031 0.002 PHE M 279 TYR 0.018 0.002 TYR D 232 ARG 0.006 0.001 ARG J 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 482 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8341 (p0) cc_final: 0.7876 (t0) REVERT: A 231 ASP cc_start: 0.7706 (t70) cc_final: 0.7344 (t70) REVERT: B 99 ARG cc_start: 0.8441 (mtt90) cc_final: 0.8217 (mtt90) REVERT: B 117 ILE cc_start: 0.8904 (mm) cc_final: 0.8584 (mm) REVERT: B 241 GLN cc_start: 0.7677 (pm20) cc_final: 0.7323 (pm20) REVERT: C 1 MET cc_start: 0.5034 (ptm) cc_final: 0.4769 (ptt) REVERT: C 124 GLN cc_start: 0.8215 (tt0) cc_final: 0.7946 (tt0) REVERT: C 178 MET cc_start: 0.8626 (pmm) cc_final: 0.8372 (pmm) REVERT: D 16 HIS cc_start: 0.8817 (m90) cc_final: 0.8328 (m90) REVERT: E 121 LEU cc_start: 0.8506 (mt) cc_final: 0.8254 (tp) REVERT: G 9 ASP cc_start: 0.7152 (p0) cc_final: 0.6771 (p0) REVERT: G 18 ASP cc_start: 0.9046 (p0) cc_final: 0.8828 (p0) REVERT: G 53 LEU cc_start: 0.8593 (tt) cc_final: 0.8313 (pp) REVERT: G 110 PRO cc_start: 0.9211 (Cg_exo) cc_final: 0.8966 (Cg_endo) REVERT: G 150 MET cc_start: 0.8037 (ttm) cc_final: 0.7520 (tpp) REVERT: G 169 ARG cc_start: 0.8477 (mtm110) cc_final: 0.8163 (mtm-85) REVERT: G 206 ASP cc_start: 0.9018 (p0) cc_final: 0.8765 (p0) REVERT: G 212 PHE cc_start: 0.8865 (p90) cc_final: 0.8426 (p90) REVERT: G 225 ASN cc_start: 0.7144 (t0) cc_final: 0.6925 (t0) REVERT: G 237 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8552 (tp40) REVERT: H 428 MET cc_start: 0.7162 (tpt) cc_final: 0.6533 (tpp) REVERT: H 448 ASP cc_start: 0.9437 (t0) cc_final: 0.9223 (t0) REVERT: I 222 TYR cc_start: 0.7174 (m-80) cc_final: 0.6631 (m-80) REVERT: I 343 ARG cc_start: 0.7288 (mtt90) cc_final: 0.6678 (mtm-85) REVERT: J 222 TYR cc_start: 0.8278 (m-80) cc_final: 0.7997 (m-80) REVERT: J 227 SER cc_start: 0.9320 (m) cc_final: 0.8916 (t) REVERT: J 236 MET cc_start: 0.8913 (ppp) cc_final: 0.8687 (ppp) REVERT: J 249 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7608 (mm-30) REVERT: J 269 GLN cc_start: 0.9247 (tt0) cc_final: 0.8379 (tm-30) REVERT: J 367 MET cc_start: 0.8646 (tpt) cc_final: 0.8406 (tpp) REVERT: K 161 MET cc_start: 0.8358 (ppp) cc_final: 0.8057 (ppp) REVERT: K 221 MET cc_start: 0.8731 (ppp) cc_final: 0.8398 (ppp) REVERT: K 222 LEU cc_start: 0.9609 (tp) cc_final: 0.9384 (tt) REVERT: K 253 MET cc_start: 0.8584 (ppp) cc_final: 0.8228 (tmm) REVERT: K 285 GLN cc_start: 0.9249 (mm-40) cc_final: 0.9035 (mm-40) REVERT: K 292 VAL cc_start: 0.9174 (m) cc_final: 0.8952 (p) REVERT: K 298 GLU cc_start: 0.8723 (pp20) cc_final: 0.8380 (pp20) REVERT: K 325 ASP cc_start: 0.9177 (p0) cc_final: 0.8728 (p0) REVERT: K 346 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.7771 (ppt170) REVERT: L 203 ASN cc_start: 0.8818 (p0) cc_final: 0.8528 (p0) REVERT: L 281 ASP cc_start: 0.7769 (p0) cc_final: 0.7408 (p0) REVERT: L 328 ASN cc_start: 0.8673 (m-40) cc_final: 0.8224 (m-40) REVERT: L 382 MET cc_start: 0.8631 (ppp) cc_final: 0.8073 (ppp) REVERT: L 386 PHE cc_start: 0.8526 (m-80) cc_final: 0.8261 (m-80) outliers start: 2 outliers final: 0 residues processed: 483 average time/residue: 0.3433 time to fit residues: 260.7881 Evaluate side-chains 403 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 106 optimal weight: 2.9990 chunk 283 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 315 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN I 238 ASN ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN M 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25141 Z= 0.255 Angle : 0.694 8.390 34112 Z= 0.352 Chirality : 0.046 0.175 3976 Planarity : 0.004 0.048 4421 Dihedral : 8.250 91.049 3694 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 0.04 % Allowed : 3.53 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.85 (0.14), residues: 3288 helix: -1.54 (0.14), residues: 1147 sheet: -2.10 (0.23), residues: 454 loop : -2.05 (0.16), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 404 HIS 0.004 0.001 HIS A 209 PHE 0.032 0.002 PHE D 174 TYR 0.021 0.002 TYR L 269 ARG 0.005 0.000 ARG J 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 499 time to evaluate : 2.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8418 (p0) cc_final: 0.7655 (t0) REVERT: A 231 ASP cc_start: 0.7477 (t70) cc_final: 0.7020 (t70) REVERT: B 4 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7335 (ttp80) REVERT: C 114 ARG cc_start: 0.8850 (tpp-160) cc_final: 0.8533 (tpp-160) REVERT: C 178 MET cc_start: 0.8611 (pmm) cc_final: 0.8367 (pmm) REVERT: D 16 HIS cc_start: 0.8834 (m90) cc_final: 0.8366 (m90) REVERT: D 19 GLN cc_start: 0.8823 (mm110) cc_final: 0.8573 (mm-40) REVERT: E 84 ASP cc_start: 0.8566 (p0) cc_final: 0.8351 (p0) REVERT: E 121 LEU cc_start: 0.8438 (mt) cc_final: 0.8187 (tp) REVERT: F 86 ASN cc_start: 0.9003 (m-40) cc_final: 0.8635 (t0) REVERT: F 102 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7692 (mtmt) REVERT: G 9 ASP cc_start: 0.7118 (p0) cc_final: 0.6681 (p0) REVERT: G 84 ASP cc_start: 0.8639 (p0) cc_final: 0.8362 (p0) REVERT: G 110 PRO cc_start: 0.9250 (Cg_exo) cc_final: 0.9018 (Cg_endo) REVERT: G 150 MET cc_start: 0.7983 (ttm) cc_final: 0.7470 (tpp) REVERT: G 206 ASP cc_start: 0.9058 (p0) cc_final: 0.8794 (p0) REVERT: G 212 PHE cc_start: 0.8805 (p90) cc_final: 0.8476 (p90) REVERT: G 225 ASN cc_start: 0.7093 (t0) cc_final: 0.6880 (t0) REVERT: G 237 GLN cc_start: 0.8913 (mm-40) cc_final: 0.8553 (tp40) REVERT: H 428 MET cc_start: 0.7075 (tpt) cc_final: 0.6393 (tpp) REVERT: I 222 TYR cc_start: 0.7151 (m-80) cc_final: 0.6675 (m-80) REVERT: J 157 ILE cc_start: 0.9669 (tt) cc_final: 0.9329 (tt) REVERT: J 227 SER cc_start: 0.9279 (m) cc_final: 0.8887 (t) REVERT: J 236 MET cc_start: 0.8760 (ppp) cc_final: 0.8231 (ppp) REVERT: J 239 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8462 (tm-30) REVERT: J 249 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7644 (mm-30) REVERT: J 269 GLN cc_start: 0.9185 (tt0) cc_final: 0.8406 (tm-30) REVERT: J 367 MET cc_start: 0.8790 (tpt) cc_final: 0.8484 (tpt) REVERT: K 161 MET cc_start: 0.8366 (ppp) cc_final: 0.8113 (ppp) REVERT: K 221 MET cc_start: 0.8707 (ppp) cc_final: 0.8293 (ppp) REVERT: K 222 LEU cc_start: 0.9608 (tp) cc_final: 0.9403 (tt) REVERT: K 235 ILE cc_start: 0.8491 (pt) cc_final: 0.7784 (mm) REVERT: K 253 MET cc_start: 0.8128 (ppp) cc_final: 0.7589 (tmm) REVERT: K 273 GLU cc_start: 0.7142 (tt0) cc_final: 0.6740 (tt0) REVERT: K 285 GLN cc_start: 0.9262 (mm-40) cc_final: 0.9036 (mm-40) REVERT: K 292 VAL cc_start: 0.9102 (m) cc_final: 0.8865 (p) REVERT: K 303 MET cc_start: 0.9009 (mtp) cc_final: 0.8683 (tpp) REVERT: K 325 ASP cc_start: 0.9141 (p0) cc_final: 0.8740 (p0) REVERT: K 346 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7756 (ppt170) REVERT: L 203 ASN cc_start: 0.8707 (p0) cc_final: 0.8342 (p0) REVERT: L 281 ASP cc_start: 0.7606 (p0) cc_final: 0.7315 (p0) REVERT: L 328 ASN cc_start: 0.8560 (m-40) cc_final: 0.8100 (m-40) REVERT: L 339 ARG cc_start: 0.7941 (ttp80) cc_final: 0.7473 (ttp80) REVERT: L 382 MET cc_start: 0.8682 (ppp) cc_final: 0.7933 (ppp) REVERT: L 386 PHE cc_start: 0.8377 (m-80) cc_final: 0.8172 (m-80) outliers start: 1 outliers final: 0 residues processed: 499 average time/residue: 0.3506 time to fit residues: 277.2266 Evaluate side-chains 416 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 304 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 179 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 314 optimal weight: 20.0000 chunk 196 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 145 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN C 177 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 ASN ** K 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 189 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25141 Z= 0.194 Angle : 0.664 10.049 34112 Z= 0.331 Chirality : 0.045 0.187 3976 Planarity : 0.004 0.050 4421 Dihedral : 7.808 79.459 3694 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.04 % Allowed : 2.60 % Favored : 97.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.55 (0.14), residues: 3288 helix: -1.29 (0.15), residues: 1133 sheet: -1.92 (0.23), residues: 464 loop : -1.88 (0.16), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 404 HIS 0.004 0.001 HIS A 209 PHE 0.037 0.001 PHE D 174 TYR 0.018 0.001 TYR D 108 ARG 0.003 0.000 ARG I 340 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 510 time to evaluate : 2.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8489 (p0) cc_final: 0.7575 (t0) REVERT: B 4 ARG cc_start: 0.7558 (ttp80) cc_final: 0.7145 (ttp80) REVERT: B 204 PHE cc_start: 0.8485 (t80) cc_final: 0.8276 (t80) REVERT: B 241 GLN cc_start: 0.7925 (mm110) cc_final: 0.7581 (mm-40) REVERT: C 114 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8283 (tpp-160) REVERT: D 16 HIS cc_start: 0.8803 (m90) cc_final: 0.8354 (m90) REVERT: D 19 GLN cc_start: 0.8801 (mm110) cc_final: 0.8557 (mm110) REVERT: E 121 LEU cc_start: 0.8414 (mt) cc_final: 0.8206 (tp) REVERT: E 225 GLN cc_start: 0.7658 (mp10) cc_final: 0.7363 (mt0) REVERT: F 102 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7694 (mtmt) REVERT: G 9 ASP cc_start: 0.7088 (p0) cc_final: 0.6747 (p0) REVERT: G 53 LEU cc_start: 0.8738 (mm) cc_final: 0.8304 (pp) REVERT: G 84 ASP cc_start: 0.8635 (p0) cc_final: 0.8302 (p0) REVERT: G 110 PRO cc_start: 0.9250 (Cg_exo) cc_final: 0.8985 (Cg_endo) REVERT: G 150 MET cc_start: 0.7843 (ttm) cc_final: 0.7426 (tpp) REVERT: G 206 ASP cc_start: 0.9061 (p0) cc_final: 0.8840 (p0) REVERT: G 212 PHE cc_start: 0.8756 (p90) cc_final: 0.8418 (p90) REVERT: G 225 ASN cc_start: 0.7053 (t0) cc_final: 0.6830 (t0) REVERT: G 237 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8564 (tp40) REVERT: H 428 MET cc_start: 0.6951 (tpt) cc_final: 0.6541 (ttm) REVERT: I 222 TYR cc_start: 0.7141 (m-80) cc_final: 0.6770 (m-80) REVERT: I 306 MET cc_start: 0.8767 (tmm) cc_final: 0.8558 (tmm) REVERT: I 417 LYS cc_start: 0.9092 (tttm) cc_final: 0.8578 (tptt) REVERT: J 183 LYS cc_start: 0.7632 (pttt) cc_final: 0.7288 (pttm) REVERT: J 227 SER cc_start: 0.9297 (m) cc_final: 0.8839 (t) REVERT: J 232 GLU cc_start: 0.8209 (mt-10) cc_final: 0.8006 (mt-10) REVERT: J 239 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8430 (tm-30) REVERT: J 249 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7636 (mm-30) REVERT: J 269 GLN cc_start: 0.9050 (tt0) cc_final: 0.8695 (tm-30) REVERT: J 327 ILE cc_start: 0.9368 (mm) cc_final: 0.8954 (tt) REVERT: J 335 MET cc_start: 0.6636 (mtm) cc_final: 0.6422 (mtm) REVERT: J 372 GLU cc_start: 0.8353 (pm20) cc_final: 0.8143 (pm20) REVERT: K 161 MET cc_start: 0.8235 (ppp) cc_final: 0.7999 (ppp) REVERT: K 221 MET cc_start: 0.8690 (ppp) cc_final: 0.8308 (ppp) REVERT: K 222 LEU cc_start: 0.9590 (tp) cc_final: 0.9356 (tt) REVERT: K 235 ILE cc_start: 0.8530 (pt) cc_final: 0.8254 (pt) REVERT: K 253 MET cc_start: 0.8209 (ppp) cc_final: 0.7716 (tmm) REVERT: K 273 GLU cc_start: 0.7680 (tt0) cc_final: 0.7442 (tt0) REVERT: K 285 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9024 (mm-40) REVERT: K 292 VAL cc_start: 0.9042 (m) cc_final: 0.8782 (p) REVERT: K 303 MET cc_start: 0.9073 (mtp) cc_final: 0.8616 (tpp) REVERT: K 325 ASP cc_start: 0.9163 (p0) cc_final: 0.8766 (p0) REVERT: K 346 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7671 (ppt170) REVERT: K 360 MET cc_start: 0.8771 (ptt) cc_final: 0.8561 (ptp) REVERT: L 203 ASN cc_start: 0.8671 (p0) cc_final: 0.8308 (p0) REVERT: L 281 ASP cc_start: 0.7540 (p0) cc_final: 0.7232 (p0) REVERT: L 328 ASN cc_start: 0.8590 (m-40) cc_final: 0.8110 (m-40) REVERT: L 339 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7502 (ttp80) REVERT: L 382 MET cc_start: 0.8694 (ppp) cc_final: 0.8259 (ppp) outliers start: 1 outliers final: 0 residues processed: 510 average time/residue: 0.3593 time to fit residues: 286.8719 Evaluate side-chains 426 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 2.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 194 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 29 optimal weight: 0.2980 chunk 246 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25141 Z= 0.220 Angle : 0.679 8.433 34112 Z= 0.340 Chirality : 0.045 0.168 3976 Planarity : 0.004 0.055 4421 Dihedral : 7.779 81.455 3694 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.04 % Allowed : 1.50 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.44 (0.14), residues: 3288 helix: -1.19 (0.15), residues: 1147 sheet: -1.77 (0.24), residues: 462 loop : -1.85 (0.16), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 160 HIS 0.004 0.001 HIS A 209 PHE 0.050 0.002 PHE D 174 TYR 0.018 0.001 TYR H 249 ARG 0.015 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 489 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8496 (p0) cc_final: 0.7588 (t0) REVERT: A 231 ASP cc_start: 0.7197 (t70) cc_final: 0.6930 (t70) REVERT: B 4 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7085 (ttp80) REVERT: B 241 GLN cc_start: 0.8074 (mm110) cc_final: 0.7750 (mm-40) REVERT: D 16 HIS cc_start: 0.8789 (m90) cc_final: 0.8403 (m90) REVERT: E 225 GLN cc_start: 0.7636 (mp10) cc_final: 0.7312 (mt0) REVERT: F 102 LYS cc_start: 0.8412 (mmmt) cc_final: 0.7771 (mtmt) REVERT: G 9 ASP cc_start: 0.7124 (p0) cc_final: 0.6687 (p0) REVERT: G 84 ASP cc_start: 0.8609 (p0) cc_final: 0.8319 (p0) REVERT: G 110 PRO cc_start: 0.9230 (Cg_exo) cc_final: 0.8968 (Cg_endo) REVERT: G 150 MET cc_start: 0.7867 (ttm) cc_final: 0.7502 (tpp) REVERT: G 169 ARG cc_start: 0.8559 (mtm110) cc_final: 0.7939 (mtm-85) REVERT: G 212 PHE cc_start: 0.8663 (p90) cc_final: 0.8447 (p90) REVERT: G 237 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8610 (tp40) REVERT: H 249 TYR cc_start: 0.7645 (p90) cc_final: 0.6813 (p90) REVERT: I 222 TYR cc_start: 0.7182 (m-80) cc_final: 0.6903 (m-80) REVERT: I 417 LYS cc_start: 0.9113 (tttm) cc_final: 0.8635 (tptt) REVERT: J 183 LYS cc_start: 0.7650 (pttt) cc_final: 0.7257 (ptmt) REVERT: J 227 SER cc_start: 0.9314 (m) cc_final: 0.8878 (t) REVERT: J 236 MET cc_start: 0.8539 (ppp) cc_final: 0.8257 (ppp) REVERT: J 239 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8482 (tm-30) REVERT: J 249 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7649 (mm-30) REVERT: J 269 GLN cc_start: 0.9013 (tt0) cc_final: 0.8718 (tm-30) REVERT: J 327 ILE cc_start: 0.9369 (mm) cc_final: 0.8947 (tt) REVERT: J 335 MET cc_start: 0.6792 (mtm) cc_final: 0.6585 (mtm) REVERT: J 367 MET cc_start: 0.8625 (tpt) cc_final: 0.7423 (tpt) REVERT: J 372 GLU cc_start: 0.8346 (pm20) cc_final: 0.8143 (pm20) REVERT: K 161 MET cc_start: 0.8304 (ppp) cc_final: 0.8072 (ppp) REVERT: K 186 GLU cc_start: 0.9191 (pt0) cc_final: 0.8665 (pt0) REVERT: K 221 MET cc_start: 0.8744 (ppp) cc_final: 0.8345 (ppp) REVERT: K 222 LEU cc_start: 0.9615 (tp) cc_final: 0.9378 (tt) REVERT: K 285 GLN cc_start: 0.9227 (mm-40) cc_final: 0.8991 (mm-40) REVERT: K 292 VAL cc_start: 0.9106 (m) cc_final: 0.8829 (p) REVERT: K 299 LEU cc_start: 0.8929 (pp) cc_final: 0.8635 (pp) REVERT: K 303 MET cc_start: 0.9147 (mtp) cc_final: 0.8741 (tpp) REVERT: K 325 ASP cc_start: 0.9216 (p0) cc_final: 0.8801 (p0) REVERT: K 334 LEU cc_start: 0.8726 (mt) cc_final: 0.7423 (pt) REVERT: K 346 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7656 (ppt170) REVERT: K 360 MET cc_start: 0.8752 (ptt) cc_final: 0.8520 (ptp) REVERT: L 203 ASN cc_start: 0.8741 (p0) cc_final: 0.8310 (p0) REVERT: L 281 ASP cc_start: 0.7616 (p0) cc_final: 0.7306 (p0) REVERT: L 328 ASN cc_start: 0.8664 (m-40) cc_final: 0.8254 (m-40) REVERT: L 339 ARG cc_start: 0.8032 (ttp80) cc_final: 0.7538 (ttp80) REVERT: L 382 MET cc_start: 0.8757 (ppp) cc_final: 0.8377 (ppp) outliers start: 1 outliers final: 0 residues processed: 489 average time/residue: 0.3601 time to fit residues: 277.4502 Evaluate side-chains 416 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 416 time to evaluate : 2.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 285 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 274 optimal weight: 9.9990 chunk 292 optimal weight: 0.9990 chunk 300 optimal weight: 10.0000 chunk 176 optimal weight: 0.0570 chunk 127 optimal weight: 5.9990 chunk 229 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 264 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 181 ASN C 152 ASN D 19 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25141 Z= 0.175 Angle : 0.670 11.425 34112 Z= 0.329 Chirality : 0.045 0.171 3976 Planarity : 0.004 0.053 4421 Dihedral : 7.497 87.473 3694 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.08 % Allowed : 1.02 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.24 (0.15), residues: 3288 helix: -0.98 (0.15), residues: 1112 sheet: -1.73 (0.23), residues: 475 loop : -1.74 (0.16), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 160 HIS 0.004 0.001 HIS G 204 PHE 0.053 0.001 PHE D 174 TYR 0.017 0.001 TYR G 78 ARG 0.011 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 493 time to evaluate : 2.855 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: A 89 ASP cc_start: 0.8508 (p0) cc_final: 0.7502 (t0) REVERT: A 162 TYR cc_start: 0.7336 (p90) cc_final: 0.7113 (p90) REVERT: B 4 ARG cc_start: 0.7384 (ttp80) cc_final: 0.6797 (ttp80) REVERT: B 241 GLN cc_start: 0.8289 (mm110) cc_final: 0.8058 (mm-40) REVERT: C 109 GLU cc_start: 0.8261 (tt0) cc_final: 0.7699 (tt0) REVERT: C 120 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8707 (tm-30) REVERT: D 16 HIS cc_start: 0.8757 (m90) cc_final: 0.8406 (m90) REVERT: E 143 LEU cc_start: 0.8962 (mt) cc_final: 0.8673 (mt) REVERT: E 182 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7562 (tm-30) REVERT: E 225 GLN cc_start: 0.7623 (mp10) cc_final: 0.7315 (mt0) REVERT: F 102 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7750 (mtmt) REVERT: G 110 PRO cc_start: 0.9237 (Cg_exo) cc_final: 0.9010 (Cg_endo) REVERT: G 150 MET cc_start: 0.7759 (ttm) cc_final: 0.7283 (tpp) REVERT: G 169 ARG cc_start: 0.8567 (mtm110) cc_final: 0.7961 (mtm-85) REVERT: G 237 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8570 (tp40) REVERT: H 428 MET cc_start: 0.6637 (tpt) cc_final: 0.6272 (ttm) REVERT: I 180 SER cc_start: 0.6776 (p) cc_final: 0.6376 (m) REVERT: I 222 TYR cc_start: 0.7118 (m-80) cc_final: 0.6687 (m-80) REVERT: I 268 PHE cc_start: 0.8761 (m-10) cc_final: 0.8543 (m-10) REVERT: J 136 LEU cc_start: 0.8680 (tt) cc_final: 0.8451 (tp) REVERT: J 183 LYS cc_start: 0.7635 (pttt) cc_final: 0.7252 (ptmt) REVERT: J 227 SER cc_start: 0.9288 (m) cc_final: 0.8929 (t) REVERT: J 239 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8509 (tm-30) REVERT: J 269 GLN cc_start: 0.8879 (tt0) cc_final: 0.8609 (tm-30) REVERT: J 296 ARG cc_start: 0.8912 (mtp-110) cc_final: 0.8623 (mtp-110) REVERT: J 335 MET cc_start: 0.6645 (mtm) cc_final: 0.6439 (mtm) REVERT: J 364 GLU cc_start: 0.8265 (mp0) cc_final: 0.7837 (mp0) REVERT: J 372 GLU cc_start: 0.8335 (pm20) cc_final: 0.8128 (pm20) REVERT: K 161 MET cc_start: 0.8282 (ppp) cc_final: 0.8076 (ppp) REVERT: K 221 MET cc_start: 0.8719 (ppp) cc_final: 0.8313 (ppp) REVERT: K 273 GLU cc_start: 0.8089 (tt0) cc_final: 0.7594 (tt0) REVERT: K 285 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8922 (mm-40) REVERT: K 303 MET cc_start: 0.9138 (mtp) cc_final: 0.8614 (tpp) REVERT: K 325 ASP cc_start: 0.9181 (p0) cc_final: 0.8837 (p0) REVERT: K 346 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.7626 (ppt170) REVERT: K 377 SER cc_start: 0.8413 (m) cc_final: 0.8122 (p) REVERT: L 203 ASN cc_start: 0.8723 (p0) cc_final: 0.8247 (p0) REVERT: L 328 ASN cc_start: 0.8662 (m-40) cc_final: 0.8238 (m-40) REVERT: L 339 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7421 (ttp80) REVERT: L 382 MET cc_start: 0.8883 (ppp) cc_final: 0.8584 (ppp) outliers start: 2 outliers final: 0 residues processed: 494 average time/residue: 0.3360 time to fit residues: 263.4140 Evaluate side-chains 422 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 291 optimal weight: 6.9990 chunk 192 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 188 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 324 optimal weight: 0.0040 chunk 298 optimal weight: 6.9990 chunk 258 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 27 GLN A 56 GLN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25141 Z= 0.199 Angle : 0.672 11.977 34112 Z= 0.332 Chirality : 0.045 0.200 3976 Planarity : 0.004 0.048 4421 Dihedral : 7.438 89.194 3694 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.04 % Allowed : 0.61 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.16 (0.15), residues: 3288 helix: -0.95 (0.15), residues: 1130 sheet: -1.72 (0.24), residues: 460 loop : -1.64 (0.16), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 404 HIS 0.005 0.001 HIS G 204 PHE 0.017 0.001 PHE A 205 TYR 0.016 0.001 TYR H 249 ARG 0.011 0.000 ARG G 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 496 time to evaluate : 2.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8336 (t0) cc_final: 0.7950 (t0) REVERT: A 89 ASP cc_start: 0.8508 (p0) cc_final: 0.7652 (t0) REVERT: A 231 ASP cc_start: 0.7146 (t70) cc_final: 0.6907 (t70) REVERT: B 4 ARG cc_start: 0.7428 (ttp80) cc_final: 0.6840 (ttp80) REVERT: B 50 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8578 (mmmt) REVERT: C 109 GLU cc_start: 0.8282 (tt0) cc_final: 0.7708 (tt0) REVERT: D 16 HIS cc_start: 0.8788 (m90) cc_final: 0.8423 (m90) REVERT: E 184 LEU cc_start: 0.8542 (tt) cc_final: 0.8327 (tt) REVERT: F 102 LYS cc_start: 0.8337 (mmmt) cc_final: 0.7797 (mtmt) REVERT: G 10 LEU cc_start: 0.8606 (pt) cc_final: 0.8003 (tt) REVERT: G 84 ASP cc_start: 0.8711 (p0) cc_final: 0.8399 (p0) REVERT: G 110 PRO cc_start: 0.9201 (Cg_exo) cc_final: 0.8957 (Cg_endo) REVERT: G 150 MET cc_start: 0.7816 (ttm) cc_final: 0.7461 (tpp) REVERT: G 169 ARG cc_start: 0.8558 (mtm110) cc_final: 0.7916 (mtm-85) REVERT: G 212 PHE cc_start: 0.8812 (p90) cc_final: 0.8444 (p90) REVERT: G 237 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8559 (tp40) REVERT: H 428 MET cc_start: 0.6875 (tpt) cc_final: 0.6415 (ttm) REVERT: I 222 TYR cc_start: 0.7127 (m-80) cc_final: 0.6703 (m-80) REVERT: I 268 PHE cc_start: 0.8784 (m-10) cc_final: 0.8559 (m-10) REVERT: I 395 MET cc_start: 0.9201 (tpp) cc_final: 0.8815 (tpp) REVERT: J 183 LYS cc_start: 0.7595 (pttt) cc_final: 0.7146 (ptmt) REVERT: J 227 SER cc_start: 0.9107 (m) cc_final: 0.8856 (t) REVERT: J 239 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8669 (tm-30) REVERT: J 269 GLN cc_start: 0.8882 (tt0) cc_final: 0.8621 (tm-30) REVERT: J 296 ARG cc_start: 0.8914 (mtp-110) cc_final: 0.8566 (mtp-110) REVERT: J 327 ILE cc_start: 0.9350 (mm) cc_final: 0.8910 (tt) REVERT: J 335 MET cc_start: 0.6793 (mtm) cc_final: 0.6513 (mtm) REVERT: K 186 GLU cc_start: 0.9193 (pt0) cc_final: 0.8827 (pt0) REVERT: K 221 MET cc_start: 0.8759 (ppp) cc_final: 0.8320 (ppp) REVERT: K 222 LEU cc_start: 0.9642 (tp) cc_final: 0.9389 (tt) REVERT: K 273 GLU cc_start: 0.8181 (tt0) cc_final: 0.7733 (tt0) REVERT: K 303 MET cc_start: 0.9187 (mtp) cc_final: 0.8673 (tpp) REVERT: K 325 ASP cc_start: 0.9165 (p0) cc_final: 0.8817 (p0) REVERT: K 334 LEU cc_start: 0.8748 (mt) cc_final: 0.7408 (pt) REVERT: K 346 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.7634 (ppt170) REVERT: K 377 SER cc_start: 0.8409 (m) cc_final: 0.8153 (p) REVERT: L 203 ASN cc_start: 0.8705 (p0) cc_final: 0.8227 (p0) REVERT: L 282 GLU cc_start: 0.7615 (pm20) cc_final: 0.7394 (pm20) REVERT: L 328 ASN cc_start: 0.8698 (m-40) cc_final: 0.8280 (m-40) REVERT: L 339 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7382 (ttp80) REVERT: L 382 MET cc_start: 0.8849 (ppp) cc_final: 0.8588 (ppp) outliers start: 1 outliers final: 1 residues processed: 497 average time/residue: 0.3438 time to fit residues: 270.5673 Evaluate side-chains 419 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 418 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 326 random chunks: chunk 158 optimal weight: 0.0770 chunk 205 optimal weight: 2.9990 chunk 275 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 259 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 265 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 HIS C 152 ASN D 19 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 244 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.067567 restraints weight = 88508.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.069262 restraints weight = 55733.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.070434 restraints weight = 39213.706| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25141 Z= 0.275 Angle : 0.718 11.683 34112 Z= 0.359 Chirality : 0.046 0.247 3976 Planarity : 0.004 0.050 4421 Dihedral : 7.722 85.925 3694 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: -2.16 (0.15), residues: 3288 helix: -0.97 (0.15), residues: 1137 sheet: -1.62 (0.24), residues: 459 loop : -1.67 (0.16), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 160 HIS 0.008 0.001 HIS G 204 PHE 0.048 0.002 PHE D 174 TYR 0.033 0.002 TYR A 162 ARG 0.010 0.001 ARG G 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5677.75 seconds wall clock time: 103 minutes 37.20 seconds (6217.20 seconds total)