Starting phenix.real_space_refine on Wed Nov 20 01:59:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k27_36830/11_2024/8k27_36830.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k27_36830/11_2024/8k27_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k27_36830/11_2024/8k27_36830.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k27_36830/11_2024/8k27_36830.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k27_36830/11_2024/8k27_36830.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k27_36830/11_2024/8k27_36830.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLU:plan': 1, 'ASN:plan1': 2} 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: {'GLU:plan': 1, 'ASN:plan1': 2} 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: {'GLU:plan': 1, 'ASN:plan1': 2} 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: {'GLU:plan': 1, 'ASN:plan1': 2} 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: {'GLU:plan': 1, 'ASN:plan1': 2} 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: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2} 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: 12.89, per 1000 atoms: 0.61 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: 5.64 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 7.43 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: 6.83 Time building geometry restraints manager: 6.44 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.160 Set scattering table: 0.220 Process input model: 52.810 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.180 ------------------------------------------------------------------------------- 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 21836 Z= 0.364 Angle : 1.151 71.649 30203 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (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 TRP 0.049 0.002 TRP C 130 HIS 0.006 0.001 HIS I 28 PHE 0.050 0.002 PHE E 182 TYR 0.057 0.002 TYR I 132 ARG 0.012 0.001 ARG D 133 *********************** 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 : 2.535 Fit side-chains revert: symmetry clash 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: 0.7261 (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: 0.6325 (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: 0.6073 (m-40) REVERT: H 86 VAL cc_start: 0.8855 (OUTLIER) cc_final: 0.8620 (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: 0.6330 (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: 0.5888 (mp) REVERT: H 213 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6594 (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: 0.5699 (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: 0.5856 (ttmm) outliers start: 218 outliers final: 29 residues processed: 430 average time/residue: 0.3736 time to fit residues: 240.6575 Evaluate side-chains 250 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 2.564 ------------------------------------------------------------------------------- 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 147 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 127 LYS 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 210 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 chunk 195 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 118 optimal weight: 20.0000 chunk 145 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 84 ASN ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 231 ASN D 294 ASN C 225 HIS F 61 ASN F 203 GLN H 73 ASN H 132 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 21836 Z= 0.362 Angle : 0.671 9.960 30203 Z= 0.367 Chirality : 0.044 0.194 3501 Planarity : 0.005 0.092 3438 Dihedral : 21.412 179.015 4396 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.42 % Favored : 94.37 % Rotamer: Outliers : 5.05 % Allowed : 18.33 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2378 helix: -1.04 (0.20), residues: 578 sheet: 0.01 (0.26), residues: 458 loop : -2.46 (0.14), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 130 HIS 0.006 0.001 HIS E 189 PHE 0.017 0.002 PHE C 205 TYR 0.016 0.002 TYR C 81 ARG 0.006 0.001 ARG A 22 *********************** 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 299 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 200 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.7852 (tpp80) REVERT: A 142 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8362 (tm-30) REVERT: B 237 THR cc_start: 0.7861 (OUTLIER) cc_final: 0.7536 (p) REVERT: D 58 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.8032 (p0) REVERT: C 30 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7285 (p0) REVERT: C 99 TYR cc_start: 0.8425 (t80) cc_final: 0.8180 (t80) REVERT: C 185 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8319 (pt) REVERT: E 260 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8433 (p) REVERT: H 127 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6519 (ttm110) REVERT: H 153 SER cc_start: 0.5070 (OUTLIER) cc_final: 0.4212 (t) REVERT: H 211 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6196 (mp) REVERT: H 213 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6640 (tppt) REVERT: H 266 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6037 (t0) REVERT: H 281 LYS cc_start: 0.6522 (OUTLIER) cc_final: 0.6044 (ttmm) REVERT: H 283 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7362 (mp) REVERT: I 41 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: I 104 ARG cc_start: 0.4714 (OUTLIER) cc_final: 0.2471 (ttp-170) outliers start: 99 outliers final: 51 residues processed: 277 average time/residue: 0.3384 time to fit residues: 145.5694 Evaluate side-chains 243 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 178 time to evaluate : 2.354 ------------------------------------------------------------------------------- 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 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 10 LEU Chi-restraints excluded: chain D residue 58 ASP Chi-restraints excluded: chain C residue 23 MET 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 185 LEU Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 139 ILE Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain F residue 62 ILE 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 144 THR Chi-restraints excluded: chain F residue 145 VAL Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 183 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 260 VAL Chi-restraints excluded: chain H residue 59 LYS 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 86 VAL Chi-restraints excluded: chain H residue 127 ARG Chi-restraints excluded: chain H residue 128 THR Chi-restraints excluded: chain H residue 153 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 255 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 283 LEU Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 41 PHE 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 146 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 chunk 153 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 226 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 224 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 181 optimal weight: 0.0010 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS H 73 ASN H 266 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21836 Z= 0.173 Angle : 0.557 9.201 30203 Z= 0.306 Chirality : 0.041 0.258 3501 Planarity : 0.004 0.075 3438 Dihedral : 21.052 177.149 4344 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.96 % Favored : 94.83 % Rotamer: Outliers : 4.49 % Allowed : 19.04 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.16), residues: 2378 helix: -0.28 (0.21), residues: 578 sheet: 0.62 (0.28), residues: 413 loop : -2.24 (0.14), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 130 HIS 0.002 0.001 HIS E 189 PHE 0.016 0.001 PHE I 18 TYR 0.016 0.001 TYR E 190 ARG 0.004 0.000 ARG E 133 *********************** 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: 88 poor density : 196 time to evaluate : 2.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.7949 (tpp80) REVERT: B 237 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7461 (p) REVERT: D 128 THR cc_start: 0.9558 (OUTLIER) cc_final: 0.9328 (m) REVERT: C 99 TYR cc_start: 0.8415 (t80) cc_final: 0.7952 (t80) REVERT: F 56 ASP cc_start: 0.6092 (OUTLIER) cc_final: 0.5867 (t0) REVERT: H 31 ARG cc_start: 0.6687 (mtm-85) cc_final: 0.6415 (mtm-85) REVERT: H 211 LEU cc_start: 0.6924 (OUTLIER) cc_final: 0.6433 (mp) REVERT: H 213 LYS cc_start: 0.7009 (OUTLIER) cc_final: 0.6544 (tppt) REVERT: H 281 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6124 (ttmm) REVERT: H 283 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7351 (mp) REVERT: I 1 TYR cc_start: 0.4543 (OUTLIER) cc_final: 0.4269 (m-80) REVERT: I 50 ASP cc_start: 0.7557 (p0) cc_final: 0.7344 (p0) REVERT: I 57 LYS cc_start: 0.4164 (OUTLIER) cc_final: 0.3312 (mttt) REVERT: I 80 LYS cc_start: 0.6013 (OUTLIER) cc_final: 0.5281 (tmtt) REVERT: I 104 ARG cc_start: 0.4562 (OUTLIER) cc_final: 0.2807 (tmm160) outliers start: 88 outliers final: 40 residues processed: 267 average time/residue: 0.3305 time to fit residues: 138.0420 Evaluate side-chains 236 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 2.174 ------------------------------------------------------------------------------- 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 64 PHE 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 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 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 31 ARG 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 268 THR Chi-restraints excluded: chain G residue 296 ILE Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 61 ASN 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 13 SER Chi-restraints excluded: chain H residue 79 VAL 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 274 MET Chi-restraints excluded: chain H residue 281 LYS 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 1 TYR Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 14 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 64 VAL Chi-restraints excluded: chain I residue 80 LYS 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 163 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 9.9990 chunk 170 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 240 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 HIS F 61 ASN E 66 ASN H 33 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 21836 Z= 0.558 Angle : 0.744 9.430 30203 Z= 0.404 Chirality : 0.049 0.219 3501 Planarity : 0.005 0.072 3438 Dihedral : 21.040 179.333 4327 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.28 % Favored : 92.39 % Rotamer: Outliers : 5.62 % Allowed : 19.19 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2378 helix: -0.42 (0.21), residues: 575 sheet: -0.00 (0.26), residues: 454 loop : -2.29 (0.14), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP F 130 HIS 0.010 0.002 HIS E 189 PHE 0.027 0.003 PHE D 85 TYR 0.019 0.002 TYR C 81 ARG 0.008 0.001 ARG A 22 *********************** 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 283 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 173 time to evaluate : 2.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8643 (t80) cc_final: 0.8190 (t80) REVERT: B 166 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8146 (p) REVERT: B 237 THR cc_start: 0.8079 (OUTLIER) cc_final: 0.7712 (p) REVERT: D 128 THR cc_start: 0.9592 (OUTLIER) cc_final: 0.9387 (m) REVERT: D 130 TRP cc_start: 0.7074 (OUTLIER) cc_final: 0.6792 (t60) REVERT: C 270 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8954 (tt) REVERT: G 22 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8285 (mt) REVERT: G 191 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7737 (mtt) REVERT: G 210 LYS cc_start: 0.7726 (ptmt) cc_final: 0.7295 (tttm) REVERT: E 93 GLU cc_start: 0.7236 (mt-10) cc_final: 0.7009 (mt-10) REVERT: H 211 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6349 (mp) REVERT: H 213 LYS cc_start: 0.7015 (OUTLIER) cc_final: 0.6661 (tppt) REVERT: H 281 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6846 (mmtt) REVERT: I 57 LYS cc_start: 0.4365 (OUTLIER) cc_final: 0.3535 (mttt) REVERT: I 104 ARG cc_start: 0.4618 (OUTLIER) cc_final: 0.2860 (tmm160) outliers start: 110 outliers final: 64 residues processed: 266 average time/residue: 0.3935 time to fit residues: 166.4690 Evaluate side-chains 239 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 163 time to evaluate : 2.605 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 237 THR 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 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 23 MET Chi-restraints excluded: chain C residue 29 SER 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 270 LEU Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain G residue 13 SER 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 139 ILE Chi-restraints excluded: chain G residue 145 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 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 13 SER Chi-restraints excluded: chain E residue 110 THR 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 74 LYS Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 128 THR 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 255 VAL Chi-restraints excluded: chain H residue 281 LYS 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 41 PHE Chi-restraints excluded: chain I residue 57 LYS Chi-restraints excluded: chain I residue 58 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 205 optimal weight: 0.9990 chunk 166 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** C 33 ASN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21836 Z= 0.185 Angle : 0.569 8.324 30203 Z= 0.311 Chirality : 0.042 0.215 3501 Planarity : 0.004 0.065 3438 Dihedral : 20.839 177.181 4326 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.92 % Favored : 94.91 % Rotamer: Outliers : 4.24 % Allowed : 20.62 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.16), residues: 2378 helix: -0.02 (0.21), residues: 575 sheet: 0.30 (0.27), residues: 439 loop : -2.09 (0.14), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 130 HIS 0.003 0.001 HIS E 189 PHE 0.014 0.001 PHE I 55 TYR 0.015 0.001 TYR H 240 ARG 0.006 0.000 ARG A 74 *********************** 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 271 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 188 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.8091 (ttp-170) REVERT: A 130 TYR cc_start: 0.8562 (t80) cc_final: 0.8041 (t80) REVERT: B 83 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8775 (m110) REVERT: B 156 MET cc_start: 0.6200 (tpt) cc_final: 0.5489 (ttt) REVERT: B 232 GLN cc_start: 0.7874 (pt0) cc_final: 0.7584 (pt0) REVERT: B 237 THR cc_start: 0.7989 (m) cc_final: 0.7638 (p) REVERT: B 240 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7720 (pmtt) REVERT: D 128 THR cc_start: 0.9553 (OUTLIER) cc_final: 0.9317 (m) REVERT: D 130 TRP cc_start: 0.6986 (OUTLIER) cc_final: 0.6318 (m-10) REVERT: D 267 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8747 (mtmm) REVERT: C 185 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8317 (pt) REVERT: G 191 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7555 (mtt) REVERT: G 210 LYS cc_start: 0.7697 (ptmt) cc_final: 0.7273 (tttm) REVERT: G 289 MET cc_start: 0.8039 (ptp) cc_final: 0.7832 (ptp) REVERT: F 99 TYR cc_start: 0.8996 (t80) cc_final: 0.8788 (t80) REVERT: H 211 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6677 (mp) REVERT: H 213 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6576 (tppt) REVERT: H 281 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6722 (ttmm) REVERT: I 57 LYS cc_start: 0.4662 (OUTLIER) cc_final: 0.3760 (mttt) REVERT: I 104 ARG cc_start: 0.4310 (OUTLIER) cc_final: 0.2859 (tmm160) REVERT: I 144 PHE cc_start: 0.7744 (p90) cc_final: 0.7485 (p90) outliers start: 83 outliers final: 45 residues processed: 253 average time/residue: 0.3403 time to fit residues: 133.3523 Evaluate side-chains 233 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 2.574 ------------------------------------------------------------------------------- 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 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 145 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 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 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 13 SER Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 74 LYS 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 221 GLN Chi-restraints excluded: chain H residue 233 ILE Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 281 LYS Chi-restraints excluded: chain H residue 284 THR Chi-restraints excluded: chain I residue 6 ILE 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 104 ARG Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 117 GLU 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 80 optimal weight: 7.9990 chunk 216 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 240 optimal weight: 0.0670 chunk 199 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 overall best weight: 2.3924 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21836 Z= 0.257 Angle : 0.575 7.452 30203 Z= 0.314 Chirality : 0.042 0.188 3501 Planarity : 0.004 0.064 3438 Dihedral : 20.753 177.174 4325 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.27 % Favored : 93.57 % Rotamer: Outliers : 4.08 % Allowed : 20.88 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.16), residues: 2378 helix: 0.13 (0.22), residues: 574 sheet: 0.41 (0.27), residues: 444 loop : -2.08 (0.14), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 130 HIS 0.006 0.001 HIS E 189 PHE 0.012 0.001 PHE A 9 TYR 0.021 0.001 TYR H 240 ARG 0.006 0.001 ARG E 133 *********************** 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 262 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 182 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8601 (t80) cc_final: 0.8069 (t80) REVERT: B 1 MET cc_start: 0.7157 (tmm) cc_final: 0.6774 (tpp) REVERT: B 83 ASN cc_start: 0.9175 (OUTLIER) cc_final: 0.8919 (m110) REVERT: B 172 GLU cc_start: 0.7560 (mp0) cc_final: 0.7089 (mp0) REVERT: B 232 GLN cc_start: 0.7872 (pt0) cc_final: 0.7663 (pt0) REVERT: B 237 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7643 (p) REVERT: B 240 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7769 (pmtt) REVERT: D 128 THR cc_start: 0.9570 (OUTLIER) cc_final: 0.9340 (m) REVERT: D 130 TRP cc_start: 0.6961 (OUTLIER) cc_final: 0.6283 (m-10) REVERT: D 267 LYS cc_start: 0.8982 (mtpt) cc_final: 0.8735 (mtmm) REVERT: D 289 MET cc_start: 0.7930 (mtm) cc_final: 0.7666 (mtm) REVERT: C 185 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8331 (pt) REVERT: C 297 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.7982 (tmt90) REVERT: G 191 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7636 (mtt) REVERT: G 210 LYS cc_start: 0.7753 (ptmt) cc_final: 0.7382 (tttm) REVERT: G 289 MET cc_start: 0.8094 (ptp) cc_final: 0.7872 (ptp) REVERT: H 38 MET cc_start: 0.8403 (mmm) cc_final: 0.8099 (mmp) REVERT: H 129 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7840 (mt) REVERT: H 211 LEU cc_start: 0.6945 (OUTLIER) cc_final: 0.6669 (mp) REVERT: H 213 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6593 (tppt) REVERT: H 262 TYR cc_start: 0.7875 (m-10) cc_final: 0.7428 (m-80) REVERT: I 57 LYS cc_start: 0.4589 (OUTLIER) cc_final: 0.3700 (mttt) REVERT: I 104 ARG cc_start: 0.4046 (OUTLIER) cc_final: 0.2742 (tmm160) REVERT: I 131 PRO cc_start: 0.6631 (Cg_endo) cc_final: 0.6381 (Cg_exo) outliers start: 80 outliers final: 54 residues processed: 244 average time/residue: 0.3436 time to fit residues: 131.4801 Evaluate side-chains 244 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 177 time to evaluate : 2.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 224 MET 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 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 G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 145 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 G residue 296 ILE Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 157 VAL 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 210 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 129 LEU 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 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 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 104 ARG Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 117 GLU 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 232 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 202 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 239 optimal weight: 0.9990 chunk 150 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 ASN H 266 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21836 Z= 0.207 Angle : 0.557 12.538 30203 Z= 0.303 Chirality : 0.041 0.192 3501 Planarity : 0.003 0.060 3438 Dihedral : 20.663 176.942 4320 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.00 % Favored : 94.83 % Rotamer: Outliers : 4.03 % Allowed : 21.18 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2378 helix: 0.30 (0.22), residues: 574 sheet: 0.56 (0.27), residues: 444 loop : -2.00 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 130 HIS 0.003 0.001 HIS B 197 PHE 0.017 0.001 PHE I 55 TYR 0.016 0.001 TYR A 73 ARG 0.006 0.000 ARG A 74 *********************** 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 265 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 186 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8027 (ttp-170) REVERT: A 130 TYR cc_start: 0.8598 (t80) cc_final: 0.8043 (t80) REVERT: B 1 MET cc_start: 0.7053 (tmm) cc_final: 0.6787 (tpp) REVERT: B 83 ASN cc_start: 0.9182 (OUTLIER) cc_final: 0.8891 (m110) REVERT: B 156 MET cc_start: 0.6020 (tpt) cc_final: 0.5506 (ttt) REVERT: B 172 GLU cc_start: 0.7576 (mp0) cc_final: 0.7096 (mp0) REVERT: B 237 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7656 (p) REVERT: B 240 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7772 (pmtt) REVERT: D 4 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8635 (pp) REVERT: D 128 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9316 (m) REVERT: D 130 TRP cc_start: 0.6879 (OUTLIER) cc_final: 0.6227 (m-10) REVERT: D 267 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8730 (mtmm) REVERT: C 137 GLU cc_start: 0.7047 (tp30) cc_final: 0.6835 (tp30) REVERT: C 185 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8339 (pt) REVERT: C 297 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.7968 (tmt90) REVERT: G 191 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7656 (mtt) REVERT: G 210 LYS cc_start: 0.7767 (ptmt) cc_final: 0.7339 (tttm) REVERT: F 140 GLU cc_start: 0.7414 (tt0) cc_final: 0.7200 (tt0) REVERT: H 38 MET cc_start: 0.8397 (mmm) cc_final: 0.8194 (mmp) REVERT: H 213 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6684 (tppt) REVERT: I 57 LYS cc_start: 0.4449 (OUTLIER) cc_final: 0.3625 (mttt) REVERT: I 104 ARG cc_start: 0.4052 (OUTLIER) cc_final: 0.2810 (tmm160) REVERT: I 131 PRO cc_start: 0.6789 (Cg_endo) cc_final: 0.6545 (Cg_exo) outliers start: 79 outliers final: 50 residues processed: 247 average time/residue: 0.3227 time to fit residues: 126.2086 Evaluate side-chains 238 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 176 time to evaluate : 2.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 182 MET Chi-restraints excluded: chain B residue 183 VAL 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 128 THR Chi-restraints excluded: chain D residue 130 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 274 MET 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 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 G residue 296 ILE Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 157 VAL 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 210 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 79 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 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 104 ARG Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 117 GLU Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 9.9990 chunk 95 optimal weight: 0.0030 chunk 143 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 118 optimal weight: 0.0050 chunk 22 optimal weight: 7.9990 chunk 188 optimal weight: 0.9980 overall best weight: 0.5606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21836 Z= 0.137 Angle : 0.534 7.958 30203 Z= 0.289 Chirality : 0.040 0.183 3501 Planarity : 0.003 0.058 3438 Dihedral : 20.591 177.748 4317 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.38 % Favored : 94.45 % Rotamer: Outliers : 3.16 % Allowed : 21.90 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2378 helix: 0.53 (0.22), residues: 574 sheet: 0.77 (0.27), residues: 449 loop : -1.93 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 130 HIS 0.002 0.000 HIS H 189 PHE 0.019 0.001 PHE I 144 TYR 0.013 0.001 TYR E 190 ARG 0.021 0.000 ARG B 63 *********************** 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 253 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 191 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8014 (ttp-170) REVERT: A 130 TYR cc_start: 0.8569 (t80) cc_final: 0.7972 (t80) REVERT: B 83 ASN cc_start: 0.9168 (OUTLIER) cc_final: 0.8778 (m110) REVERT: B 156 MET cc_start: 0.5895 (tpt) cc_final: 0.5515 (ttt) REVERT: B 172 GLU cc_start: 0.7503 (mp0) cc_final: 0.7034 (mp0) REVERT: B 237 THR cc_start: 0.8014 (OUTLIER) cc_final: 0.7719 (p) REVERT: B 240 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7510 (pmtt) REVERT: D 4 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8573 (pp) REVERT: D 130 TRP cc_start: 0.6618 (OUTLIER) cc_final: 0.5860 (m-10) REVERT: D 267 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8727 (mtmm) REVERT: C 137 GLU cc_start: 0.7010 (tp30) cc_final: 0.6791 (tp30) REVERT: C 297 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.7967 (tmt90) REVERT: G 191 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7491 (mtt) REVERT: G 210 LYS cc_start: 0.7781 (ptmt) cc_final: 0.7360 (tttm) REVERT: F 140 GLU cc_start: 0.7442 (tt0) cc_final: 0.7208 (tt0) REVERT: H 38 MET cc_start: 0.8372 (mmm) cc_final: 0.8166 (mmp) REVERT: H 192 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7108 (tt) REVERT: H 213 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6793 (tppt) REVERT: I 57 LYS cc_start: 0.4440 (OUTLIER) cc_final: 0.3602 (mttt) REVERT: I 104 ARG cc_start: 0.3799 (OUTLIER) cc_final: 0.2652 (tmm160) outliers start: 62 outliers final: 41 residues processed: 237 average time/residue: 0.3229 time to fit residues: 121.4260 Evaluate side-chains 233 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 181 time to evaluate : 2.302 ------------------------------------------------------------------------------- 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 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 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 145 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 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 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 G residue 296 ILE Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain E residue 210 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 192 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 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 104 ARG Chi-restraints excluded: chain I residue 105 CYS 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 218 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 chunk 209 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 222 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 GLN D 146 ASN D 279 ASN F 66 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 21836 Z= 0.417 Angle : 0.645 10.110 30203 Z= 0.346 Chirality : 0.045 0.183 3501 Planarity : 0.004 0.059 3438 Dihedral : 20.632 177.055 4314 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 3.62 % Allowed : 21.69 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.16), residues: 2378 helix: 0.31 (0.22), residues: 574 sheet: 0.50 (0.26), residues: 449 loop : -2.03 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 239 HIS 0.006 0.001 HIS E 189 PHE 0.014 0.002 PHE D 160 TYR 0.022 0.002 TYR H 262 ARG 0.007 0.001 ARG A 22 *********************** 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 251 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 180 time to evaluate : 2.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 TYR cc_start: 0.8719 (t80) cc_final: 0.8211 (t80) REVERT: B 2 ARG cc_start: 0.7174 (ptp-170) cc_final: 0.6925 (ptp-170) REVERT: B 83 ASN cc_start: 0.9241 (OUTLIER) cc_final: 0.8943 (m110) REVERT: B 156 MET cc_start: 0.6044 (tpt) cc_final: 0.5445 (ttt) REVERT: B 237 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7696 (p) REVERT: B 240 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.7948 (pmtt) REVERT: D 128 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9377 (m) REVERT: D 130 TRP cc_start: 0.7052 (OUTLIER) cc_final: 0.6424 (m-10) REVERT: D 267 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8766 (mtmm) REVERT: C 185 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8369 (pt) REVERT: C 297 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8045 (tmt90) REVERT: G 191 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7765 (mtt) REVERT: G 210 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7540 (tttm) REVERT: H 38 MET cc_start: 0.8406 (mmm) cc_final: 0.8202 (mmp) REVERT: H 192 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7208 (tt) REVERT: H 213 LYS cc_start: 0.7203 (OUTLIER) cc_final: 0.6814 (tppt) REVERT: I 57 LYS cc_start: 0.4721 (OUTLIER) cc_final: 0.3805 (mttt) REVERT: I 104 ARG cc_start: 0.3878 (OUTLIER) cc_final: 0.2643 (tmm160) outliers start: 71 outliers final: 51 residues processed: 236 average time/residue: 0.3333 time to fit residues: 124.2580 Evaluate side-chains 235 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 172 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU 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 168 VAL 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 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 224 MET Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 23 MET 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 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 145 VAL Chi-restraints excluded: chain G residue 156 LEU Chi-restraints excluded: chain G residue 191 MET Chi-restraints excluded: chain G residue 203 GLN Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 176 VAL 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 145 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 192 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 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 104 ARG Chi-restraints excluded: chain I residue 105 CYS Chi-restraints excluded: chain I residue 140 THR Chi-restraints excluded: chain I residue 163 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 248 optimal weight: 20.0000 chunk 228 optimal weight: 0.0670 chunk 197 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 152 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21836 Z= 0.145 Angle : 0.558 9.062 30203 Z= 0.301 Chirality : 0.041 0.176 3501 Planarity : 0.003 0.057 3438 Dihedral : 20.569 177.560 4314 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.21 % Favored : 94.66 % Rotamer: Outliers : 2.55 % Allowed : 23.12 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.17), residues: 2378 helix: 0.50 (0.22), residues: 574 sheet: 0.75 (0.27), residues: 449 loop : -1.91 (0.15), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 130 HIS 0.001 0.000 HIS G 189 PHE 0.018 0.001 PHE I 144 TYR 0.014 0.001 TYR H 117 ARG 0.009 0.000 ARG E 133 ********************** 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 235 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 3.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8041 (ttp-170) REVERT: A 130 TYR cc_start: 0.8651 (t80) cc_final: 0.8125 (t80) REVERT: B 83 ASN cc_start: 0.9194 (OUTLIER) cc_final: 0.8848 (m110) REVERT: B 156 MET cc_start: 0.5847 (tpt) cc_final: 0.5505 (ttt) REVERT: B 237 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7751 (p) REVERT: B 240 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.7832 (pmtt) REVERT: D 128 THR cc_start: 0.9528 (OUTLIER) cc_final: 0.9296 (m) REVERT: D 130 TRP cc_start: 0.6765 (OUTLIER) cc_final: 0.6170 (m-10) REVERT: D 267 LYS cc_start: 0.8968 (mtpt) cc_final: 0.8754 (mtmm) REVERT: C 185 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8304 (pt) REVERT: C 297 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7973 (tmt90) REVERT: G 191 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7595 (mtt) REVERT: G 210 LYS cc_start: 0.7776 (ptmt) cc_final: 0.7487 (tttm) REVERT: G 284 THR cc_start: 0.8619 (p) cc_final: 0.8386 (t) REVERT: F 140 GLU cc_start: 0.7444 (tt0) cc_final: 0.7203 (tt0) REVERT: H 38 MET cc_start: 0.8376 (mmm) cc_final: 0.8174 (mmp) REVERT: H 192 LEU cc_start: 0.7770 (OUTLIER) cc_final: 0.7133 (tt) REVERT: H 213 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6884 (tppt) REVERT: I 57 LYS cc_start: 0.4614 (OUTLIER) cc_final: 0.3762 (mttt) REVERT: I 104 ARG cc_start: 0.3907 (OUTLIER) cc_final: 0.2687 (tmm160) outliers start: 50 outliers final: 37 residues processed: 224 average time/residue: 0.3323 time to fit residues: 118.1734 Evaluate side-chains 229 residues out of total 1997 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 LEU 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 168 VAL Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 183 VAL 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 151 THR Chi-restraints excluded: chain C residue 183 VAL 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 C residue 297 ARG Chi-restraints excluded: chain G residue 64 THR Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 145 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 61 ASN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 157 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain E residue 176 VAL Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 156 LEU Chi-restraints excluded: chain H residue 192 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 255 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 104 ARG 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 156 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 182 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 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 = 0.3541 r_free = 0.3541 target = 0.124002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.088370 restraints weight = 35401.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088780 restraints weight = 47246.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.089162 restraints weight = 45250.948| |-----------------------------------------------------------------------------| r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 21836 Z= 0.305 Angle : 0.598 9.313 30203 Z= 0.322 Chirality : 0.043 0.174 3501 Planarity : 0.004 0.058 3438 Dihedral : 20.580 176.736 4314 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.35 % Favored : 93.52 % Rotamer: Outliers : 2.65 % Allowed : 22.87 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.17), residues: 2378 helix: 0.44 (0.22), residues: 574 sheet: 0.57 (0.27), residues: 450 loop : -1.93 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 239 HIS 0.004 0.001 HIS D 189 PHE 0.016 0.001 PHE I 144 TYR 0.018 0.002 TYR E 190 ARG 0.008 0.001 ARG E 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3787.78 seconds wall clock time: 71 minutes 29.43 seconds (4289.43 seconds total)