Starting phenix.real_space_refine on Sun Aug 24 14:54:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k27_36830/08_2025/8k27_36830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k27_36830/08_2025/8k27_36830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k27_36830/08_2025/8k27_36830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k27_36830/08_2025/8k27_36830.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k27_36830/08_2025/8k27_36830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k27_36830/08_2025/8k27_36830.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 sd= 0.004 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 134 5.49 5 S 72 5.16 5 C 12914 2.51 5 N 3608 2.21 5 O 4455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21183 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1382 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 6, 'TRANS': 166} Chain: "B" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1903 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 10, 'TRANS': 235} Chain: "D" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "P" Number of atoms: 1260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1260 Classifications: {'RNA': 60} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 17, 'rna3p_pur': 14, 'rna3p_pyr': 18} Link IDs: {'rna2p': 27, 'rna3p': 32} Chain: "Q" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1013 Classifications: {'DNA': 49} Link IDs: {'rna3p': 48} Chain: "R" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 515 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2301 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2305 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2299 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 294} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1290 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Time building chain proxies: 5.02, per 1000 atoms: 0.24 Number of scatterers: 21183 At special positions: 0 Unit cell: (171.72, 131.76, 153.36, 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 72 16.00 P 134 15.00 O 4455 8.00 N 3608 7.00 C 12914 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 156 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.95 Conformation dependent library (CDL) restraints added in 825.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4372 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 43 sheets defined 27.1% alpha, 22.5% beta 37 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.798A pdb=" N ASP A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.544A pdb=" N ALA A 52 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 68 removed outlier: 3.823A pdb=" N LYS A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 81 through 90 removed outlier: 3.565A pdb=" N GLN A 85 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.746A pdb=" N ILE A 125 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.796A pdb=" N ASN A 151 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 148 through 152' Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.732A pdb=" N MET A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.972A pdb=" N PHE B 32 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 122 removed outlier: 3.575A pdb=" N PHE B 120 " --> pdb=" O LYS B 116 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN B 122 " --> pdb=" O THR B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 155 removed outlier: 3.682A pdb=" N ALA B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N MET B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 178 Processing helix chain 'B' and resid 219 through 223 removed outlier: 3.675A pdb=" N VAL B 223 " --> pdb=" O VAL B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 229 Processing helix chain 'D' and resid 53 through 57 removed outlier: 3.623A pdb=" N ALA D 57 " --> pdb=" O PRO D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.521A pdb=" N THR D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 removed outlier: 3.785A pdb=" N LEU D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 120 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE D 123 " --> pdb=" O TYR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 178 removed outlier: 3.726A pdb=" N ILE D 169 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N MET D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.579A pdb=" N ASN D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA D 232 " --> pdb=" O LYS D 228 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE D 233 " --> pdb=" O ILE D 229 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG D 234 " --> pdb=" O GLY D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 287 through 298 Processing helix chain 'C' and resid 53 through 57 removed outlier: 3.513A pdb=" N ALA C 57 " --> pdb=" O PRO C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 105 Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.766A pdb=" N LEU C 115 " --> pdb=" O ASP C 111 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 123 " --> pdb=" O TYR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 179 removed outlier: 3.973A pdb=" N ALA C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU C 168 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE C 169 " --> pdb=" O ASP C 165 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 176 " --> pdb=" O MET C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 234 removed outlier: 3.825A pdb=" N ASN C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE C 233 " --> pdb=" O ILE C 229 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG C 234 " --> pdb=" O GLY C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 removed outlier: 3.509A pdb=" N LEU C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ASP C 275 " --> pdb=" O PHE C 271 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 298 removed outlier: 3.605A pdb=" N MET C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL C 291 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 58 removed outlier: 3.730A pdb=" N ALA G 57 " --> pdb=" O PRO G 54 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP G 58 " --> pdb=" O ASN G 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 54 through 58' Processing helix chain 'G' and resid 99 through 107 Processing helix chain 'G' and resid 111 through 126 removed outlier: 3.747A pdb=" N LEU G 115 " --> pdb=" O ASP G 111 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN G 122 " --> pdb=" O ARG G 118 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE G 123 " --> pdb=" O TYR G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 179 removed outlier: 3.643A pdb=" N MET G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 234 removed outlier: 3.629A pdb=" N ILE G 229 " --> pdb=" O HIS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 280 removed outlier: 3.500A pdb=" N LEU G 273 " --> pdb=" O ASP G 269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP G 275 " --> pdb=" O PHE G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 288 through 298 Processing helix chain 'F' and resid 98 through 104 removed outlier: 3.527A pdb=" N GLN F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 126 removed outlier: 3.731A pdb=" N LEU F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 130 Processing helix chain 'F' and resid 164 through 178 removed outlier: 3.845A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.704A pdb=" N ILE F 229 " --> pdb=" O HIS F 225 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA F 232 " --> pdb=" O LYS F 228 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG F 234 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 279 removed outlier: 3.739A pdb=" N ASN F 279 " --> pdb=" O ASP F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 298 removed outlier: 3.773A pdb=" N GLN F 288 " --> pdb=" O THR F 284 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N MET F 289 " --> pdb=" O GLU F 285 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N PHE F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 removed outlier: 3.708A pdb=" N ALA E 57 " --> pdb=" O PRO E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 105 removed outlier: 3.871A pdb=" N THR E 105 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.752A pdb=" N LEU E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL E 120 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN E 122 " --> pdb=" O ARG E 118 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE E 123 " --> pdb=" O TYR E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 178 removed outlier: 3.767A pdb=" N ILE E 169 " --> pdb=" O ASP E 165 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.579A pdb=" N ILE E 229 " --> pdb=" O HIS E 225 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA E 232 " --> pdb=" O LYS E 228 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 234 " --> pdb=" O GLY E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 280 removed outlier: 3.938A pdb=" N ASP E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN E 279 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 298 Processing helix chain 'H' and resid 54 through 58 removed outlier: 4.084A pdb=" N ALA H 57 " --> pdb=" O PRO H 54 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP H 58 " --> pdb=" O ASN H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 58' Processing helix chain 'H' and resid 99 through 105 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.879A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 179 removed outlier: 3.658A pdb=" N MET H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 234 Processing helix chain 'H' and resid 269 through 280 Processing helix chain 'H' and resid 284 through 298 removed outlier: 3.664A pdb=" N PHE H 290 " --> pdb=" O GLU H 286 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL H 291 " --> pdb=" O ASP H 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 15 through 30 Processing helix chain 'I' and resid 61 through 69 removed outlier: 3.877A pdb=" N LEU I 65 " --> pdb=" O ASP I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 71 No H-bonds generated for 'chain 'I' and resid 70 through 71' Processing helix chain 'I' and resid 72 through 74 No H-bonds generated for 'chain 'I' and resid 72 through 74' Processing helix chain 'I' and resid 98 through 109 Processing helix chain 'I' and resid 112 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.770A pdb=" N GLY A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.770A pdb=" N GLY A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N TYR B 206 " --> pdb=" O TYR A 112 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE A 114 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ALA B 208 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 116 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA B 205 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYS B 191 " --> pdb=" O ALA B 205 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU B 207 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY B 185 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR B 213 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL B 183 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B 215 " --> pdb=" O PRO B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 142 removed outlier: 8.251A pdb=" N VAL B 24 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N PHE A 166 " --> pdb=" O VAL B 24 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.093A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.093A pdb=" N ALA B 49 " --> pdb=" O GLU B 103 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ALA B 94 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 100 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LYS B 8 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N PHE B 102 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE B 6 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 104 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHE B 4 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 6 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 138 " --> pdb=" O ILE B 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 231 through 232 Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.734A pdb=" N TYR D 12 " --> pdb=" O GLY D 299 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY D 299 " --> pdb=" O TYR D 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB2, first strand: chain 'D' and resid 16 through 18 Processing sheet with id=AB3, first strand: chain 'D' and resid 40 through 44 Processing sheet with id=AB4, first strand: chain 'D' and resid 217 through 218 Processing sheet with id=AB5, first strand: chain 'D' and resid 254 through 255 removed outlier: 3.653A pdb=" N VAL D 260 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 Processing sheet with id=AB7, first strand: chain 'C' and resid 16 through 18 Processing sheet with id=AB8, first strand: chain 'C' and resid 16 through 18 removed outlier: 3.631A pdb=" N THR C 141 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL C 145 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 40 through 47 removed outlier: 3.528A pdb=" N PHE C 67 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 217 through 218 Processing sheet with id=AC2, first strand: chain 'C' and resid 254 through 255 Processing sheet with id=AC3, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.661A pdb=" N THR G 35 " --> pdb=" O ALA G 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.645A pdb=" N VAL G 145 " --> pdb=" O GLN G 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 40 through 45 Processing sheet with id=AC6, first strand: chain 'G' and resid 235 through 237 Processing sheet with id=AC7, first strand: chain 'G' and resid 254 through 255 Processing sheet with id=AC8, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AC9, first strand: chain 'F' and resid 16 through 18 Processing sheet with id=AD1, first strand: chain 'F' and resid 40 through 45 removed outlier: 3.679A pdb=" N PHE F 67 " --> pdb=" O GLY F 40 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 217 through 218 Processing sheet with id=AD3, first strand: chain 'F' and resid 254 through 255 removed outlier: 3.784A pdb=" N VAL F 260 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 16 through 18 Processing sheet with id=AD5, first strand: chain 'E' and resid 16 through 18 Processing sheet with id=AD6, first strand: chain 'E' and resid 40 through 47 Processing sheet with id=AD7, first strand: chain 'E' and resid 217 through 218 Processing sheet with id=AD8, first strand: chain 'E' and resid 254 through 255 Processing sheet with id=AD9, first strand: chain 'H' and resid 92 through 94 removed outlier: 3.569A pdb=" N LEU H 94 " --> pdb=" O ALA H 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 16 through 18 Processing sheet with id=AE2, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.730A pdb=" N MET H 224 " --> pdb=" O ALA H 21 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 40 through 42 Processing sheet with id=AE4, first strand: chain 'H' and resid 235 through 237 Processing sheet with id=AE5, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AE6, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AE7, first strand: chain 'I' and resid 90 through 93 removed outlier: 3.711A pdb=" N GLU I 149 " --> pdb=" O ARG I 91 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE I 147 " --> pdb=" O VAL I 93 " (cutoff:3.500A) 643 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 3.57 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4249 1.33 - 1.45: 5849 1.45 - 1.57: 11345 1.57 - 1.70: 264 1.70 - 1.82: 129 Bond restraints: 21836 Sorted by residual: bond pdb=" C LYS I 156 " pdb=" N PHE I 157 " ideal model delta sigma weight residual 1.331 1.509 -0.178 1.38e-02 5.25e+03 1.67e+02 bond pdb=" O3' A P 36 " pdb=" P G P 37 " ideal model delta sigma weight residual 1.607 1.462 0.145 1.50e-02 4.44e+03 9.33e+01 bond pdb=" CA ALA I 113 " pdb=" C ALA I 113 " ideal model delta sigma weight residual 1.524 1.463 0.061 1.32e-02 5.74e+03 2.13e+01 bond pdb=" CA SER I 112 " pdb=" C SER I 112 " ideal model delta sigma weight residual 1.524 1.469 0.055 1.31e-02 5.83e+03 1.76e+01 bond pdb=" CA ASN I 34 " pdb=" C ASN I 34 " ideal model delta sigma weight residual 1.524 1.472 0.051 1.26e-02 6.30e+03 1.66e+01 ... (remaining 21831 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.33: 30196 14.33 - 28.66: 5 28.66 - 42.99: 1 42.99 - 57.32: 0 57.32 - 71.65: 1 Bond angle restraints: 30203 Sorted by residual: angle pdb=" O3' A P 36 " pdb=" P G P 37 " pdb=" O5' G P 37 " ideal model delta sigma weight residual 104.00 32.35 71.65 1.50e+00 4.44e-01 2.28e+03 angle pdb=" CA THR I 58 " pdb=" C THR I 58 " pdb=" N GLY I 59 " ideal model delta sigma weight residual 118.14 94.06 24.08 1.31e+00 5.83e-01 3.38e+02 angle pdb=" O THR I 58 " pdb=" C THR I 58 " pdb=" N GLY I 59 " ideal model delta sigma weight residual 122.43 144.38 -21.95 1.34e+00 5.57e-01 2.68e+02 angle pdb=" C3' A P 36 " pdb=" O3' A P 36 " pdb=" P G P 37 " ideal model delta sigma weight residual 120.20 99.14 21.06 1.50e+00 4.44e-01 1.97e+02 angle pdb=" C THR I 58 " pdb=" N GLY I 59 " pdb=" CA GLY I 59 " ideal model delta sigma weight residual 121.41 96.90 24.51 1.96e+00 2.60e-01 1.56e+02 ... (remaining 30198 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 11835 35.45 - 70.89: 908 70.89 - 106.34: 53 106.34 - 141.79: 2 141.79 - 177.23: 10 Dihedral angle restraints: 12808 sinusoidal: 5965 harmonic: 6843 Sorted by residual: dihedral pdb=" O4' C P 44 " pdb=" C1' C P 44 " pdb=" N1 C P 44 " pdb=" C2 C P 44 " ideal model delta sinusoidal sigma weight residual 200.00 34.49 165.51 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" CB CYS A 152 " pdb=" SG CYS A 152 " pdb=" SG CYS A 156 " pdb=" CB CYS A 156 " ideal model delta sinusoidal sigma weight residual -86.00 -144.16 58.16 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" C5' U P 35 " pdb=" C4' U P 35 " pdb=" C3' U P 35 " pdb=" O3' U P 35 " ideal model delta sinusoidal sigma weight residual 147.00 112.60 34.40 1 8.00e+00 1.56e-02 2.62e+01 ... (remaining 12805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.142: 3361 0.142 - 0.285: 124 0.285 - 0.427: 12 0.427 - 0.570: 3 0.570 - 0.712: 1 Chirality restraints: 3501 Sorted by residual: chirality pdb=" C3' C P 41 " pdb=" C4' C P 41 " pdb=" O3' C P 41 " pdb=" C2' C P 41 " both_signs ideal model delta sigma weight residual False -2.74 -2.03 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CA LYS I 124 " pdb=" N LYS I 124 " pdb=" C LYS I 124 " pdb=" CB LYS I 124 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CA PHE I 55 " pdb=" N PHE I 55 " pdb=" C PHE I 55 " pdb=" CB PHE I 55 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.78e+00 ... (remaining 3498 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 86 " -0.090 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO B 87 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO B 87 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO B 87 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 61 " 0.022 2.00e-02 2.50e+03 4.44e-02 1.97e+01 pdb=" C ASP I 61 " -0.077 2.00e-02 2.50e+03 pdb=" O ASP I 61 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG I 62 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR I 58 " 0.013 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C THR I 58 " -0.061 2.00e-02 2.50e+03 pdb=" O THR I 58 " 0.027 2.00e-02 2.50e+03 pdb=" N GLY I 59 " 0.022 2.00e-02 2.50e+03 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 7 2.30 - 2.95: 9204 2.95 - 3.60: 28777 3.60 - 4.25: 49422 4.25 - 4.90: 80459 Nonbonded interactions: 167869 Sorted by model distance: nonbonded pdb=" CG1 VAL H 134 " pdb=" CZ PHE I 75 " model vdw 1.649 3.760 nonbonded pdb=" O3' A P 36 " pdb=" C5' G P 37 " model vdw 2.132 2.752 nonbonded pdb=" N THR I 58 " pdb=" N GLY I 59 " model vdw 2.158 2.560 nonbonded pdb=" O SER A 51 " pdb=" OG SER A 51 " model vdw 2.266 3.040 nonbonded pdb=" C3' A P 36 " pdb=" O5' G P 37 " model vdw 2.269 2.776 ... (remaining 167864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'D' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'F' and (resid 2 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'G' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB )) or resid 52 through 303)) selection = (chain 'H' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 303)) } 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 20.430 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.178 21837 Z= 0.353 Angle : 1.152 71.649 30205 Z= 0.716 Chirality : 0.066 0.712 3501 Planarity : 0.006 0.134 3438 Dihedral : 21.737 177.233 8433 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.50 % Allowed : 7.32 % Favored : 92.18 % Rotamer: Outliers : 11.13 % Allowed : 16.08 % Favored : 72.79 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.14), residues: 2378 helix: -2.58 (0.15), residues: 572 sheet: -0.12 (0.26), residues: 450 loop : -2.81 (0.13), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 133 TYR 0.057 0.002 TYR I 132 PHE 0.050 0.002 PHE E 182 TRP 0.049 0.002 TRP C 130 HIS 0.006 0.001 HIS I 28 Details of bonding type rmsd covalent geometry : bond 0.00571 (21836) covalent geometry : angle 1.15077 (30203) SS BOND : bond 0.00369 ( 1) SS BOND : angle 7.46609 ( 2) hydrogen bonds : bond 0.20377 ( 708) hydrogen bonds : angle 7.70195 ( 1926) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 293 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7218 (tt0) REVERT: A 142 GLN cc_start: 0.8604 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 195 ASN cc_start: 0.7882 (p0) cc_final: 0.7262 (t0) REVERT: D 58 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7740 (p0) REVERT: C 22 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8564 (mt) REVERT: C 30 ASP cc_start: 0.7339 (OUTLIER) cc_final: 0.6643 (p0) REVERT: C 58 ASP cc_start: 0.8937 (OUTLIER) cc_final: 0.8727 (p0) REVERT: F 58 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6322 (m-30) REVERT: F 59 LYS cc_start: 0.6335 (OUTLIER) cc_final: 0.5954 (tptp) REVERT: F 61 ASN cc_start: 0.6497 (OUTLIER) cc_final: 0.6077 (m-40) REVERT: H 86 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8621 (t) REVERT: H 127 ARG cc_start: 0.7128 (OUTLIER) cc_final: 0.6301 (ttm110) REVERT: H 130 TRP cc_start: 0.6532 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: H 192 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6693 (tt) REVERT: H 211 LEU cc_start: 0.6323 (OUTLIER) cc_final: 0.5889 (mp) REVERT: H 213 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6496 (tppt) REVERT: H 228 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7061 (tttp) REVERT: H 260 VAL cc_start: 0.5983 (OUTLIER) cc_final: 0.5698 (m) REVERT: H 266 ASN cc_start: 0.7064 (OUTLIER) cc_final: 0.6430 (p0) REVERT: H 281 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5855 (ttmm) outliers start: 218 outliers final: 27 residues processed: 430 average time/residue: 0.1592 time to fit residues: 103.1424 Evaluate side-chains 248 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 203 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 58 ASP Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 114 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 228 LYS Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 260 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 0.0570 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 8.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN D 294 ASN G 294 ASN F 61 ASN F 203 GLN H 73 ASN H 132 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.096860 restraints weight = 35477.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096530 restraints weight = 48012.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097461 restraints weight = 45570.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.097997 restraints weight = 27963.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.098543 restraints weight = 25376.777| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 21837 Z= 0.142 Angle : 0.607 10.390 30205 Z= 0.333 Chirality : 0.042 0.201 3501 Planarity : 0.004 0.088 3438 Dihedral : 21.375 177.250 4390 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.96 % Favored : 94.83 % Rotamer: Outliers : 4.34 % Allowed : 18.43 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.16), residues: 2378 helix: -0.92 (0.20), residues: 575 sheet: 0.43 (0.27), residues: 418 loop : -2.44 (0.14), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 43 TYR 0.013 0.001 TYR H 121 PHE 0.014 0.001 PHE B 64 TRP 0.014 0.001 TRP C 130 HIS 0.005 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00311 (21836) covalent geometry : angle 0.60606 (30203) SS BOND : bond 0.00304 ( 1) SS BOND : angle 4.04387 ( 2) hydrogen bonds : bond 0.04624 ( 708) hydrogen bonds : angle 4.93604 ( 1926) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 197 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8154 (ttm-80) cc_final: 0.7891 (tpp80) REVERT: B 237 THR cc_start: 0.7801 (OUTLIER) cc_final: 0.7486 (p) REVERT: D 58 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7813 (p0) REVERT: C 30 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.6960 (p0) REVERT: C 99 TYR cc_start: 0.8449 (t80) cc_final: 0.8119 (t80) REVERT: G 228 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8399 (mmtt) REVERT: G 289 MET cc_start: 0.7876 (ptp) cc_final: 0.7670 (ptp) REVERT: G 294 ASN cc_start: 0.9258 (OUTLIER) cc_final: 0.9051 (t0) REVERT: H 33 ASN cc_start: 0.7415 (m-40) cc_final: 0.6735 (m110) REVERT: H 127 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.6366 (ttm110) REVERT: H 130 TRP cc_start: 0.6581 (OUTLIER) cc_final: 0.6321 (m-10) REVERT: H 211 LEU cc_start: 0.6413 (OUTLIER) cc_final: 0.5945 (mp) REVERT: H 213 LYS cc_start: 0.7165 (OUTLIER) cc_final: 0.6758 (tppt) REVERT: H 227 GLN cc_start: 0.7959 (pt0) cc_final: 0.7684 (mt0) REVERT: H 266 ASN cc_start: 0.6937 (OUTLIER) cc_final: 0.6024 (t0) REVERT: H 283 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7340 (mp) REVERT: I 44 MET cc_start: 0.8039 (tmm) cc_final: 0.7810 (tmm) REVERT: I 104 ARG cc_start: 0.4897 (OUTLIER) cc_final: 0.2670 (ttp-170) outliers start: 85 outliers final: 37 residues processed: 267 average time/residue: 0.1382 time to fit residues: 57.8101 Evaluate side-chains 226 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 164 VAL Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 294 ASN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 171 ASP Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 74 LYS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 268 THR Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 69 LEU Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 235 optimal weight: 3.9990 chunk 203 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 243 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN A 123 ASN B 85 ASN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN E 66 ASN E 72 HIS H 73 ASN ** H 294 ASN ** 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 = 0.3576 r_free = 0.3576 target = 0.126618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.090868 restraints weight = 35677.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091534 restraints weight = 46734.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.091882 restraints weight = 44877.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.092552 restraints weight = 27158.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.092829 restraints weight = 23795.245| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21837 Z= 0.224 Angle : 0.625 10.643 30205 Z= 0.340 Chirality : 0.043 0.212 3501 Planarity : 0.004 0.075 3438 Dihedral : 21.106 178.785 4344 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.93 % Favored : 93.82 % Rotamer: Outliers : 4.85 % Allowed : 18.43 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.16), residues: 2378 helix: -0.38 (0.21), residues: 579 sheet: 0.24 (0.26), residues: 463 loop : -2.33 (0.14), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 22 TYR 0.015 0.002 TYR C 81 PHE 0.014 0.002 PHE C 205 TRP 0.015 0.001 TRP G 239 HIS 0.007 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00522 (21836) covalent geometry : angle 0.62478 (30203) SS BOND : bond 0.00419 ( 1) SS BOND : angle 3.43934 ( 2) hydrogen bonds : bond 0.04898 ( 708) hydrogen bonds : angle 4.69104 ( 1926) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 189 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7941 (tpp80) REVERT: B 198 MET cc_start: 0.8674 (mmm) cc_final: 0.8340 (mmm) REVERT: B 237 THR cc_start: 0.8027 (OUTLIER) cc_final: 0.7718 (p) REVERT: D 128 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9343 (m) REVERT: C 30 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7584 (p0) REVERT: C 99 TYR cc_start: 0.8535 (t80) cc_final: 0.8029 (t80) REVERT: C 185 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8338 (pt) REVERT: G 191 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7431 (mtt) REVERT: G 210 LYS cc_start: 0.7386 (ptmt) cc_final: 0.6973 (tttm) REVERT: H 127 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6250 (ttm110) REVERT: H 130 TRP cc_start: 0.6361 (OUTLIER) cc_final: 0.6100 (m-10) REVERT: H 211 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6030 (mp) REVERT: H 213 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6699 (tppt) REVERT: H 283 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7455 (mp) REVERT: I 50 ASP cc_start: 0.7506 (p0) cc_final: 0.7271 (p0) REVERT: I 104 ARG cc_start: 0.4778 (OUTLIER) cc_final: 0.2978 (tmm160) outliers start: 95 outliers final: 57 residues processed: 265 average time/residue: 0.1299 time to fit residues: 54.4570 Evaluate side-chains 244 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 176 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 29 SER Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 53 THR Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 168 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 241 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 244 optimal weight: 0.0870 chunk 78 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.126239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090568 restraints weight = 35577.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.091010 restraints weight = 48712.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091690 restraints weight = 44907.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092027 restraints weight = 28747.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.092647 restraints weight = 25815.564| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21837 Z= 0.183 Angle : 0.580 9.371 30205 Z= 0.318 Chirality : 0.043 0.211 3501 Planarity : 0.004 0.068 3438 Dihedral : 20.956 177.739 4332 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.76 % Favored : 94.03 % Rotamer: Outliers : 5.05 % Allowed : 18.63 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.16), residues: 2378 helix: -0.05 (0.22), residues: 575 sheet: 0.31 (0.27), residues: 444 loop : -2.21 (0.14), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 22 TYR 0.014 0.001 TYR H 81 PHE 0.020 0.001 PHE I 18 TRP 0.018 0.001 TRP F 130 HIS 0.005 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00421 (21836) covalent geometry : angle 0.57985 (30203) SS BOND : bond 0.00326 ( 1) SS BOND : angle 3.05634 ( 2) hydrogen bonds : bond 0.04309 ( 708) hydrogen bonds : angle 4.49240 ( 1926) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 188 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7888 (ttp-170) REVERT: B 172 GLU cc_start: 0.7362 (mp0) cc_final: 0.7044 (mp0) REVERT: B 237 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7659 (p) REVERT: B 240 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7835 (pmtt) REVERT: D 128 THR cc_start: 0.9529 (OUTLIER) cc_final: 0.9285 (m) REVERT: D 130 TRP cc_start: 0.6802 (OUTLIER) cc_final: 0.6028 (m-10) REVERT: C 185 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8342 (pt) REVERT: G 129 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8728 (mt) REVERT: G 191 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7406 (mtt) REVERT: G 210 LYS cc_start: 0.7506 (ptmt) cc_final: 0.7160 (tttm) REVERT: H 127 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6105 (ttm110) REVERT: H 130 TRP cc_start: 0.6282 (OUTLIER) cc_final: 0.6041 (m-10) REVERT: H 211 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6123 (mp) REVERT: H 213 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6737 (tppt) REVERT: H 283 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7455 (mp) REVERT: I 50 ASP cc_start: 0.7563 (p0) cc_final: 0.7341 (p0) REVERT: I 57 LYS cc_start: 0.4209 (OUTLIER) cc_final: 0.3564 (mttt) REVERT: I 80 LYS cc_start: 0.6168 (OUTLIER) cc_final: 0.5267 (tmtt) REVERT: I 91 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.6110 (ptt180) REVERT: I 104 ARG cc_start: 0.4810 (OUTLIER) cc_final: 0.3007 (tmm160) outliers start: 99 outliers final: 55 residues processed: 265 average time/residue: 0.1350 time to fit residues: 56.9360 Evaluate side-chains 247 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 129 LEU Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 91 ARG Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 146 MET Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 100 optimal weight: 7.9990 chunk 238 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN F 61 ASN H 33 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.122645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.088629 restraints weight = 35540.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088910 restraints weight = 61568.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.089719 restraints weight = 50813.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.089684 restraints weight = 34129.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.090840 restraints weight = 30260.561| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 21837 Z= 0.292 Angle : 0.673 8.777 30205 Z= 0.365 Chirality : 0.046 0.212 3501 Planarity : 0.004 0.067 3438 Dihedral : 20.925 178.994 4327 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.94 % Favored : 92.81 % Rotamer: Outliers : 5.36 % Allowed : 19.14 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.16), residues: 2378 helix: -0.16 (0.21), residues: 574 sheet: 0.12 (0.26), residues: 444 loop : -2.23 (0.14), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 63 TYR 0.015 0.002 TYR C 81 PHE 0.023 0.002 PHE D 85 TRP 0.016 0.002 TRP F 130 HIS 0.008 0.002 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00687 (21836) covalent geometry : angle 0.67266 (30203) SS BOND : bond 0.00349 ( 1) SS BOND : angle 3.24641 ( 2) hydrogen bonds : bond 0.05132 ( 708) hydrogen bonds : angle 4.63897 ( 1926) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 178 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8642 (tp40) REVERT: B 83 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8875 (m110) REVERT: B 166 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8188 (p) REVERT: B 237 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7677 (p) REVERT: B 240 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.7818 (pmtt) REVERT: D 128 THR cc_start: 0.9589 (OUTLIER) cc_final: 0.9385 (m) REVERT: D 130 TRP cc_start: 0.7012 (OUTLIER) cc_final: 0.6477 (m-10) REVERT: D 289 MET cc_start: 0.7883 (mtm) cc_final: 0.7654 (mtm) REVERT: C 185 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8425 (pt) REVERT: G 210 LYS cc_start: 0.7567 (ptmt) cc_final: 0.7267 (tttm) REVERT: H 127 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6129 (ttm110) REVERT: H 130 TRP cc_start: 0.6437 (OUTLIER) cc_final: 0.5751 (m-10) REVERT: H 211 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6132 (mp) REVERT: H 213 LYS cc_start: 0.7130 (OUTLIER) cc_final: 0.6693 (tppt) REVERT: I 50 ASP cc_start: 0.7748 (p0) cc_final: 0.7547 (p0) REVERT: I 57 LYS cc_start: 0.4495 (OUTLIER) cc_final: 0.3961 (mptt) REVERT: I 91 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6443 (ptt180) REVERT: I 104 ARG cc_start: 0.4820 (OUTLIER) cc_final: 0.2962 (tmm160) outliers start: 105 outliers final: 64 residues processed: 263 average time/residue: 0.1360 time to fit residues: 55.7349 Evaluate side-chains 240 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 162 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 145 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 221 GLN Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain I residue 6 ILE Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 91 ARG Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 178 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 192 optimal weight: 0.3980 chunk 243 optimal weight: 20.0000 chunk 146 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 245 optimal weight: 0.0040 overall best weight: 1.0594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.126160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.092246 restraints weight = 35379.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.091907 restraints weight = 56492.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092410 restraints weight = 51691.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094891 restraints weight = 35787.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094721 restraints weight = 24099.638| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21837 Z= 0.125 Angle : 0.564 9.642 30205 Z= 0.307 Chirality : 0.042 0.224 3501 Planarity : 0.004 0.061 3438 Dihedral : 20.754 176.811 4324 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.13 % Favored : 94.70 % Rotamer: Outliers : 3.01 % Allowed : 20.67 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.16), residues: 2378 helix: 0.20 (0.22), residues: 574 sheet: 0.38 (0.26), residues: 455 loop : -2.11 (0.14), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 74 TYR 0.018 0.001 TYR H 81 PHE 0.014 0.001 PHE I 18 TRP 0.017 0.001 TRP G 130 HIS 0.003 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00268 (21836) covalent geometry : angle 0.56368 (30203) SS BOND : bond 0.00361 ( 1) SS BOND : angle 2.56728 ( 2) hydrogen bonds : bond 0.03851 ( 708) hydrogen bonds : angle 4.38616 ( 1926) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8353 (m-10) cc_final: 0.8123 (m-80) REVERT: B 26 MET cc_start: 0.8676 (tpp) cc_final: 0.8169 (mtp) REVERT: B 83 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8865 (m110) REVERT: B 156 MET cc_start: 0.6117 (tpt) cc_final: 0.5439 (ttt) REVERT: B 172 GLU cc_start: 0.7407 (mp0) cc_final: 0.7089 (mp0) REVERT: B 237 THR cc_start: 0.7954 (m) cc_final: 0.7636 (p) REVERT: B 240 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.7784 (pmtt) REVERT: D 128 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9289 (m) REVERT: D 130 TRP cc_start: 0.6922 (OUTLIER) cc_final: 0.6307 (m-10) REVERT: D 289 MET cc_start: 0.7791 (mtm) cc_final: 0.7529 (mtm) REVERT: C 185 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8363 (pt) REVERT: G 191 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7448 (mtt) REVERT: G 210 LYS cc_start: 0.7560 (ptmt) cc_final: 0.7276 (tttm) REVERT: H 127 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.5928 (ttm110) REVERT: H 130 TRP cc_start: 0.6215 (OUTLIER) cc_final: 0.5747 (m-10) REVERT: H 211 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6429 (mp) REVERT: H 213 LYS cc_start: 0.7131 (OUTLIER) cc_final: 0.6724 (tppt) REVERT: I 57 LYS cc_start: 0.4336 (OUTLIER) cc_final: 0.3662 (mttt) REVERT: I 91 ARG cc_start: 0.6944 (OUTLIER) cc_final: 0.6242 (ptt180) REVERT: I 104 ARG cc_start: 0.4777 (OUTLIER) cc_final: 0.2930 (tmm160) REVERT: I 144 PHE cc_start: 0.7847 (p90) cc_final: 0.7621 (p90) outliers start: 59 outliers final: 36 residues processed: 229 average time/residue: 0.1512 time to fit residues: 54.1000 Evaluate side-chains 223 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 221 GLN Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 91 ARG Chi-restraints excluded: chain I residue 104 ARG Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 45 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 167 optimal weight: 0.0980 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.124375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088796 restraints weight = 35261.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088635 restraints weight = 47280.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.089381 restraints weight = 45039.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.089644 restraints weight = 29217.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.090592 restraints weight = 26334.112| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21837 Z= 0.184 Angle : 0.587 9.987 30205 Z= 0.317 Chirality : 0.043 0.191 3501 Planarity : 0.004 0.061 3438 Dihedral : 20.702 176.988 4322 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.56 % Favored : 93.27 % Rotamer: Outliers : 3.88 % Allowed : 20.57 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.16), residues: 2378 helix: 0.30 (0.22), residues: 574 sheet: 0.39 (0.27), residues: 444 loop : -2.06 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 133 TYR 0.019 0.002 TYR H 262 PHE 0.013 0.001 PHE I 18 TRP 0.013 0.001 TRP G 239 HIS 0.006 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00429 (21836) covalent geometry : angle 0.58692 (30203) SS BOND : bond 0.00358 ( 1) SS BOND : angle 2.70997 ( 2) hydrogen bonds : bond 0.04203 ( 708) hydrogen bonds : angle 4.37250 ( 1926) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 171 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 TYR cc_start: 0.8337 (m-10) cc_final: 0.8118 (m-80) REVERT: B 1 MET cc_start: 0.7267 (tmm) cc_final: 0.6833 (tpp) REVERT: B 83 ASN cc_start: 0.9209 (OUTLIER) cc_final: 0.8865 (m110) REVERT: B 237 THR cc_start: 0.7966 (m) cc_final: 0.7653 (p) REVERT: B 240 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.7773 (pmtt) REVERT: D 128 THR cc_start: 0.9580 (OUTLIER) cc_final: 0.9362 (m) REVERT: D 130 TRP cc_start: 0.6995 (OUTLIER) cc_final: 0.6291 (m-10) REVERT: C 185 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8361 (pt) REVERT: C 297 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8051 (tmt90) REVERT: G 191 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7646 (mtt) REVERT: G 210 LYS cc_start: 0.7669 (ptmt) cc_final: 0.7352 (tttm) REVERT: H 127 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.5966 (ttm110) REVERT: H 130 TRP cc_start: 0.6340 (OUTLIER) cc_final: 0.5791 (m-10) REVERT: H 213 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6759 (tppt) REVERT: I 57 LYS cc_start: 0.4181 (OUTLIER) cc_final: 0.3525 (mttt) REVERT: I 104 ARG cc_start: 0.4817 (ttm-80) cc_final: 0.3025 (tmm160) REVERT: I 144 PHE cc_start: 0.7918 (p90) cc_final: 0.7651 (p90) outliers start: 76 outliers final: 53 residues processed: 234 average time/residue: 0.1653 time to fit residues: 60.1942 Evaluate side-chains 232 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 142 GLN Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 221 GLN Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 52 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 153 optimal weight: 5.9990 chunk 81 optimal weight: 20.0000 chunk 207 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN H 266 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088934 restraints weight = 35414.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.089689 restraints weight = 58866.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.090218 restraints weight = 48370.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.090193 restraints weight = 33211.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.090597 restraints weight = 29331.608| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 21837 Z= 0.262 Angle : 0.647 12.368 30205 Z= 0.347 Chirality : 0.045 0.194 3501 Planarity : 0.004 0.060 3438 Dihedral : 20.739 177.764 4320 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer: Outliers : 4.44 % Allowed : 19.96 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.16), residues: 2378 helix: 0.16 (0.21), residues: 580 sheet: 0.25 (0.27), residues: 442 loop : -2.12 (0.14), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 133 TYR 0.025 0.002 TYR H 262 PHE 0.016 0.002 PHE A 163 TRP 0.015 0.002 TRP G 239 HIS 0.007 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00615 (21836) covalent geometry : angle 0.64682 (30203) SS BOND : bond 0.00435 ( 1) SS BOND : angle 3.00000 ( 2) hydrogen bonds : bond 0.04770 ( 708) hydrogen bonds : angle 4.50997 ( 1926) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 171 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8683 (t80) cc_final: 0.8123 (t80) REVERT: B 83 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8886 (m110) REVERT: B 166 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8188 (p) REVERT: B 237 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7719 (p) REVERT: B 240 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7801 (pmtt) REVERT: D 130 TRP cc_start: 0.6971 (OUTLIER) cc_final: 0.6408 (m-10) REVERT: C 185 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8441 (pt) REVERT: C 297 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8092 (tmt90) REVERT: G 210 LYS cc_start: 0.7702 (ptmt) cc_final: 0.7474 (tttm) REVERT: H 127 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6161 (ttm110) REVERT: H 130 TRP cc_start: 0.6499 (OUTLIER) cc_final: 0.5853 (m-10) REVERT: H 213 LYS cc_start: 0.7126 (OUTLIER) cc_final: 0.6776 (tppt) REVERT: I 57 LYS cc_start: 0.4389 (OUTLIER) cc_final: 0.3700 (mttt) REVERT: I 91 ARG cc_start: 0.6572 (ttt-90) cc_final: 0.6277 (ttt180) REVERT: I 104 ARG cc_start: 0.4472 (ttm-80) cc_final: 0.2773 (tmm160) outliers start: 87 outliers final: 66 residues processed: 245 average time/residue: 0.1637 time to fit residues: 62.4377 Evaluate side-chains 244 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 167 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain B residue 241 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 105 THR Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 221 GLN Chi-restraints excluded: chain H residue 227 GLN Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 151 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN D 146 ASN H 266 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.124255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088690 restraints weight = 35194.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088909 restraints weight = 44807.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.089399 restraints weight = 43775.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.089933 restraints weight = 27581.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.090375 restraints weight = 24637.767| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21837 Z= 0.162 Angle : 0.590 12.647 30205 Z= 0.317 Chirality : 0.042 0.189 3501 Planarity : 0.004 0.059 3438 Dihedral : 20.692 176.606 4320 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.55 % Favored : 94.28 % Rotamer: Outliers : 3.73 % Allowed : 20.72 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.16), residues: 2378 helix: 0.31 (0.22), residues: 580 sheet: 0.36 (0.27), residues: 442 loop : -2.05 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 133 TYR 0.019 0.001 TYR H 262 PHE 0.015 0.001 PHE I 18 TRP 0.013 0.001 TRP G 239 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00373 (21836) covalent geometry : angle 0.59006 (30203) SS BOND : bond 0.00404 ( 1) SS BOND : angle 2.66388 ( 2) hydrogen bonds : bond 0.04074 ( 708) hydrogen bonds : angle 4.38482 ( 1926) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 174 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8616 (t80) cc_final: 0.8034 (t80) REVERT: B 1 MET cc_start: 0.7223 (tmm) cc_final: 0.6895 (tpp) REVERT: B 83 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8904 (m110) REVERT: B 156 MET cc_start: 0.6134 (tpt) cc_final: 0.5576 (ttt) REVERT: B 166 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8157 (p) REVERT: B 172 GLU cc_start: 0.7467 (mp0) cc_final: 0.7013 (mp0) REVERT: B 237 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7698 (p) REVERT: B 240 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7748 (pmtt) REVERT: D 130 TRP cc_start: 0.7006 (OUTLIER) cc_final: 0.6298 (m-10) REVERT: C 185 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8386 (pt) REVERT: C 297 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8015 (tmt90) REVERT: G 210 LYS cc_start: 0.7710 (ptmt) cc_final: 0.7491 (tttm) REVERT: H 127 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.5975 (ttm110) REVERT: H 130 TRP cc_start: 0.6429 (OUTLIER) cc_final: 0.5812 (m-10) REVERT: H 213 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6737 (tppt) REVERT: H 283 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7884 (mt) REVERT: I 57 LYS cc_start: 0.4377 (OUTLIER) cc_final: 0.3669 (mttt) outliers start: 73 outliers final: 52 residues processed: 234 average time/residue: 0.1570 time to fit residues: 57.8678 Evaluate side-chains 234 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 170 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 13 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 214 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 146 ASN H 266 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.124875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.089976 restraints weight = 35259.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.090421 restraints weight = 46031.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091147 restraints weight = 42102.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.091389 restraints weight = 27865.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.091735 restraints weight = 25401.627| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 21837 Z= 0.161 Angle : 0.586 12.350 30205 Z= 0.314 Chirality : 0.042 0.183 3501 Planarity : 0.004 0.059 3438 Dihedral : 20.676 176.507 4320 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.06 % Favored : 93.78 % Rotamer: Outliers : 3.47 % Allowed : 21.08 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.16), residues: 2378 helix: 0.38 (0.22), residues: 580 sheet: 0.38 (0.27), residues: 442 loop : -2.02 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 133 TYR 0.022 0.001 TYR H 262 PHE 0.015 0.001 PHE I 18 TRP 0.012 0.001 TRP G 239 HIS 0.004 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00371 (21836) covalent geometry : angle 0.58562 (30203) SS BOND : bond 0.00392 ( 1) SS BOND : angle 2.63438 ( 2) hydrogen bonds : bond 0.04018 ( 708) hydrogen bonds : angle 4.36177 ( 1926) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4756 Ramachandran restraints generated. 2378 Oldfield, 0 Emsley, 2378 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 175 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8617 (t80) cc_final: 0.8035 (t80) REVERT: B 83 ASN cc_start: 0.9227 (OUTLIER) cc_final: 0.8929 (m110) REVERT: B 156 MET cc_start: 0.6098 (tpt) cc_final: 0.5557 (ttt) REVERT: B 166 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8153 (p) REVERT: B 172 GLU cc_start: 0.7485 (mp0) cc_final: 0.7018 (mp0) REVERT: B 237 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7701 (p) REVERT: B 240 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.7750 (pmtt) REVERT: D 4 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8681 (pp) REVERT: D 130 TRP cc_start: 0.6972 (OUTLIER) cc_final: 0.6231 (m-10) REVERT: C 185 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8353 (pt) REVERT: C 297 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7990 (tmt90) REVERT: G 210 LYS cc_start: 0.7722 (ptmt) cc_final: 0.7507 (tttm) REVERT: G 289 MET cc_start: 0.8093 (ptp) cc_final: 0.7866 (ptp) REVERT: H 127 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.5906 (ttm110) REVERT: H 130 TRP cc_start: 0.6432 (OUTLIER) cc_final: 0.5930 (m-10) REVERT: H 213 LYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6847 (tppt) REVERT: H 283 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7968 (mt) REVERT: I 57 LYS cc_start: 0.4420 (OUTLIER) cc_final: 0.3708 (mttt) outliers start: 68 outliers final: 52 residues processed: 231 average time/residue: 0.1598 time to fit residues: 58.0363 Evaluate side-chains 236 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 171 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain B residue 7 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 83 ASN Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain B residue 240 LYS Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 172 MET Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 297 ARG Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 191 MET Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 130 TRP Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 153 SER Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 202 SER Chi-restraints excluded: chain H residue 210 LYS Chi-restraints excluded: chain H residue 213 LYS Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 283 LEU Chi-restraints excluded: chain H residue 295 LEU Chi-restraints excluded: chain I residue 16 VAL Chi-restraints excluded: chain I residue 34 ASN Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 140 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 105 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 147 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088813 restraints weight = 35466.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.088614 restraints weight = 45045.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.089233 restraints weight = 45171.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.089776 restraints weight = 28000.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090161 restraints weight = 25044.494| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21837 Z= 0.209 Angle : 0.611 12.283 30205 Z= 0.327 Chirality : 0.043 0.183 3501 Planarity : 0.004 0.058 3438 Dihedral : 20.683 177.037 4320 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.31 % Rotamer: Outliers : 3.73 % Allowed : 20.93 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.16), residues: 2378 helix: 0.34 (0.22), residues: 581 sheet: 0.37 (0.26), residues: 458 loop : -2.04 (0.15), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 133 TYR 0.016 0.002 TYR H 262 PHE 0.015 0.001 PHE I 18 TRP 0.016 0.001 TRP G 239 HIS 0.005 0.001 HIS E 189 Details of bonding type rmsd covalent geometry : bond 0.00488 (21836) covalent geometry : angle 0.61101 (30203) SS BOND : bond 0.00398 ( 1) SS BOND : angle 2.73382 ( 2) hydrogen bonds : bond 0.04316 ( 708) hydrogen bonds : angle 4.40677 ( 1926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3024.68 seconds wall clock time: 53 minutes 20.37 seconds (3200.37 seconds total)