Starting phenix.real_space_refine on Wed Jul 24 04:55:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/07_2024/6ef0_9042.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/07_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_9042/07_2024/6ef0_9042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/07_2024/6ef0_9042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/07_2024/6ef0_9042.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ef0_9042/07_2024/6ef0_9042.cif" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 13.99, per 1000 atoms: 0.57 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: 9.96 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... Secondary structure from input PDB file: 129 helices and 23 sheets defined 39.6% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.67 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 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) Processing helix chain 'A' and resid 87 through 109 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 113 through 118 removed outlier: 3.535A pdb=" N LEU A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.526A pdb=" N ILE A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.545A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 removed outlier: 3.653A pdb=" N GLU A 204 " --> pdb=" O GLU A 200 " (cutoff:3.500A) 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 238 through 245 removed outlier: 3.557A pdb=" N ILE A 241 " --> pdb=" O ALA A 238 " (cutoff:3.500A) 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 31 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 82 through 96 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 97 through 102 Processing helix chain 'B' and resid 109 through 120 removed outlier: 3.731A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 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 184 through 198 removed outlier: 4.255A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 81 through 84 removed outlier: 3.674A pdb=" N ALA C 84 " --> pdb=" O THR C 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 81 through 84' Processing helix chain 'C' and resid 86 through 103 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 111 through 123 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) removed outlier: 3.586A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 177 removed outlier: 3.774A pdb=" N THR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 198 Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 231 through 242 removed outlier: 4.118A pdb=" N ILE C 238 " --> pdb=" O GLU C 234 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 27 removed outlier: 3.780A pdb=" N GLU D 21 " --> pdb=" O ILE D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 81 through 100 removed outlier: 3.843A pdb=" N LEU D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) 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 108 through 120 removed outlier: 3.700A pdb=" N TYR D 112 " --> pdb=" O TYR D 108 " (cutoff:3.500A) 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 171 through 179 removed outlier: 3.523A pdb=" N LYS D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 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) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 216 through 220 removed outlier: 3.509A pdb=" N ASP D 220 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 239 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) Processing helix chain 'E' and resid 21 through 30 removed outlier: 4.359A pdb=" N GLU E 25 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 103 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 109 through 118 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 122 removed outlier: 3.603A pdb=" N ARG E 122 " --> pdb=" O LEU E 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 119 through 122' Processing helix chain 'E' and resid 176 through 185 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) removed outlier: 3.608A pdb=" N ASN E 185 " --> pdb=" O ALA E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 192 through 208 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 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 232 through 240 Processing helix chain 'E' and resid 241 through 248 removed outlier: 3.567A pdb=" N LYS E 244 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLU E 245 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 32 removed outlier: 3.684A pdb=" N GLU F 23 " --> pdb=" O LEU F 19 " (cutoff:3.500A) 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 78 through 95 removed outlier: 3.573A pdb=" N ARG F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) 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) Processing helix chain 'F' and resid 105 through 119 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 165 through 175 Processing helix chain 'F' and resid 185 through 196 removed outlier: 4.045A pdb=" N LEU F 189 " --> pdb=" O ASN F 185 " (cutoff:3.500A) 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 226 through 234 removed outlier: 4.356A pdb=" N ALA F 229 " --> pdb=" O ASP F 226 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS F 232 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 33 Processing helix chain 'G' and resid 82 through 104 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 108 through 120 removed outlier: 4.582A pdb=" N GLN G 118 " --> pdb=" O ASP G 114 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL G 120 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 124 Processing helix chain 'G' and resid 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' Processing helix chain 'G' and resid 168 through 181 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) Processing helix chain 'G' and resid 188 through 204 removed outlier: 3.833A pdb=" N ALA G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) 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) Processing helix chain 'G' and resid 205 through 208 removed outlier: 4.135A pdb=" N LYS G 208 " --> pdb=" O GLU G 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 221 through 225 Processing helix chain 'G' and resid 233 through 246 removed outlier: 3.629A pdb=" N GLN G 237 " --> pdb=" O GLY G 233 " (cutoff:3.500A) 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) Processing helix chain 'H' and resid 215 through 221 removed outlier: 4.390A pdb=" N GLU H 219 " --> pdb=" O LYS H 215 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 removed outlier: 4.513A pdb=" N THR H 237 " --> pdb=" O GLU H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 255 through 265 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) removed outlier: 4.071A pdb=" N ASN H 265 " --> pdb=" O ARG H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 269 Processing helix chain 'H' and resid 275 through 280 removed outlier: 4.069A pdb=" N LEU H 279 " --> pdb=" O ILE H 275 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL H 280 " --> pdb=" O GLY H 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 275 through 280' Processing helix chain 'H' and resid 286 through 299 Processing helix chain 'H' and resid 311 through 316 Processing helix chain 'H' and resid 318 through 322 removed outlier: 4.022A pdb=" N ASP H 321 " --> pdb=" O ARG H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 327 through 341 removed outlier: 4.401A pdb=" N ASP H 341 " --> pdb=" O ILE H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 387 Processing helix chain 'H' and resid 405 through 410 Processing helix chain 'H' and resid 418 through 427 Processing helix chain 'H' and resid 428 through 434 Processing helix chain 'H' and resid 440 through 451 removed outlier: 3.509A pdb=" N LEU H 444 " --> pdb=" O GLU H 440 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS H 449 " --> pdb=" O LYS H 445 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 450 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE H 451 " --> pdb=" O VAL H 447 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 198 removed outlier: 3.974A pdb=" N ILE I 194 " --> pdb=" O GLN I 190 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS I 195 " --> pdb=" O ILE I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 204 Processing helix chain 'I' and resid 205 through 212 removed outlier: 3.700A pdb=" N GLU I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 240 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 250 through 253 removed outlier: 3.710A pdb=" N ILE I 253 " --> pdb=" O SER I 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 250 through 253' Processing helix chain 'I' and resid 260 through 274 removed outlier: 3.980A pdb=" N CYS I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) 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 283 through 287 Processing helix chain 'I' and resid 298 through 316 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 354 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 362 through 367 Processing helix chain 'I' and resid 376 through 380 Processing helix chain 'I' and resid 391 through 405 removed outlier: 4.248A pdb=" N GLY I 400 " --> pdb=" O CYS I 396 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 427 removed outlier: 3.901A pdb=" N PHE I 416 " --> pdb=" O THR I 412 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN I 426 " --> pdb=" O ARG I 422 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 139 removed outlier: 3.969A pdb=" N LEU J 136 " --> pdb=" O LEU J 133 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET J 138 " --> pdb=" O SER J 135 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL J 139 " --> pdb=" O LEU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 161 Processing helix chain 'J' and resid 161 through 166 removed outlier: 4.117A pdb=" N LEU J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 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 241 removed outlier: 4.249A pdb=" N SER J 227 " --> pdb=" O ILE J 223 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE J 234 " --> pdb=" O VAL J 230 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL J 235 " --> pdb=" O ARG J 231 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA J 237 " --> pdb=" O LEU J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 276 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 301 through 306 removed outlier: 4.532A pdb=" N LEU J 305 " --> pdb=" O ASP J 301 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG J 306 " --> pdb=" O PRO J 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 301 through 306' Processing helix chain 'J' and resid 320 through 331 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) removed outlier: 4.080A pdb=" N HIS J 331 " --> pdb=" O ILE J 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 350 Processing helix chain 'J' and resid 357 through 371 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) Processing helix chain 'J' and resid 378 through 391 removed outlier: 4.215A pdb=" N PHE J 382 " --> pdb=" O THR J 378 " (cutoff:3.500A) 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) removed outlier: 4.505A pdb=" N MET J 390 " --> pdb=" O VAL J 386 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN J 391 " --> pdb=" O GLY J 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 189 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 189 through 194 Processing helix chain 'K' and resid 195 through 200 Processing helix chain 'K' and resid 221 through 229 removed outlier: 4.069A pdb=" N ALA K 225 " --> pdb=" O MET K 221 " (cutoff:3.500A) 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 265 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 274 through 278 removed outlier: 3.657A pdb=" N ALA K 278 " --> pdb=" O ASP K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 305 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 345 through 359 removed outlier: 3.723A pdb=" N ARG K 349 " --> pdb=" O ASP K 345 " (cutoff:3.500A) 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) removed outlier: 3.650A pdb=" N LYS K 359 " --> pdb=" O THR K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 381 through 396 removed outlier: 4.004A pdb=" N ALA K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) 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) Processing helix chain 'K' and resid 404 through 415 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) removed outlier: 3.742A pdb=" N VAL K 415 " --> pdb=" O TYR K 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 171 removed outlier: 4.574A pdb=" N THR L 171 " --> pdb=" O VAL L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 183 removed outlier: 3.554A pdb=" N GLY L 182 " --> pdb=" O THR L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 204 through 211 removed outlier: 3.822A pdb=" N GLN L 208 " --> pdb=" O PRO L 204 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 240 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 257 through 272 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 282 through 287 Processing helix chain 'L' and resid 298 through 312 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) removed outlier: 3.599A pdb=" N MET L 312 " --> pdb=" O LEU L 308 " (cutoff:3.500A) Processing helix chain 'L' and resid 334 through 339 removed outlier: 3.772A pdb=" N LEU L 338 " --> pdb=" O ASP L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 355 through 366 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 379 through 385 removed outlier: 4.204A pdb=" N ASP L 384 " --> pdb=" O LYS L 381 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY L 385 " --> pdb=" O MET L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 403 removed outlier: 4.449A pdb=" N ASN L 393 " --> pdb=" O ALA L 389 " (cutoff:3.500A) 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) removed outlier: 3.519A pdb=" N ILE L 403 " --> pdb=" O GLY L 399 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 428 removed outlier: 3.558A pdb=" N ALA L 418 " --> pdb=" O ASP L 414 " (cutoff:3.500A) 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) Processing helix chain 'M' and resid 186 through 194 removed outlier: 3.588A pdb=" N ILE M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 202 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 206 through 211 Processing helix chain 'M' and resid 227 through 236 removed outlier: 3.588A pdb=" N ALA M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 247 through 251 Processing helix chain 'M' and resid 257 through 271 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 298 through 311 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 353 through 364 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 375 through 380 Processing helix chain 'M' and resid 387 through 404 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) Processing helix chain 'M' and resid 415 through 420 removed outlier: 4.251A pdb=" N SER M 420 " --> pdb=" O VAL M 416 " (cutoff:3.500A) Processing helix chain 'M' and resid 421 through 423 No H-bonds generated for 'chain 'M' and resid 421 through 423' Processing sheet with id=AA1, 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=AA2, first strand: chain 'A' and resid 79 through 80 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=AA3, 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=AA4, 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=AA5, first strand: chain 'B' and resid 65 through 68 removed outlier: 3.745A pdb=" N LEU B 67 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 163 through 164 removed outlier: 3.947A pdb=" N ILE C 38 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL C 45 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C 46 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ALA C 214 " --> pdb=" O LEU C 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 74 through 75 removed outlier: 4.093A pdb=" N GLY C 139 " --> pdb=" O GLN C 147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA9, first strand: chain 'C' and resid 149 through 150 Processing sheet with id=AB1, 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) removed outlier: 4.020A pdb=" N VAL D 222 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 72 through 74 removed outlier: 3.648A pdb=" N ALA D 136 " --> pdb=" O VAL D 72 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, 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=AB5, 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=AB6, first strand: chain 'F' and resid 63 through 67 removed outlier: 3.937A pdb=" N CYS F 66 " --> pdb=" O MET F 70 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N MET F 70 " --> pdb=" O CYS F 66 " (cutoff:3.500A) 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) removed outlier: 3.508A pdb=" N THR F 154 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 37 through 41 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=AB8, first strand: chain 'G' and resid 37 through 41 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: 3.746A pdb=" N CYS G 219 " --> pdb=" O VAL G 46 " (cutoff:3.500A) Processing sheet with id=AB9, 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) removed outlier: 3.571A pdb=" N GLY G 75 " --> pdb=" O GLY G 139 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE G 137 " --> pdb=" O VAL G 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 141 through 142 Processing sheet with id=AC2, first strand: chain 'H' and resid 246 through 248 removed outlier: 7.120A pdb=" N LEU H 247 " --> pdb=" O VAL H 375 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'I' and resid 246 through 248 removed outlier: 3.844A pdb=" N ASP I 282 " --> pdb=" O ILE I 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 291 through 293 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=AC5, first strand: chain 'L' and resid 218 through 219 removed outlier: 6.884A pdb=" N VAL L 218 " --> pdb=" O MET L 325 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1935 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: 6.83 Time building geometry restraints manager: 10.88 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: 735 2.65 - 3.21: 27179 3.21 - 3.78: 37074 3.78 - 4.34: 50102 4.34 - 4.90: 76401 Nonbonded interactions: 191491 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 GLN F 166 " pdb=" OG1 THR F 170 " model vdw 2.184 2.440 ... (remaining 191486 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: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.030 Extract box with map and model: 1.000 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 64.100 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.090 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.250 ------------------------------------------------------------------------------- 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= 0.704 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 : 3.045 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: 0.4011 time to fit residues: 381.7904 Evaluate side-chains 422 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 3.125 ------------------------------------------------------------------------------- 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: 0.9990 chunk 247 optimal weight: 0.1980 chunk 137 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 166 optimal weight: 0.0000 chunk 132 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 155 optimal weight: 0.0070 chunk 190 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 overall best weight: 0.3404 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 25141 Z= 0.201 Angle : 0.761 8.866 34112 Z= 0.383 Chirality : 0.047 0.177 3976 Planarity : 0.005 0.048 4421 Dihedral : 9.587 158.173 3694 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % 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: -4.24 (0.13), residues: 3288 helix: -2.63 (0.12), residues: 1156 sheet: -3.33 (0.22), residues: 390 loop : -2.83 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 218 HIS 0.006 0.001 HIS M 364 PHE 0.021 0.002 PHE A 205 TYR 0.023 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 628 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 623 time to evaluate : 3.054 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: 0.8312 (t70) cc_final: 0.8002 (t0) REVERT: A 89 ASP cc_start: 0.8392 (p0) cc_final: 0.7532 (t0) REVERT: A 92 ASN cc_start: 0.8094 (p0) cc_final: 0.7543 (t0) REVERT: A 106 TYR cc_start: 0.7708 (t80) cc_final: 0.6662 (m-10) REVERT: A 162 TYR cc_start: 0.6839 (p90) cc_final: 0.6543 (p90) REVERT: A 231 ASP cc_start: 0.7389 (t70) cc_final: 0.7026 (t70) REVERT: B 65 SER cc_start: 0.7582 (p) cc_final: 0.7331 (t) REVERT: B 103 GLU cc_start: 0.8184 (pm20) cc_final: 0.7924 (pm20) REVERT: B 117 ILE cc_start: 0.8892 (mm) cc_final: 0.8616 (mm) REVERT: B 241 GLN cc_start: 0.7798 (pm20) cc_final: 0.7336 (pm20) REVERT: C 1 MET cc_start: 0.5010 (ptm) cc_final: 0.4649 (ptt) REVERT: C 114 ARG cc_start: 0.8628 (tpm170) cc_final: 0.8254 (tpp-160) REVERT: C 120 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 213 PHE cc_start: 0.8094 (p90) cc_final: 0.7822 (p90) REVERT: D 56 ASP cc_start: 0.7161 (t70) cc_final: 0.6841 (m-30) REVERT: D 120 TYR cc_start: 0.8065 (m-80) cc_final: 0.7418 (m-80) REVERT: D 149 GLN cc_start: 0.7306 (tm-30) cc_final: 0.7055 (tm-30) REVERT: E 84 ASP cc_start: 0.8749 (p0) cc_final: 0.8347 (p0) REVERT: E 90 GLU cc_start: 0.8488 (tt0) cc_final: 0.8202 (tt0) REVERT: E 208 MET cc_start: 0.7908 (tpt) cc_final: 0.7652 (tpp) REVERT: F 24 TYR cc_start: 0.8615 (m-80) cc_final: 0.8288 (m-80) REVERT: F 128 TYR cc_start: 0.8050 (m-10) cc_final: 0.7803 (m-10) REVERT: F 144 LEU cc_start: 0.8967 (tp) cc_final: 0.8701 (tp) REVERT: F 147 PHE cc_start: 0.8686 (t80) cc_final: 0.8278 (t80) REVERT: F 228 GLU cc_start: 0.8437 (mp0) cc_final: 0.8226 (mm-30) REVERT: G 18 ASP cc_start: 0.8907 (p0) cc_final: 0.8652 (p0) REVERT: G 43 ASN cc_start: 0.8763 (p0) cc_final: 0.8510 (p0) REVERT: G 53 LEU cc_start: 0.8614 (tt) cc_final: 0.8121 (pp) REVERT: G 115 ARG cc_start: 0.7283 (mmt-90) cc_final: 0.6822 (mmt-90) REVERT: G 212 PHE cc_start: 0.8711 (p90) cc_final: 0.8442 (p90) REVERT: G 225 ASN cc_start: 0.6969 (t0) cc_final: 0.6639 (t0) REVERT: H 392 HIS cc_start: 0.7854 (m90) cc_final: 0.7292 (m90) REVERT: H 448 ASP cc_start: 0.8985 (t0) cc_final: 0.8717 (t0) REVERT: I 219 VAL cc_start: 0.7527 (p) cc_final: 0.6798 (m) REVERT: I 222 TYR cc_start: 0.6952 (m-80) cc_final: 0.6692 (m-80) REVERT: I 306 MET cc_start: 0.8407 (tmm) cc_final: 0.8199 (tmm) REVERT: I 326 MET cc_start: 0.8121 (pmm) cc_final: 0.7848 (pmm) REVERT: I 355 LEU cc_start: 0.8831 (tt) cc_final: 0.8562 (mt) REVERT: I 417 LYS cc_start: 0.9035 (tttm) cc_final: 0.8670 (tptt) REVERT: J 156 GLN cc_start: 0.9002 (mp10) cc_final: 0.8276 (mp10) REVERT: J 327 ILE cc_start: 0.9379 (mm) cc_final: 0.9037 (mm) REVERT: J 328 LEU cc_start: 0.9428 (tt) cc_final: 0.9218 (pp) REVERT: J 359 LYS cc_start: 0.9072 (ptmt) cc_final: 0.8752 (ptmt) REVERT: K 161 MET cc_start: 0.7539 (ppp) cc_final: 0.7081 (ppp) REVERT: K 204 ASP cc_start: 0.8597 (p0) cc_final: 0.7857 (p0) REVERT: K 273 GLU cc_start: 0.7534 (tt0) cc_final: 0.7269 (tt0) REVERT: K 285 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8903 (mm-40) REVERT: K 289 ASP cc_start: 0.8712 (p0) cc_final: 0.8488 (p0) REVERT: K 298 GLU cc_start: 0.8422 (pp20) cc_final: 0.8221 (pp20) REVERT: K 322 ASP cc_start: 0.8123 (p0) cc_final: 0.7903 (p0) REVERT: K 334 LEU cc_start: 0.8590 (mt) cc_final: 0.8231 (mt) REVERT: K 339 GLU cc_start: 0.8667 (pm20) cc_final: 0.8439 (pm20) REVERT: K 346 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7565 (ppt170) REVERT: L 221 TYR cc_start: 0.8525 (p90) cc_final: 0.8291 (p90) REVERT: L 274 GLU cc_start: 0.8132 (pm20) cc_final: 0.7922 (pm20) REVERT: L 306 MET cc_start: 0.8531 (mtt) cc_final: 0.7930 (mtt) REVERT: L 328 ASN cc_start: 0.8643 (m-40) cc_final: 0.8219 (m-40) REVERT: M 265 ASP cc_start: 0.8518 (p0) cc_final: 0.8252 (m-30) REVERT: M 368 MET cc_start: 0.6252 (ptp) cc_final: 0.5955 (ptt) outliers start: 5 outliers final: 2 residues processed: 625 average time/residue: 0.3731 time to fit residues: 355.6907 Evaluate side-chains 463 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 461 time to evaluate : 2.792 ------------------------------------------------------------------------------- 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: 2.9990 chunk 91 optimal weight: 6.9990 chunk 246 optimal weight: 0.3980 chunk 201 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 296 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 264 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 218 ASN ** C 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN L 311 GLN M 310 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25141 Z= 0.268 Angle : 0.714 8.235 34112 Z= 0.368 Chirality : 0.047 0.160 3976 Planarity : 0.004 0.055 4421 Dihedral : 8.774 120.326 3694 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 0.12 % Allowed : 5.81 % Favored : 94.07 % 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: -3.61 (0.14), residues: 3288 helix: -2.02 (0.13), residues: 1183 sheet: -2.91 (0.22), residues: 433 loop : -2.52 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 218 HIS 0.007 0.001 HIS A 209 PHE 0.018 0.002 PHE A 205 TYR 0.015 0.001 TYR A 162 ARG 0.020 0.001 ARG L 357 *********************** 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 552 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 549 time to evaluate : 2.954 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: A 49 ASP cc_start: 0.8365 (t70) cc_final: 0.7885 (t0) REVERT: A 89 ASP cc_start: 0.8480 (p0) cc_final: 0.7663 (t0) REVERT: A 162 TYR cc_start: 0.7087 (p90) cc_final: 0.6758 (p90) REVERT: A 231 ASP cc_start: 0.7459 (t70) cc_final: 0.7183 (t70) REVERT: B 75 TYR cc_start: 0.8237 (p90) cc_final: 0.7831 (p90) REVERT: B 103 GLU cc_start: 0.8153 (pm20) cc_final: 0.7919 (pm20) REVERT: B 117 ILE cc_start: 0.8795 (mm) cc_final: 0.8414 (mm) REVERT: B 119 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7597 (tp-100) REVERT: B 241 GLN cc_start: 0.7754 (pm20) cc_final: 0.7314 (pm20) REVERT: C 1 MET cc_start: 0.5143 (ptm) cc_final: 0.4594 (ptt) REVERT: C 114 ARG cc_start: 0.8928 (tpm170) cc_final: 0.8607 (tpp-160) REVERT: D 16 HIS cc_start: 0.8732 (m90) cc_final: 0.8305 (m90) REVERT: D 56 ASP cc_start: 0.7327 (t70) cc_final: 0.7078 (m-30) REVERT: D 120 TYR cc_start: 0.8138 (m-80) cc_final: 0.7624 (m-80) REVERT: D 149 GLN cc_start: 0.7377 (tm-30) cc_final: 0.6962 (tm-30) REVERT: E 84 ASP cc_start: 0.8777 (p0) cc_final: 0.8575 (p0) REVERT: E 90 GLU cc_start: 0.8410 (tt0) cc_final: 0.7567 (tp30) REVERT: E 134 MET cc_start: 0.8068 (ptp) cc_final: 0.7592 (ptm) REVERT: F 24 TYR cc_start: 0.9001 (m-80) cc_final: 0.8712 (m-10) REVERT: F 87 TYR cc_start: 0.9035 (t80) cc_final: 0.8658 (t80) REVERT: F 90 GLN cc_start: 0.8374 (mp-120) cc_final: 0.7586 (mp10) REVERT: F 147 PHE cc_start: 0.8404 (t80) cc_final: 0.8088 (t80) REVERT: F 185 ASN cc_start: 0.9145 (t0) cc_final: 0.8903 (t0) REVERT: G 18 ASP cc_start: 0.8880 (p0) cc_final: 0.8643 (p0) REVERT: G 53 LEU cc_start: 0.8700 (tt) cc_final: 0.8291 (pt) REVERT: G 86 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7283 (ttm-80) REVERT: G 110 PRO cc_start: 0.9130 (Cg_exo) cc_final: 0.8852 (Cg_endo) REVERT: G 212 PHE cc_start: 0.8719 (p90) cc_final: 0.8409 (p90) REVERT: G 225 ASN cc_start: 0.7076 (t0) cc_final: 0.6771 (t0) REVERT: H 392 HIS cc_start: 0.7720 (m90) cc_final: 0.7183 (m90) REVERT: H 448 ASP cc_start: 0.9266 (t0) cc_final: 0.8946 (t0) REVERT: I 193 GLU cc_start: 0.9017 (mp0) cc_final: 0.8482 (mp0) REVERT: I 222 TYR cc_start: 0.7093 (m-80) cc_final: 0.6739 (m-80) REVERT: I 289 THR cc_start: 0.8582 (p) cc_final: 0.8334 (p) REVERT: I 343 ARG cc_start: 0.7165 (mtt90) cc_final: 0.6844 (mtt90) REVERT: I 395 MET cc_start: 0.9097 (tpp) cc_final: 0.8893 (tpp) REVERT: I 417 LYS cc_start: 0.9065 (tttm) cc_final: 0.8660 (tptt) REVERT: J 161 LYS cc_start: 0.8906 (mtmm) cc_final: 0.8246 (tptt) REVERT: J 269 GLN cc_start: 0.9243 (tt0) cc_final: 0.8419 (tm-30) REVERT: K 161 MET cc_start: 0.7943 (ppp) cc_final: 0.7544 (ppp) REVERT: K 221 MET cc_start: 0.8477 (ppp) cc_final: 0.8208 (ppp) REVERT: K 285 GLN cc_start: 0.9256 (mm-40) cc_final: 0.9007 (mm-40) REVERT: K 292 VAL cc_start: 0.8975 (m) cc_final: 0.8686 (p) REVERT: K 298 GLU cc_start: 0.8545 (pp20) cc_final: 0.8332 (pp20) REVERT: K 322 ASP cc_start: 0.8273 (p0) cc_final: 0.8029 (p0) REVERT: K 325 ASP cc_start: 0.9105 (p0) cc_final: 0.8778 (p0) REVERT: K 346 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7598 (ppt170) REVERT: L 328 ASN cc_start: 0.8631 (m-40) cc_final: 0.8233 (m-40) REVERT: L 339 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7175 (ttp80) REVERT: M 334 ASP cc_start: 0.7830 (m-30) cc_final: 0.7410 (m-30) outliers start: 3 outliers final: 0 residues processed: 551 average time/residue: 0.3722 time to fit residues: 315.5270 Evaluate side-chains 432 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 2.903 ------------------------------------------------------------------------------- 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: 4.9990 chunk 222 optimal weight: 0.0980 chunk 153 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 297 optimal weight: 20.0000 chunk 315 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 282 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 56 GLN A 84 ASN ** A 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 218 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 25141 Z= 0.342 Angle : 0.757 9.105 34112 Z= 0.393 Chirality : 0.048 0.208 3976 Planarity : 0.005 0.073 4421 Dihedral : 8.759 92.640 3694 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.74 % Favored : 89.26 % Rotamer: Outliers : 0.20 % Allowed : 6.74 % Favored : 93.05 % 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: -3.36 (0.14), residues: 3288 helix: -1.80 (0.14), residues: 1190 sheet: -2.50 (0.23), residues: 437 loop : -2.46 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 160 HIS 0.006 0.001 HIS A 209 PHE 0.021 0.002 PHE F 13 TYR 0.019 0.002 TYR F 94 ARG 0.007 0.001 ARG B 4 *********************** 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 512 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 507 time to evaluate : 2.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.8521 (m110) cc_final: 0.8220 (m-40) REVERT: A 89 ASP cc_start: 0.8453 (p0) cc_final: 0.7748 (t0) REVERT: A 231 ASP cc_start: 0.7689 (t70) cc_final: 0.7312 (t70) REVERT: B 75 TYR cc_start: 0.8629 (p90) cc_final: 0.8348 (p90) REVERT: B 99 ARG cc_start: 0.8587 (mtt90) cc_final: 0.8253 (mtt90) REVERT: B 103 GLU cc_start: 0.8363 (pm20) cc_final: 0.7987 (pm20) REVERT: B 117 ILE cc_start: 0.8895 (mm) cc_final: 0.8585 (mm) REVERT: B 241 GLN cc_start: 0.7656 (pm20) cc_final: 0.7246 (pm20) REVERT: C 1 MET cc_start: 0.5156 (ptm) cc_final: 0.4879 (ptt) REVERT: C 93 ILE cc_start: 0.8635 (pt) cc_final: 0.8403 (mt) REVERT: C 114 ARG cc_start: 0.8951 (tpm170) cc_final: 0.8672 (tpp-160) REVERT: C 124 GLN cc_start: 0.8188 (tt0) cc_final: 0.7908 (tt0) REVERT: C 173 GLN cc_start: 0.9336 (mm110) cc_final: 0.9117 (mm-40) REVERT: D 16 HIS cc_start: 0.8808 (m90) cc_final: 0.8282 (m90) REVERT: D 56 ASP cc_start: 0.7725 (t70) cc_final: 0.7267 (m-30) REVERT: D 120 TYR cc_start: 0.8128 (m-80) cc_final: 0.7607 (m-80) REVERT: E 84 ASP cc_start: 0.8720 (p0) cc_final: 0.8513 (p0) REVERT: E 206 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8261 (tm-30) REVERT: F 19 LEU cc_start: 0.8880 (mp) cc_final: 0.8603 (mp) REVERT: F 52 ASN cc_start: 0.8580 (p0) cc_final: 0.8230 (p0) REVERT: F 86 ASN cc_start: 0.8858 (m-40) cc_final: 0.8589 (t0) REVERT: F 102 LYS cc_start: 0.8286 (mmmt) cc_final: 0.7457 (mtmt) REVERT: F 228 GLU cc_start: 0.8368 (mp0) cc_final: 0.8163 (mm-30) REVERT: G 18 ASP cc_start: 0.8986 (p0) cc_final: 0.8776 (p0) REVERT: G 53 LEU cc_start: 0.8647 (tt) cc_final: 0.8362 (pt) REVERT: G 110 PRO cc_start: 0.9184 (Cg_exo) cc_final: 0.8939 (Cg_endo) REVERT: G 150 MET cc_start: 0.7943 (ttm) cc_final: 0.7422 (tpp) REVERT: G 206 ASP cc_start: 0.9003 (p0) cc_final: 0.8723 (p0) REVERT: G 212 PHE cc_start: 0.8845 (p90) cc_final: 0.8404 (p90) REVERT: G 225 ASN cc_start: 0.7231 (t0) cc_final: 0.7029 (t0) REVERT: I 222 TYR cc_start: 0.7069 (m-80) cc_final: 0.6593 (m-80) REVERT: I 232 LEU cc_start: 0.9534 (mt) cc_final: 0.9291 (mp) REVERT: I 395 MET cc_start: 0.9240 (tpp) cc_final: 0.8894 (tpp) REVERT: J 161 LYS cc_start: 0.9056 (mtmm) cc_final: 0.8670 (mtmm) REVERT: J 240 HIS cc_start: 0.8255 (m90) cc_final: 0.7472 (m90) REVERT: J 249 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7460 (mm-30) REVERT: J 327 ILE cc_start: 0.9433 (mm) cc_final: 0.9043 (tt) REVERT: K 161 MET cc_start: 0.8149 (ppp) cc_final: 0.7766 (ppp) REVERT: K 221 MET cc_start: 0.8654 (ppp) cc_final: 0.8344 (ppp) REVERT: K 285 GLN cc_start: 0.9266 (mm-40) cc_final: 0.9054 (mm-40) REVERT: K 292 VAL cc_start: 0.9071 (m) cc_final: 0.8853 (p) REVERT: K 298 GLU cc_start: 0.8630 (pp20) cc_final: 0.8352 (pp20) REVERT: K 325 ASP cc_start: 0.9103 (p0) cc_final: 0.8784 (p0) REVERT: K 346 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.7762 (ppt170) REVERT: L 213 LYS cc_start: 0.9281 (mmtt) cc_final: 0.8923 (mtpt) REVERT: L 255 TYR cc_start: 0.8590 (m-10) cc_final: 0.8364 (m-10) REVERT: L 306 MET cc_start: 0.8620 (mtt) cc_final: 0.8250 (mtt) REVERT: L 328 ASN cc_start: 0.8660 (m-40) cc_final: 0.8215 (m-40) REVERT: L 339 ARG cc_start: 0.8044 (ttp80) cc_final: 0.7270 (ttp80) REVERT: M 334 ASP cc_start: 0.7614 (m-30) cc_final: 0.7167 (m-30) outliers start: 5 outliers final: 1 residues processed: 510 average time/residue: 0.3557 time to fit residues: 282.4690 Evaluate side-chains 422 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 421 time to evaluate : 2.707 ------------------------------------------------------------------------------- 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: 4.9990 chunk 178 optimal weight: 30.0000 chunk 4 optimal weight: 6.9990 chunk 234 optimal weight: 0.3980 chunk 130 optimal weight: 10.0000 chunk 268 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 160 optimal weight: 5.9990 chunk 282 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 19 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 392 HIS I 238 ASN I 239 GLN ** J 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25141 Z= 0.266 Angle : 0.698 10.524 34112 Z= 0.357 Chirality : 0.047 0.227 3976 Planarity : 0.004 0.050 4421 Dihedral : 8.410 94.993 3694 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.20 % Allowed : 4.22 % Favored : 95.57 % 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: -3.02 (0.14), residues: 3288 helix: -1.54 (0.14), residues: 1193 sheet: -2.24 (0.23), residues: 442 loop : -2.26 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 160 HIS 0.008 0.001 HIS J 240 PHE 0.024 0.002 PHE M 279 TYR 0.019 0.001 TYR E 167 ARG 0.006 0.000 ARG E 166 *********************** 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 513 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 508 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8509 (p0) cc_final: 0.7632 (t0) REVERT: A 210 MET cc_start: 0.8913 (ttp) cc_final: 0.8711 (ttm) REVERT: A 231 ASP cc_start: 0.7590 (t70) cc_final: 0.7232 (t70) REVERT: B 75 TYR cc_start: 0.8649 (p90) cc_final: 0.8350 (p90) REVERT: B 99 ARG cc_start: 0.8542 (mtt90) cc_final: 0.8136 (mtt90) REVERT: B 103 GLU cc_start: 0.8369 (pm20) cc_final: 0.8020 (pm20) REVERT: C 1 MET cc_start: 0.5032 (ptm) cc_final: 0.4650 (ptt) REVERT: C 93 ILE cc_start: 0.8681 (pt) cc_final: 0.8440 (mt) REVERT: C 114 ARG cc_start: 0.8917 (tpm170) cc_final: 0.8646 (tpp-160) REVERT: C 124 GLN cc_start: 0.8168 (tt0) cc_final: 0.7514 (tt0) REVERT: C 173 GLN cc_start: 0.9265 (mm110) cc_final: 0.9037 (mm-40) REVERT: D 16 HIS cc_start: 0.8789 (m90) cc_final: 0.8324 (m90) REVERT: D 48 ARG cc_start: 0.7333 (ppt170) cc_final: 0.7086 (ptm-80) REVERT: D 56 ASP cc_start: 0.7779 (t70) cc_final: 0.7374 (m-30) REVERT: D 120 TYR cc_start: 0.8081 (m-80) cc_final: 0.7543 (m-80) REVERT: E 84 ASP cc_start: 0.8732 (p0) cc_final: 0.8464 (p0) REVERT: E 206 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8176 (tm-30) REVERT: F 86 ASN cc_start: 0.8969 (m-40) cc_final: 0.8522 (t0) REVERT: G 9 ASP cc_start: 0.7157 (p0) cc_final: 0.6811 (p0) REVERT: G 53 LEU cc_start: 0.8701 (tt) cc_final: 0.8365 (pt) REVERT: G 84 ASP cc_start: 0.8529 (p0) cc_final: 0.8310 (p0) REVERT: G 110 PRO cc_start: 0.9242 (Cg_exo) cc_final: 0.8997 (Cg_endo) REVERT: G 150 MET cc_start: 0.7897 (ttm) cc_final: 0.7413 (tpp) REVERT: G 206 ASP cc_start: 0.9029 (p0) cc_final: 0.8690 (p0) REVERT: G 212 PHE cc_start: 0.8752 (p90) cc_final: 0.8464 (p90) REVERT: G 225 ASN cc_start: 0.7261 (t0) cc_final: 0.7042 (t0) REVERT: H 428 MET cc_start: 0.5978 (tpt) cc_final: 0.5612 (ttm) REVERT: I 222 TYR cc_start: 0.7213 (m-80) cc_final: 0.6647 (m-80) REVERT: I 395 MET cc_start: 0.9192 (tpp) cc_final: 0.8804 (tpp) REVERT: I 398 GLU cc_start: 0.8255 (tp30) cc_final: 0.7837 (tp30) REVERT: J 161 LYS cc_start: 0.8968 (mtmm) cc_final: 0.8633 (mtmm) REVERT: J 327 ILE cc_start: 0.9387 (mm) cc_final: 0.8993 (tt) REVERT: J 367 MET cc_start: 0.8556 (tpt) cc_final: 0.7755 (tpt) REVERT: K 161 MET cc_start: 0.8270 (ppp) cc_final: 0.7872 (ppp) REVERT: K 186 GLU cc_start: 0.9080 (pt0) cc_final: 0.8636 (pt0) REVERT: K 221 MET cc_start: 0.8715 (ppp) cc_final: 0.8333 (ppp) REVERT: K 222 LEU cc_start: 0.9587 (tp) cc_final: 0.9368 (tt) REVERT: K 273 GLU cc_start: 0.7149 (tt0) cc_final: 0.6878 (tt0) REVERT: K 285 GLN cc_start: 0.9269 (mm-40) cc_final: 0.9052 (mm-40) REVERT: K 292 VAL cc_start: 0.9082 (m) cc_final: 0.8829 (p) REVERT: K 325 ASP cc_start: 0.9125 (p0) cc_final: 0.8849 (p0) REVERT: K 346 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.7778 (ppt170) REVERT: L 281 ASP cc_start: 0.8360 (p0) cc_final: 0.7092 (p0) REVERT: L 328 ASN cc_start: 0.8700 (m-40) cc_final: 0.8216 (m-40) REVERT: L 339 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7531 (ttp80) REVERT: M 221 TYR cc_start: 0.7798 (p90) cc_final: 0.7400 (p90) REVERT: M 334 ASP cc_start: 0.7417 (m-30) cc_final: 0.6956 (m-30) REVERT: M 346 LYS cc_start: 0.6979 (pttm) cc_final: 0.6742 (pttm) outliers start: 5 outliers final: 1 residues processed: 511 average time/residue: 0.3450 time to fit residues: 277.3236 Evaluate side-chains 416 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 2.706 ------------------------------------------------------------------------------- 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: 5.9990 chunk 283 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 185 optimal weight: 0.1980 chunk 77 optimal weight: 8.9990 chunk 315 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 165 optimal weight: 9.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- 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** C 152 ASN D 19 GLN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 178 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 348 ASN K 302 GLN L 311 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25141 Z= 0.230 Angle : 0.680 8.710 34112 Z= 0.346 Chirality : 0.045 0.183 3976 Planarity : 0.004 0.048 4421 Dihedral : 8.100 87.303 3694 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.34 % 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: -2.77 (0.14), residues: 3288 helix: -1.34 (0.14), residues: 1185 sheet: -2.04 (0.23), residues: 436 loop : -2.13 (0.16), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 218 HIS 0.009 0.001 HIS J 240 PHE 0.034 0.002 PHE D 174 TYR 0.016 0.001 TYR E 167 ARG 0.007 0.000 ARG G 169 *********************** 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 502 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 500 time to evaluate : 2.767 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: 0.8497 (p0) cc_final: 0.7616 (t0) REVERT: B 4 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7181 (ttp80) REVERT: B 57 MET cc_start: 0.8296 (mmp) cc_final: 0.7978 (mmm) REVERT: B 75 TYR cc_start: 0.8704 (p90) cc_final: 0.8471 (p90) REVERT: B 78 MET cc_start: 0.8052 (ttm) cc_final: 0.7815 (ttm) REVERT: B 103 GLU cc_start: 0.8378 (pm20) cc_final: 0.8015 (pm20) REVERT: B 108 LYS cc_start: 0.6952 (ttpt) cc_final: 0.6523 (tmtt) REVERT: B 117 ILE cc_start: 0.9006 (mm) cc_final: 0.8801 (mm) REVERT: B 241 GLN cc_start: 0.7976 (mm110) cc_final: 0.7649 (mm-40) REVERT: C 93 ILE cc_start: 0.8659 (pt) cc_final: 0.8426 (mt) REVERT: C 114 ARG cc_start: 0.8916 (tpm170) cc_final: 0.8624 (tpp-160) REVERT: C 124 GLN cc_start: 0.7958 (tt0) cc_final: 0.7555 (tt0) REVERT: C 173 GLN cc_start: 0.9276 (mm110) cc_final: 0.9019 (mm-40) REVERT: D 16 HIS cc_start: 0.8845 (m90) cc_final: 0.8421 (m90) REVERT: D 19 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8409 (mm-40) REVERT: D 48 ARG cc_start: 0.7362 (ppt170) cc_final: 0.7140 (ptm-80) REVERT: D 56 ASP cc_start: 0.7800 (t70) cc_final: 0.7371 (m-30) REVERT: D 120 TYR cc_start: 0.8045 (m-80) cc_final: 0.7455 (m-80) REVERT: E 84 ASP cc_start: 0.8719 (p0) cc_final: 0.8464 (p0) REVERT: E 206 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8233 (tm-30) REVERT: F 86 ASN cc_start: 0.8997 (m-40) cc_final: 0.8635 (t0) REVERT: F 102 LYS cc_start: 0.8365 (mmmt) cc_final: 0.7606 (mtmt) REVERT: G 9 ASP cc_start: 0.7124 (p0) cc_final: 0.6750 (p0) REVERT: G 53 LEU cc_start: 0.8625 (tt) cc_final: 0.8357 (pp) REVERT: G 110 PRO cc_start: 0.9236 (Cg_exo) cc_final: 0.8990 (Cg_endo) REVERT: G 150 MET cc_start: 0.7910 (ttm) cc_final: 0.7389 (tpp) REVERT: G 206 ASP cc_start: 0.9044 (p0) cc_final: 0.8761 (p0) REVERT: G 212 PHE cc_start: 0.8737 (p90) cc_final: 0.8437 (p90) REVERT: G 225 ASN cc_start: 0.7212 (t0) cc_final: 0.6962 (t0) REVERT: H 428 MET cc_start: 0.6080 (tpt) cc_final: 0.5742 (ttm) REVERT: I 222 TYR cc_start: 0.7114 (m-80) cc_final: 0.6575 (m-80) REVERT: I 306 MET cc_start: 0.8794 (tmm) cc_final: 0.8579 (tmm) REVERT: I 326 MET cc_start: 0.7796 (pmm) cc_final: 0.7582 (pmm) REVERT: I 398 GLU cc_start: 0.8225 (tp30) cc_final: 0.7814 (tp30) REVERT: J 161 LYS cc_start: 0.8946 (mtmm) cc_final: 0.8706 (ttmm) REVERT: J 327 ILE cc_start: 0.9361 (mm) cc_final: 0.8953 (tt) REVERT: J 367 MET cc_start: 0.8511 (tpt) cc_final: 0.7506 (tpp) REVERT: K 161 MET cc_start: 0.8380 (ppp) cc_final: 0.8007 (ppp) REVERT: K 186 GLU cc_start: 0.9102 (pt0) cc_final: 0.8454 (pt0) REVERT: K 221 MET cc_start: 0.8731 (ppp) cc_final: 0.8354 (ppp) REVERT: K 222 LEU cc_start: 0.9571 (tp) cc_final: 0.9312 (tt) REVERT: K 273 GLU cc_start: 0.7441 (tt0) cc_final: 0.6888 (tt0) REVERT: K 285 GLN cc_start: 0.9274 (mm-40) cc_final: 0.9051 (mm-40) REVERT: K 292 VAL cc_start: 0.9072 (m) cc_final: 0.8809 (p) REVERT: K 303 MET cc_start: 0.9052 (mtp) cc_final: 0.8657 (tpp) REVERT: K 325 ASP cc_start: 0.9122 (p0) cc_final: 0.8873 (p0) REVERT: K 346 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.7770 (ppt170) REVERT: L 312 MET cc_start: 0.9116 (mtm) cc_final: 0.8868 (mtp) REVERT: L 328 ASN cc_start: 0.8685 (m-40) cc_final: 0.8227 (m-40) REVERT: L 339 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7493 (ttp80) REVERT: L 386 PHE cc_start: 0.8541 (m-10) cc_final: 0.8316 (m-80) REVERT: M 334 ASP cc_start: 0.7554 (m-30) cc_final: 0.7077 (m-30) outliers start: 2 outliers final: 0 residues processed: 501 average time/residue: 0.3496 time to fit residues: 278.1721 Evaluate side-chains 418 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 3.765 ------------------------------------------------------------------------------- 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: 0.5980 chunk 35 optimal weight: 5.9990 chunk 179 optimal weight: 0.0770 chunk 230 optimal weight: 1.9990 chunk 178 optimal weight: 30.0000 chunk 265 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 314 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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** A 240 ASN B 139 HIS ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 ASN D 178 ASN D 204 GLN E 114 GLN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 302 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5023 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= 0.174 Angle : 0.666 9.358 34112 Z= 0.331 Chirality : 0.045 0.178 3976 Planarity : 0.004 0.045 4421 Dihedral : 7.597 78.269 3694 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.12 % Allowed : 2.27 % Favored : 97.60 % 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: -2.54 (0.14), residues: 3288 helix: -1.11 (0.15), residues: 1181 sheet: -1.97 (0.23), residues: 471 loop : -1.99 (0.16), residues: 1636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 160 HIS 0.007 0.001 HIS J 240 PHE 0.031 0.002 PHE D 174 TYR 0.018 0.001 TYR E 167 ARG 0.006 0.000 ARG M 303 *********************** 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 529 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 526 time to evaluate : 2.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8500 (p0) cc_final: 0.7564 (t0) REVERT: A 231 ASP cc_start: 0.7308 (t70) cc_final: 0.6984 (t70) REVERT: B 103 GLU cc_start: 0.8338 (pm20) cc_final: 0.8004 (pm20) REVERT: B 108 LYS cc_start: 0.7050 (ttpt) cc_final: 0.6647 (tmtt) REVERT: B 241 GLN cc_start: 0.8182 (mm110) cc_final: 0.7968 (mm-40) REVERT: C 114 ARG cc_start: 0.8840 (tpm170) cc_final: 0.8542 (tpp-160) REVERT: C 120 GLN cc_start: 0.8569 (tm-30) cc_final: 0.8279 (tm-30) REVERT: C 124 GLN cc_start: 0.7628 (tt0) cc_final: 0.7301 (tt0) REVERT: C 173 GLN cc_start: 0.9261 (mm110) cc_final: 0.9039 (mm-40) REVERT: D 16 HIS cc_start: 0.8781 (m90) cc_final: 0.8363 (m90) REVERT: D 19 GLN cc_start: 0.8839 (mm-40) cc_final: 0.8432 (mm110) REVERT: D 56 ASP cc_start: 0.7677 (t70) cc_final: 0.7439 (m-30) REVERT: D 120 TYR cc_start: 0.7973 (m-80) cc_final: 0.7532 (m-80) REVERT: E 84 ASP cc_start: 0.8620 (p0) cc_final: 0.8378 (p0) REVERT: E 206 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8223 (tm-30) REVERT: F 23 GLU cc_start: 0.8624 (mp0) cc_final: 0.8326 (mp0) REVERT: F 102 LYS cc_start: 0.8344 (mmmt) cc_final: 0.7569 (mtmt) REVERT: G 9 ASP cc_start: 0.7044 (p0) cc_final: 0.6641 (p0) REVERT: G 110 PRO cc_start: 0.9208 (Cg_exo) cc_final: 0.8994 (Cg_endo) REVERT: G 150 MET cc_start: 0.7678 (ttm) cc_final: 0.7147 (tpp) REVERT: G 206 ASP cc_start: 0.9085 (p0) cc_final: 0.8844 (p0) REVERT: G 225 ASN cc_start: 0.7100 (t0) cc_final: 0.6861 (t0) REVERT: I 199 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8131 (tm-30) REVERT: I 200 LEU cc_start: 0.8822 (tt) cc_final: 0.8613 (tt) REVERT: I 222 TYR cc_start: 0.7112 (m-80) cc_final: 0.6688 (m-80) REVERT: I 352 ASN cc_start: 0.8579 (m-40) cc_final: 0.8200 (m-40) REVERT: I 398 GLU cc_start: 0.8421 (tp30) cc_final: 0.8118 (tp30) REVERT: I 417 LYS cc_start: 0.9078 (tttm) cc_final: 0.8607 (tptt) REVERT: J 183 LYS cc_start: 0.7461 (pttt) cc_final: 0.7112 (ptmt) REVERT: J 327 ILE cc_start: 0.9302 (mm) cc_final: 0.8878 (tt) REVERT: J 367 MET cc_start: 0.8602 (tpt) cc_final: 0.7666 (tpt) REVERT: K 161 MET cc_start: 0.8199 (ppp) cc_final: 0.7945 (ppp) REVERT: K 186 GLU cc_start: 0.9135 (pt0) cc_final: 0.8760 (pt0) REVERT: K 221 MET cc_start: 0.8740 (ppp) cc_final: 0.8350 (ppp) REVERT: K 222 LEU cc_start: 0.9561 (tp) cc_final: 0.9291 (tt) REVERT: K 235 ILE cc_start: 0.8237 (pt) cc_final: 0.7893 (pt) REVERT: K 273 GLU cc_start: 0.7076 (tt0) cc_final: 0.6660 (tt0) REVERT: K 292 VAL cc_start: 0.9009 (m) cc_final: 0.8732 (p) REVERT: K 303 MET cc_start: 0.9071 (mtp) cc_final: 0.8727 (tpp) REVERT: K 325 ASP cc_start: 0.9115 (p0) cc_final: 0.8729 (t70) REVERT: K 346 ARG cc_start: 0.8406 (mtm-85) cc_final: 0.7757 (ppt170) REVERT: L 281 ASP cc_start: 0.7441 (p0) cc_final: 0.7230 (p0) REVERT: L 328 ASN cc_start: 0.8649 (m-40) cc_final: 0.8161 (m-40) REVERT: L 397 GLU cc_start: 0.8529 (tp30) cc_final: 0.8055 (tp30) REVERT: M 307 GLU cc_start: 0.8183 (pp20) cc_final: 0.7950 (pp20) REVERT: M 334 ASP cc_start: 0.7650 (m-30) cc_final: 0.7179 (m-30) outliers start: 3 outliers final: 0 residues processed: 528 average time/residue: 0.3496 time to fit residues: 288.8484 Evaluate side-chains 428 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 2.969 ------------------------------------------------------------------------------- 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: 4.9990 chunk 125 optimal weight: 6.9990 chunk 187 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 199 optimal weight: 0.0670 chunk 214 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 246 optimal weight: 0.7980 overall best weight: 1.1722 ------------------------------------------------------------------------------- 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 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 ASN D 178 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 217 GLN J 269 GLN K 302 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25141 Z= 0.180 Angle : 0.673 9.185 34112 Z= 0.334 Chirality : 0.045 0.170 3976 Planarity : 0.004 0.054 4421 Dihedral : 7.390 78.018 3694 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.08 % Allowed : 1.71 % Favored : 98.21 % 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: -2.35 (0.15), residues: 3288 helix: -0.94 (0.15), residues: 1178 sheet: -1.83 (0.23), residues: 460 loop : -1.91 (0.16), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 404 HIS 0.008 0.001 HIS J 240 PHE 0.043 0.001 PHE D 174 TYR 0.017 0.001 TYR E 167 ARG 0.014 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 509 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 507 time to evaluate : 2.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.6780 (mpp-170) cc_final: 0.6517 (mpp-170) REVERT: A 77 ARG cc_start: 0.7193 (mmm160) cc_final: 0.6866 (mtp180) REVERT: A 89 ASP cc_start: 0.8511 (p0) cc_final: 0.7604 (t0) REVERT: B 50 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8576 (mmmt) REVERT: B 57 MET cc_start: 0.8530 (mmp) cc_final: 0.8284 (mmp) REVERT: B 103 GLU cc_start: 0.8370 (pm20) cc_final: 0.8032 (pm20) REVERT: B 108 LYS cc_start: 0.7038 (ttpt) cc_final: 0.6677 (tmtt) REVERT: B 241 GLN cc_start: 0.8298 (mm110) cc_final: 0.8091 (mm-40) REVERT: C 109 GLU cc_start: 0.8346 (tt0) cc_final: 0.7748 (tt0) REVERT: C 114 ARG cc_start: 0.8850 (tpm170) cc_final: 0.8563 (tpp-160) REVERT: C 120 GLN cc_start: 0.8551 (tm-30) cc_final: 0.8241 (tm-30) REVERT: C 124 GLN cc_start: 0.7563 (tt0) cc_final: 0.7282 (tt0) REVERT: C 173 GLN cc_start: 0.9249 (mm110) cc_final: 0.8989 (mm-40) REVERT: D 16 HIS cc_start: 0.8752 (m90) cc_final: 0.8376 (m90) REVERT: D 48 ARG cc_start: 0.7362 (ppt170) cc_final: 0.7149 (ptm-80) REVERT: D 56 ASP cc_start: 0.7648 (t70) cc_final: 0.7425 (m-30) REVERT: D 120 TYR cc_start: 0.7975 (m-80) cc_final: 0.7580 (m-80) REVERT: E 206 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8131 (tm-30) REVERT: F 23 GLU cc_start: 0.8536 (mp0) cc_final: 0.8222 (mp0) REVERT: F 102 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7608 (mtmt) REVERT: F 190 ILE cc_start: 0.8890 (pt) cc_final: 0.8435 (mt) REVERT: G 110 PRO cc_start: 0.9199 (Cg_exo) cc_final: 0.8986 (Cg_endo) REVERT: G 150 MET cc_start: 0.7665 (ttm) cc_final: 0.7147 (tpp) REVERT: G 169 ARG cc_start: 0.8548 (mtm110) cc_final: 0.7949 (mtm-85) REVERT: G 206 ASP cc_start: 0.9056 (p0) cc_final: 0.8855 (p0) REVERT: G 225 ASN cc_start: 0.7100 (t0) cc_final: 0.6868 (t0) REVERT: H 428 MET cc_start: 0.6132 (tpt) cc_final: 0.5804 (ttm) REVERT: I 199 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8028 (tm-30) REVERT: I 222 TYR cc_start: 0.7101 (m-80) cc_final: 0.6684 (m-80) REVERT: I 326 MET cc_start: 0.7712 (pmm) cc_final: 0.7484 (pmm) REVERT: I 352 ASN cc_start: 0.8558 (m-40) cc_final: 0.8177 (m-40) REVERT: I 395 MET cc_start: 0.9023 (tpp) cc_final: 0.8738 (mmt) REVERT: I 398 GLU cc_start: 0.8389 (tp30) cc_final: 0.8002 (tp30) REVERT: I 417 LYS cc_start: 0.9059 (tttm) cc_final: 0.8599 (tptt) REVERT: J 183 LYS cc_start: 0.7500 (pttt) cc_final: 0.7196 (ptmt) REVERT: J 269 GLN cc_start: 0.9165 (tt0) cc_final: 0.8589 (tm-30) REVERT: J 327 ILE cc_start: 0.9308 (mm) cc_final: 0.8868 (tt) REVERT: J 367 MET cc_start: 0.8603 (tpt) cc_final: 0.8039 (tpt) REVERT: K 161 MET cc_start: 0.8280 (ppp) cc_final: 0.7994 (ppp) REVERT: K 179 MET cc_start: 0.9019 (ppp) cc_final: 0.8587 (ppp) REVERT: K 186 GLU cc_start: 0.9120 (pt0) cc_final: 0.8869 (pt0) REVERT: K 221 MET cc_start: 0.8755 (ppp) cc_final: 0.8388 (ppp) REVERT: K 222 LEU cc_start: 0.9571 (tp) cc_final: 0.9294 (tt) REVERT: K 273 GLU cc_start: 0.6982 (tt0) cc_final: 0.6747 (tt0) REVERT: K 292 VAL cc_start: 0.9034 (m) cc_final: 0.8753 (p) REVERT: K 303 MET cc_start: 0.9109 (mtp) cc_final: 0.8726 (tpp) REVERT: K 325 ASP cc_start: 0.9098 (p0) cc_final: 0.8719 (t70) REVERT: K 346 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.7765 (ppt170) REVERT: K 377 SER cc_start: 0.8448 (m) cc_final: 0.8164 (p) REVERT: L 203 ASN cc_start: 0.8934 (p0) cc_final: 0.8684 (p0) REVERT: L 281 ASP cc_start: 0.7506 (p0) cc_final: 0.7278 (p0) REVERT: L 328 ASN cc_start: 0.8731 (m-40) cc_final: 0.8303 (m-40) REVERT: L 397 GLU cc_start: 0.8520 (tp30) cc_final: 0.8046 (tp30) REVERT: M 307 GLU cc_start: 0.8160 (pp20) cc_final: 0.7948 (pp20) REVERT: M 334 ASP cc_start: 0.7502 (m-30) cc_final: 0.7199 (m-30) outliers start: 2 outliers final: 0 residues processed: 509 average time/residue: 0.3820 time to fit residues: 308.5538 Evaluate side-chains 431 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 2.974 ------------------------------------------------------------------------------- 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: 7.9990 chunk 301 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 300 optimal weight: 8.9990 chunk 176 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 229 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 276 optimal weight: 0.0670 overall best weight: 1.1922 ------------------------------------------------------------------------------- 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 181 ASN D 178 ASN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5384 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= 0.175 Angle : 0.664 9.648 34112 Z= 0.328 Chirality : 0.044 0.171 3976 Planarity : 0.004 0.050 4421 Dihedral : 7.201 80.896 3694 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.04 % Allowed : 0.81 % Favored : 99.15 % 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: -2.20 (0.15), residues: 3288 helix: -0.80 (0.15), residues: 1176 sheet: -1.69 (0.23), residues: 467 loop : -1.86 (0.16), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 160 HIS 0.010 0.001 HIS J 240 PHE 0.041 0.001 PHE D 174 TYR 0.017 0.001 TYR E 167 ARG 0.012 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 507 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 506 time to evaluate : 2.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ASP cc_start: 0.8510 (p0) cc_final: 0.7563 (t0) REVERT: A 231 ASP cc_start: 0.7162 (t70) cc_final: 0.6811 (t70) REVERT: B 4 ARG cc_start: 0.7463 (ttp80) cc_final: 0.6677 (ttp80) REVERT: B 50 LYS cc_start: 0.8806 (mmmt) cc_final: 0.8525 (mmmt) REVERT: B 108 LYS cc_start: 0.7151 (ttpt) cc_final: 0.6826 (tmtt) REVERT: C 109 GLU cc_start: 0.8345 (tt0) cc_final: 0.7752 (tt0) REVERT: C 114 ARG cc_start: 0.8840 (tpm170) cc_final: 0.8551 (tpp-160) REVERT: C 120 GLN cc_start: 0.8510 (tm-30) cc_final: 0.8207 (tm-30) REVERT: C 124 GLN cc_start: 0.7513 (tt0) cc_final: 0.7214 (tt0) REVERT: C 164 SER cc_start: 0.8283 (p) cc_final: 0.8066 (p) REVERT: C 173 GLN cc_start: 0.9248 (mm110) cc_final: 0.8970 (mm-40) REVERT: D 16 HIS cc_start: 0.8737 (m90) cc_final: 0.8486 (m90) REVERT: D 120 TYR cc_start: 0.7924 (m-80) cc_final: 0.7509 (m-80) REVERT: E 78 MET cc_start: 0.8407 (mtp) cc_final: 0.8002 (mmm) REVERT: E 84 ASP cc_start: 0.8619 (p0) cc_final: 0.8297 (p0) REVERT: E 206 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8132 (tm-30) REVERT: F 23 GLU cc_start: 0.8534 (mp0) cc_final: 0.8205 (mp0) REVERT: F 102 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7643 (mtmt) REVERT: F 190 ILE cc_start: 0.8910 (pt) cc_final: 0.8473 (mt) REVERT: G 9 ASP cc_start: 0.6864 (p0) cc_final: 0.6117 (p0) REVERT: G 110 PRO cc_start: 0.9204 (Cg_exo) cc_final: 0.8985 (Cg_endo) REVERT: G 150 MET cc_start: 0.7666 (ttm) cc_final: 0.7143 (tpp) REVERT: G 206 ASP cc_start: 0.9026 (p0) cc_final: 0.8803 (p0) REVERT: G 225 ASN cc_start: 0.7047 (t0) cc_final: 0.6813 (t0) REVERT: H 428 MET cc_start: 0.6201 (tpt) cc_final: 0.5806 (ttm) REVERT: I 199 GLU cc_start: 0.8384 (tm-30) cc_final: 0.8035 (tm-30) REVERT: I 222 TYR cc_start: 0.7105 (m-80) cc_final: 0.6693 (m-80) REVERT: I 352 ASN cc_start: 0.8580 (m-40) cc_final: 0.8200 (m-40) REVERT: I 395 MET cc_start: 0.9023 (tpp) cc_final: 0.8758 (mmt) REVERT: I 398 GLU cc_start: 0.8410 (tp30) cc_final: 0.8038 (tp30) REVERT: I 417 LYS cc_start: 0.9054 (tttm) cc_final: 0.8587 (tptt) REVERT: J 137 MET cc_start: 0.8973 (pmm) cc_final: 0.8741 (pmm) REVERT: J 183 LYS cc_start: 0.7523 (pttt) cc_final: 0.7145 (ptmt) REVERT: J 269 GLN cc_start: 0.9121 (tt0) cc_final: 0.8555 (tm-30) REVERT: J 327 ILE cc_start: 0.9293 (mm) cc_final: 0.8858 (tt) REVERT: J 367 MET cc_start: 0.8600 (tpt) cc_final: 0.7964 (tpt) REVERT: K 161 MET cc_start: 0.8233 (ppp) cc_final: 0.7977 (ppp) REVERT: K 186 GLU cc_start: 0.9128 (pt0) cc_final: 0.8807 (pt0) REVERT: K 221 MET cc_start: 0.8749 (ppp) cc_final: 0.8360 (ppp) REVERT: K 222 LEU cc_start: 0.9578 (tp) cc_final: 0.9287 (tt) REVERT: K 303 MET cc_start: 0.9144 (mtp) cc_final: 0.8717 (tpp) REVERT: K 325 ASP cc_start: 0.9079 (p0) cc_final: 0.8785 (p0) REVERT: K 346 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.7680 (ppt170) REVERT: K 377 SER cc_start: 0.8412 (m) cc_final: 0.8105 (p) REVERT: L 203 ASN cc_start: 0.8901 (p0) cc_final: 0.8673 (p0) REVERT: L 281 ASP cc_start: 0.7520 (p0) cc_final: 0.7274 (p0) REVERT: L 312 MET cc_start: 0.9184 (mtm) cc_final: 0.8955 (mtp) REVERT: L 328 ASN cc_start: 0.8783 (m-40) cc_final: 0.8356 (m-40) REVERT: L 397 GLU cc_start: 0.8548 (tp30) cc_final: 0.8083 (tp30) REVERT: M 238 GLN cc_start: 0.6844 (tm-30) cc_final: 0.6562 (tm-30) REVERT: M 303 ARG cc_start: 0.8375 (ptt-90) cc_final: 0.8018 (ptp90) REVERT: M 334 ASP cc_start: 0.7528 (m-30) cc_final: 0.7203 (m-30) outliers start: 1 outliers final: 0 residues processed: 507 average time/residue: 0.3457 time to fit residues: 277.4887 Evaluate side-chains 439 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 439 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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: 2.9990 chunk 192 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 188 optimal weight: 0.0970 chunk 146 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 324 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 258 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 199 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 181 ASN B 94 HIS C 152 ASN D 178 ASN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 390 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5484 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= 0.191 Angle : 0.676 9.411 34112 Z= 0.335 Chirality : 0.045 0.250 3976 Planarity : 0.004 0.041 4421 Dihedral : 7.182 84.982 3694 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 0.12 % Allowed : 0.32 % 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: -2.10 (0.15), residues: 3288 helix: -0.73 (0.15), residues: 1173 sheet: -1.62 (0.23), residues: 477 loop : -1.78 (0.16), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 160 HIS 0.010 0.001 HIS J 240 PHE 0.041 0.002 PHE D 174 TYR 0.016 0.001 TYR E 167 ARG 0.007 0.000 ARG D 119 ********************** 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 506 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 503 time to evaluate : 2.718 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 14 ARG cc_start: 0.6807 (mpp-170) cc_final: 0.6406 (mpp-170) REVERT: A 41 ASN cc_start: 0.8486 (m110) cc_final: 0.8100 (m-40) REVERT: A 49 ASP cc_start: 0.8355 (t0) cc_final: 0.7951 (t0) REVERT: A 89 ASP cc_start: 0.8525 (p0) cc_final: 0.7563 (t0) REVERT: B 50 LYS cc_start: 0.8833 (mmmt) cc_final: 0.8583 (mmmt) REVERT: B 108 LYS cc_start: 0.7220 (ttpt) cc_final: 0.6920 (tptp) REVERT: C 114 ARG cc_start: 0.8876 (tpm170) cc_final: 0.8600 (tpp-160) REVERT: C 120 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8180 (tm-30) REVERT: C 124 GLN cc_start: 0.7500 (tt0) cc_final: 0.7242 (tt0) REVERT: C 164 SER cc_start: 0.8206 (p) cc_final: 0.7960 (p) REVERT: C 173 GLN cc_start: 0.9237 (mm110) cc_final: 0.8951 (mm-40) REVERT: D 16 HIS cc_start: 0.8729 (m90) cc_final: 0.8435 (m90) REVERT: D 56 ASP cc_start: 0.7243 (m-30) cc_final: 0.6514 (m-30) REVERT: E 78 MET cc_start: 0.8430 (mtp) cc_final: 0.7992 (mmm) REVERT: E 84 ASP cc_start: 0.8611 (p0) cc_final: 0.8374 (p0) REVERT: E 206 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8059 (tm-30) REVERT: F 23 GLU cc_start: 0.8551 (mp0) cc_final: 0.8262 (mp0) REVERT: F 72 LEU cc_start: 0.9176 (pp) cc_final: 0.8968 (pp) REVERT: F 102 LYS cc_start: 0.8339 (mmmt) cc_final: 0.7744 (mtmt) REVERT: G 110 PRO cc_start: 0.9212 (Cg_exo) cc_final: 0.9004 (Cg_endo) REVERT: G 150 MET cc_start: 0.7680 (ttm) cc_final: 0.7195 (tpp) REVERT: G 225 ASN cc_start: 0.7046 (t0) cc_final: 0.6827 (t0) REVERT: H 428 MET cc_start: 0.6206 (tpt) cc_final: 0.5788 (ttm) REVERT: I 199 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8089 (tm-30) REVERT: I 222 TYR cc_start: 0.7160 (m-80) cc_final: 0.6722 (m-80) REVERT: I 352 ASN cc_start: 0.8563 (m-40) cc_final: 0.8206 (m-40) REVERT: I 395 MET cc_start: 0.9031 (tpp) cc_final: 0.8764 (mmt) REVERT: I 398 GLU cc_start: 0.8317 (tp30) cc_final: 0.7867 (tp30) REVERT: I 417 LYS cc_start: 0.9059 (tttm) cc_final: 0.8598 (tptt) REVERT: J 183 LYS cc_start: 0.7526 (pttt) cc_final: 0.7148 (ptmt) REVERT: J 269 GLN cc_start: 0.9150 (tt0) cc_final: 0.8565 (tm-30) REVERT: J 327 ILE cc_start: 0.9303 (mm) cc_final: 0.8877 (tt) REVERT: J 367 MET cc_start: 0.8600 (tpt) cc_final: 0.7735 (tpt) REVERT: K 161 MET cc_start: 0.8244 (ppp) cc_final: 0.7984 (ppp) REVERT: K 179 MET cc_start: 0.9033 (ppp) cc_final: 0.8812 (ppp) REVERT: K 186 GLU cc_start: 0.9163 (pt0) cc_final: 0.8694 (pt0) REVERT: K 221 MET cc_start: 0.8775 (ppp) cc_final: 0.8400 (ppp) REVERT: K 222 LEU cc_start: 0.9588 (tp) cc_final: 0.9298 (tt) REVERT: K 303 MET cc_start: 0.9177 (mtp) cc_final: 0.8714 (tpp) REVERT: K 325 ASP cc_start: 0.9032 (p0) cc_final: 0.8786 (p0) REVERT: K 346 ARG cc_start: 0.8356 (mtm-85) cc_final: 0.7642 (ppt170) REVERT: K 377 SER cc_start: 0.8415 (m) cc_final: 0.8120 (p) REVERT: L 203 ASN cc_start: 0.8911 (p0) cc_final: 0.8674 (p0) REVERT: L 281 ASP cc_start: 0.7557 (p0) cc_final: 0.7338 (p0) REVERT: L 328 ASN cc_start: 0.8813 (m-40) cc_final: 0.8389 (m-40) REVERT: L 397 GLU cc_start: 0.8567 (tp30) cc_final: 0.8094 (tp30) REVERT: M 238 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6621 (tm-30) REVERT: M 303 ARG cc_start: 0.8386 (ptt-90) cc_final: 0.8127 (ptp90) REVERT: M 334 ASP cc_start: 0.7428 (m-30) cc_final: 0.7117 (m-30) outliers start: 3 outliers final: 0 residues processed: 504 average time/residue: 0.3392 time to fit residues: 269.5138 Evaluate side-chains 430 residues out of total 2787 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 430 time to evaluate : 2.866 ------------------------------------------------------------------------------- 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: 0.7980 chunk 205 optimal weight: 7.9990 chunk 275 optimal weight: 9.9990 chunk 79 optimal weight: 0.0670 chunk 238 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 265 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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 181 ASN A 209 HIS C 227 GLN ** D 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN F 60 GLN ** G 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.084954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.072148 restraints weight = 88773.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.074025 restraints weight = 57626.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.075547 restraints weight = 37829.271| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25141 Z= 0.169 Angle : 0.670 10.510 34112 Z= 0.330 Chirality : 0.044 0.173 3976 Planarity : 0.004 0.058 4421 Dihedral : 7.063 89.837 3694 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % Favored : 99.39 % 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: -2.05 (0.15), residues: 3288 helix: -0.66 (0.15), residues: 1165 sheet: -1.64 (0.23), residues: 455 loop : -1.76 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 160 HIS 0.010 0.001 HIS J 240 PHE 0.026 0.001 PHE A 205 TYR 0.017 0.001 TYR E 167 ARG 0.014 0.000 ARG G 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5724.03 seconds wall clock time: 102 minutes 19.63 seconds (6139.63 seconds total)