Starting phenix.real_space_refine on Tue Feb 20 12:36:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319_neut_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnn_33319/02_2024/7xnn_33319_neut_trim_updated.pdb" } resolution = 2.5 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= 0.002 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: 7 Type Number sf(0) Gaussians K 4 8.98 5 P 12 5.49 5 S 60 5.16 5 C 9268 2.51 5 N 2484 2.21 5 O 2452 1.98 5 H 13096 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27376 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1377 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5387 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 7, 'TRANS': 322} Chain breaks: 2 Chain: "C" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5387 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 7, 'TRANS': 322} Chain breaks: 2 Chain: "D" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1377 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "E" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5387 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 7, 'TRANS': 322} Chain breaks: 2 Chain: "F" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1377 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "G" Number of atoms: 5387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5387 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 7, 'TRANS': 322} Chain breaks: 2 Chain: "H" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1377 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 309 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 235 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 5, 'ASP:plan': 16, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "B" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 82 Unusual residues: {' K': 3, 'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 4} Link IDs: {None: 4} Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' K': 1, 'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 2} Link IDs: {None: 2} Chain: "E" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'PIO': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Time building chain proxies: 11.89, per 1000 atoms: 0.43 Number of scatterers: 27376 At special positions: 0 Unit cell: (126.75, 126.75, 114.582, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 4 19.00 S 60 16.00 P 12 15.00 O 2452 8.00 N 2484 7.00 C 9268 6.00 H 13096 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 22.90 Conformation dependent library (CDL) restraints added in 3.1 seconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB I0S B 704 " pdb=" CB I0S C 702 " pdb=" CB I0S E 901 " pdb=" CB I0S G 901 " Number of C-beta restraints generated: 3512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 88 helices and 0 sheets defined 68.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'A' and resid 12 through 20 removed outlier: 3.854A pdb=" N ALA A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE A 20 " --> pdb=" O ALA A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 40 removed outlier: 3.782A pdb=" N GLY A 34 " --> pdb=" O THR A 30 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.922A pdb=" N ILE A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 119 through 129 removed outlier: 3.561A pdb=" N ILE A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 3.523A pdb=" N GLN A 144 " --> pdb=" O GLU A 140 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N MET A 145 " --> pdb=" O GLU A 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 121 through 143 removed outlier: 3.582A pdb=" N LEU B 142 " --> pdb=" O ILE B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 151 through 178 removed outlier: 3.764A pdb=" N PHE B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 161 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 186 through 194 Processing helix chain 'B' and resid 197 through 215 Processing helix chain 'B' and resid 224 through 240 removed outlier: 4.460A pdb=" N PHE B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET B 238 " --> pdb=" O GLN B 234 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N HIS B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 284 removed outlier: 5.497A pdb=" N GLN B 260 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLU B 261 " --> pdb=" O ILE B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 310 Processing helix chain 'B' and resid 323 through 335 Processing helix chain 'B' and resid 337 through 340 Processing helix chain 'B' and resid 342 through 382 Proline residue: B 369 - end of helix removed outlier: 3.788A pdb=" N ILE B 375 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 533 removed outlier: 3.769A pdb=" N LYS B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 554 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 121 through 143 removed outlier: 3.582A pdb=" N LEU C 142 " --> pdb=" O ILE C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 151 through 178 removed outlier: 3.764A pdb=" N PHE C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP C 158 " --> pdb=" O GLY C 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 197 through 215 Processing helix chain 'C' and resid 224 through 240 removed outlier: 4.461A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET C 238 " --> pdb=" O GLN C 234 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N HIS C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 284 removed outlier: 5.497A pdb=" N GLN C 260 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU C 261 " --> pdb=" O ILE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 310 Processing helix chain 'C' and resid 323 through 335 Processing helix chain 'C' and resid 337 through 340 Processing helix chain 'C' and resid 342 through 382 Proline residue: C 369 - end of helix removed outlier: 3.788A pdb=" N ILE C 375 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 533 removed outlier: 3.768A pdb=" N LYS C 527 " --> pdb=" O PHE C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 554 Processing helix chain 'D' and resid 12 through 20 removed outlier: 3.855A pdb=" N ALA D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 removed outlier: 3.782A pdb=" N GLY D 34 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.923A pdb=" N ILE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 103 through 110 Processing helix chain 'D' and resid 119 through 129 removed outlier: 3.561A pdb=" N ILE D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 removed outlier: 3.523A pdb=" N GLN D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET D 145 " --> pdb=" O GLU D 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 114 Processing helix chain 'E' and resid 121 through 143 removed outlier: 3.582A pdb=" N LEU E 142 " --> pdb=" O ILE E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 151 through 178 removed outlier: 3.764A pdb=" N PHE E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP E 158 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 186 through 194 Processing helix chain 'E' and resid 197 through 215 Processing helix chain 'E' and resid 224 through 240 removed outlier: 4.461A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N MET E 238 " --> pdb=" O GLN E 234 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N LEU E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N HIS E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 284 removed outlier: 5.496A pdb=" N GLN E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 310 Processing helix chain 'E' and resid 323 through 335 Processing helix chain 'E' and resid 337 through 340 Processing helix chain 'E' and resid 342 through 382 Proline residue: E 369 - end of helix removed outlier: 3.788A pdb=" N ILE E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 533 removed outlier: 3.769A pdb=" N LYS E 527 " --> pdb=" O PHE E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 554 Processing helix chain 'F' and resid 12 through 20 removed outlier: 3.854A pdb=" N ALA F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 40 removed outlier: 3.782A pdb=" N GLY F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 54 removed outlier: 3.922A pdb=" N ILE F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 92 Processing helix chain 'F' and resid 103 through 110 Processing helix chain 'F' and resid 119 through 129 removed outlier: 3.562A pdb=" N ILE F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 removed outlier: 3.523A pdb=" N GLN F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET F 145 " --> pdb=" O GLU F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 114 Processing helix chain 'G' and resid 121 through 143 removed outlier: 3.581A pdb=" N LEU G 142 " --> pdb=" O ILE G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 151 through 178 removed outlier: 3.764A pdb=" N PHE G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP G 158 " --> pdb=" O GLY G 154 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 186 through 194 Processing helix chain 'G' and resid 197 through 215 Processing helix chain 'G' and resid 224 through 240 removed outlier: 4.460A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET G 238 " --> pdb=" O GLN G 234 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU G 239 " --> pdb=" O ILE G 235 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N HIS G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 284 removed outlier: 5.497A pdb=" N GLN G 260 " --> pdb=" O PHE G 256 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N GLU G 261 " --> pdb=" O ILE G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 310 Processing helix chain 'G' and resid 323 through 335 Processing helix chain 'G' and resid 337 through 340 Processing helix chain 'G' and resid 342 through 382 Proline residue: G 369 - end of helix removed outlier: 3.787A pdb=" N ILE G 375 " --> pdb=" O ALA G 371 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG G 380 " --> pdb=" O GLN G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 533 removed outlier: 3.768A pdb=" N LYS G 527 " --> pdb=" O PHE G 523 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 554 Processing helix chain 'H' and resid 12 through 20 removed outlier: 3.854A pdb=" N ALA H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 40 removed outlier: 3.782A pdb=" N GLY H 34 " --> pdb=" O THR H 30 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR H 35 " --> pdb=" O LYS H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 54 removed outlier: 3.922A pdb=" N ILE H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 92 Processing helix chain 'H' and resid 103 through 110 Processing helix chain 'H' and resid 119 through 129 removed outlier: 3.561A pdb=" N ILE H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 146 removed outlier: 3.523A pdb=" N GLN H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET H 145 " --> pdb=" O GLU H 141 " (cutoff:3.500A) 852 hydrogen bonds defined for protein. 2544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.05 Time building geometry restraints manager: 23.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13072 1.02 - 1.22: 36 1.22 - 1.42: 6534 1.42 - 1.61: 7946 1.61 - 1.81: 104 Bond restraints: 27692 Sorted by residual: bond pdb=" CAT I0S C 702 " pdb=" SBF I0S C 702 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S B 704 " pdb=" SBF I0S B 704 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S E 901 " pdb=" SBF I0S E 901 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CAT I0S G 901 " pdb=" SBF I0S G 901 " ideal model delta sigma weight residual 1.739 1.606 0.133 2.00e-02 2.50e+03 4.42e+01 bond pdb=" CBE I0S E 901 " pdb=" SBF I0S E 901 " ideal model delta sigma weight residual 1.717 1.584 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 27687 not shown) Histogram of bond angle deviations from ideal: 96.55 - 104.07: 168 104.07 - 111.59: 28601 111.59 - 119.10: 7835 119.10 - 126.62: 12661 126.62 - 134.14: 235 Bond angle restraints: 49500 Sorted by residual: angle pdb=" OAQ I0S E 901 " pdb=" SAI I0S E 901 " pdb=" OAR I0S E 901 " ideal model delta sigma weight residual 119.45 103.60 15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S G 901 " pdb=" SAI I0S G 901 " pdb=" OAR I0S G 901 " ideal model delta sigma weight residual 119.45 103.61 15.84 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S B 704 " pdb=" SAI I0S B 704 " pdb=" OAR I0S B 704 " ideal model delta sigma weight residual 119.45 103.62 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" OAQ I0S C 702 " pdb=" SAI I0S C 702 " pdb=" OAR I0S C 702 " ideal model delta sigma weight residual 119.45 103.62 15.83 3.00e+00 1.11e-01 2.79e+01 angle pdb=" CA I0S C 702 " pdb=" N I0S C 702 " pdb=" CAG I0S C 702 " ideal model delta sigma weight residual 121.42 107.76 13.66 3.00e+00 1.11e-01 2.07e+01 ... (remaining 49495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.18: 12912 34.18 - 68.36: 360 68.36 - 102.55: 24 102.55 - 136.73: 4 136.73 - 170.91: 8 Dihedral angle restraints: 13308 sinusoidal: 6692 harmonic: 6616 Sorted by residual: dihedral pdb=" CA TYR E 545 " pdb=" C TYR E 545 " pdb=" N SER E 546 " pdb=" CA SER E 546 " ideal model delta harmonic sigma weight residual 180.00 156.52 23.48 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA TYR B 545 " pdb=" C TYR B 545 " pdb=" N SER B 546 " pdb=" CA SER B 546 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TYR G 545 " pdb=" C TYR G 545 " pdb=" N SER G 546 " pdb=" CA SER G 546 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 13305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1681 0.074 - 0.147: 359 0.147 - 0.220: 93 0.220 - 0.294: 63 0.294 - 0.367: 44 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CB THR B 311 " pdb=" CA THR B 311 " pdb=" OG1 THR B 311 " pdb=" CG2 THR B 311 " both_signs ideal model delta sigma weight residual False 2.55 2.18 0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" CB THR C 311 " pdb=" CA THR C 311 " pdb=" OG1 THR C 311 " pdb=" CG2 THR C 311 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR G 311 " pdb=" CA THR G 311 " pdb=" OG1 THR G 311 " pdb=" CG2 THR G 311 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.32e+00 ... (remaining 2237 not shown) Planarity restraints: 4312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PIO G 902 " 0.150 2.00e-02 2.50e+03 9.69e-01 2.82e+04 pdb=" C2 PIO G 902 " 0.797 2.00e-02 2.50e+03 pdb=" C3 PIO G 902 " 0.116 2.00e-02 2.50e+03 pdb=" C4 PIO G 902 " 0.342 2.00e-02 2.50e+03 pdb=" C5 PIO G 902 " -0.461 2.00e-02 2.50e+03 pdb=" C6 PIO G 902 " -0.170 2.00e-02 2.50e+03 pdb=" O1 PIO G 902 " -1.039 2.00e-02 2.50e+03 pdb=" O2 PIO G 902 " 0.701 2.00e-02 2.50e+03 pdb=" O3 PIO G 902 " -1.268 2.00e-02 2.50e+03 pdb=" O4 PIO G 902 " 1.712 2.00e-02 2.50e+03 pdb=" O5 PIO G 902 " -1.809 2.00e-02 2.50e+03 pdb=" O6 PIO G 902 " 0.930 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO E 902 " 0.151 2.00e-02 2.50e+03 9.69e-01 2.82e+04 pdb=" C2 PIO E 902 " 0.797 2.00e-02 2.50e+03 pdb=" C3 PIO E 902 " 0.115 2.00e-02 2.50e+03 pdb=" C4 PIO E 902 " 0.341 2.00e-02 2.50e+03 pdb=" C5 PIO E 902 " -0.462 2.00e-02 2.50e+03 pdb=" C6 PIO E 902 " -0.169 2.00e-02 2.50e+03 pdb=" O1 PIO E 902 " -1.037 2.00e-02 2.50e+03 pdb=" O2 PIO E 902 " 0.701 2.00e-02 2.50e+03 pdb=" O3 PIO E 902 " -1.268 2.00e-02 2.50e+03 pdb=" O4 PIO E 902 " 1.710 2.00e-02 2.50e+03 pdb=" O5 PIO E 902 " -1.810 2.00e-02 2.50e+03 pdb=" O6 PIO E 902 " 0.931 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 PIO B 705 " -0.151 2.00e-02 2.50e+03 9.69e-01 2.82e+04 pdb=" C2 PIO B 705 " -0.796 2.00e-02 2.50e+03 pdb=" C3 PIO B 705 " -0.114 2.00e-02 2.50e+03 pdb=" C4 PIO B 705 " -0.341 2.00e-02 2.50e+03 pdb=" C5 PIO B 705 " 0.461 2.00e-02 2.50e+03 pdb=" C6 PIO B 705 " 0.169 2.00e-02 2.50e+03 pdb=" O1 PIO B 705 " 1.038 2.00e-02 2.50e+03 pdb=" O2 PIO B 705 " -0.701 2.00e-02 2.50e+03 pdb=" O3 PIO B 705 " 1.269 2.00e-02 2.50e+03 pdb=" O4 PIO B 705 " -1.711 2.00e-02 2.50e+03 pdb=" O5 PIO B 705 " 1.809 2.00e-02 2.50e+03 pdb=" O6 PIO B 705 " -0.932 2.00e-02 2.50e+03 ... (remaining 4309 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.24: 4362 2.24 - 2.97: 72199 2.97 - 3.69: 92299 3.69 - 4.42: 140387 4.42 - 5.14: 218869 Nonbonded interactions: 528116 Sorted by model distance: nonbonded pdb=" O HIS F 108 " pdb="HD21 ASN F 112 " model vdw 1.521 1.850 nonbonded pdb=" O HIS A 108 " pdb="HD21 ASN A 112 " model vdw 1.522 1.850 nonbonded pdb=" O HIS H 108 " pdb="HD21 ASN H 112 " model vdw 1.522 1.850 nonbonded pdb=" O HIS D 108 " pdb="HD21 ASN D 112 " model vdw 1.522 1.850 nonbonded pdb=" O ILE A 101 " pdb=" H VAL A 137 " model vdw 1.526 1.850 ... (remaining 528111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = (chain 'B' and resid 104 through 555) selection = (chain 'C' and resid 104 through 555) selection = (chain 'E' and resid 104 through 555) selection = (chain 'G' and resid 104 through 555) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.400 Extract box with map and model: 4.350 Check model and map are aligned: 0.410 Set scattering table: 0.220 Process input model: 89.860 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 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 : 0.026 0.202 14596 Z= 1.673 Angle : 1.139 15.849 19848 Z= 0.613 Chirality : 0.089 0.367 2240 Planarity : 0.039 0.969 2468 Dihedral : 14.265 170.912 4996 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -4.55 (0.16), residues: 1864 helix: -2.90 (0.11), residues: 1372 sheet: None (None), residues: 0 loop : -2.63 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 323 HIS 0.009 0.003 HIS G 363 PHE 0.034 0.005 PHE C 351 TYR 0.047 0.006 TYR B 299 ARG 0.009 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 347 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 158 TRP cc_start: 0.5801 (m100) cc_final: 0.5537 (m-10) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 2.4924 time to fit residues: 948.9241 Evaluate side-chains 237 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.153 14596 Z= 0.364 Angle : 1.908 76.496 19848 Z= 0.679 Chirality : 0.037 0.130 2240 Planarity : 0.004 0.041 2468 Dihedral : 13.171 179.704 2340 Min Nonbonded Distance : 1.211 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.81 % Allowed : 10.56 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.19), residues: 1864 helix: -0.79 (0.13), residues: 1356 sheet: None (None), residues: 0 loop : -1.27 (0.31), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 304 HIS 0.002 0.001 HIS B 549 PHE 0.012 0.002 PHE D 13 TYR 0.016 0.002 TYR B 545 ARG 0.003 0.000 ARG G 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 301 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 LEU cc_start: 0.8518 (tp) cc_final: 0.8265 (tp) REVERT: B 361 GLN cc_start: 0.7866 (tt0) cc_final: 0.7381 (tp-100) REVERT: C 236 LEU cc_start: 0.8475 (tp) cc_final: 0.8194 (tp) REVERT: C 361 GLN cc_start: 0.7969 (tt0) cc_final: 0.7466 (tp-100) REVERT: E 202 ASP cc_start: 0.8020 (t0) cc_final: 0.7647 (t0) REVERT: E 236 LEU cc_start: 0.8477 (tp) cc_final: 0.8201 (tp) REVERT: E 361 GLN cc_start: 0.7977 (tt0) cc_final: 0.7456 (tp-100) REVERT: F 102 SER cc_start: 0.7476 (p) cc_final: 0.7204 (m) REVERT: G 202 ASP cc_start: 0.8050 (t0) cc_final: 0.7662 (t0) REVERT: G 236 LEU cc_start: 0.8478 (tp) cc_final: 0.8212 (tp) REVERT: G 361 GLN cc_start: 0.7822 (tt0) cc_final: 0.7352 (tp-100) outliers start: 10 outliers final: 1 residues processed: 304 average time/residue: 2.2316 time to fit residues: 756.6054 Evaluate side-chains 243 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 242 time to evaluate : 2.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 290 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 142 optimal weight: 0.0870 chunk 116 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 184 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 169 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 10.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 GLN B 510 HIS C 356 GLN C 510 HIS E 359 GLN E 510 HIS G 359 GLN G 510 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.126 14596 Z= 0.555 Angle : 1.924 77.530 19848 Z= 0.702 Chirality : 0.041 0.148 2240 Planarity : 0.004 0.037 2468 Dihedral : 13.536 173.997 2340 Min Nonbonded Distance : 1.185 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.82 % Allowed : 14.35 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1864 helix: -0.23 (0.13), residues: 1380 sheet: None (None), residues: 0 loop : -1.14 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 304 HIS 0.005 0.001 HIS B 549 PHE 0.023 0.003 PHE B 296 TYR 0.022 0.002 TYR B 545 ARG 0.007 0.001 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 242 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8300 (t0) cc_final: 0.7877 (t0) REVERT: B 361 GLN cc_start: 0.8017 (tt0) cc_final: 0.7684 (tp-100) REVERT: C 202 ASP cc_start: 0.8258 (t0) cc_final: 0.7860 (t0) REVERT: C 361 GLN cc_start: 0.8171 (tt0) cc_final: 0.7782 (tp-100) REVERT: E 202 ASP cc_start: 0.8347 (t0) cc_final: 0.7955 (t0) REVERT: E 361 GLN cc_start: 0.8200 (tt0) cc_final: 0.7792 (tp-100) REVERT: F 102 SER cc_start: 0.7542 (p) cc_final: 0.7255 (m) REVERT: G 202 ASP cc_start: 0.8328 (t0) cc_final: 0.7935 (t0) REVERT: G 361 GLN cc_start: 0.8011 (tt0) cc_final: 0.7643 (tp-100) outliers start: 35 outliers final: 24 residues processed: 262 average time/residue: 2.0990 time to fit residues: 615.2963 Evaluate side-chains 243 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 219 time to evaluate : 2.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain C residue 143 SER Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 143 SER Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 chunk 88 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 81 optimal weight: 40.0000 chunk 114 optimal weight: 0.0980 chunk 171 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 162 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 GLN G 359 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 14596 Z= 0.418 Angle : 1.895 77.609 19848 Z= 0.676 Chirality : 0.037 0.148 2240 Planarity : 0.004 0.041 2468 Dihedral : 13.108 172.794 2340 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.66 % Allowed : 16.53 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1864 helix: 0.46 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -0.24 (0.34), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 304 HIS 0.002 0.001 HIS G 258 PHE 0.022 0.002 PHE G 296 TYR 0.022 0.002 TYR C 545 ARG 0.003 0.000 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 226 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8287 (t0) cc_final: 0.7874 (t0) REVERT: B 361 GLN cc_start: 0.8031 (tt0) cc_final: 0.7816 (tp-100) REVERT: C 202 ASP cc_start: 0.8313 (t0) cc_final: 0.7918 (t0) REVERT: C 361 GLN cc_start: 0.8138 (tt0) cc_final: 0.7784 (tp-100) REVERT: D 102 SER cc_start: 0.7428 (p) cc_final: 0.7172 (m) REVERT: E 202 ASP cc_start: 0.8340 (t0) cc_final: 0.7937 (t0) REVERT: E 361 GLN cc_start: 0.8122 (tt0) cc_final: 0.7774 (tp-100) REVERT: F 102 SER cc_start: 0.7537 (p) cc_final: 0.7288 (m) REVERT: G 170 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: G 202 ASP cc_start: 0.8347 (t0) cc_final: 0.7943 (t0) REVERT: G 361 GLN cc_start: 0.8021 (tt0) cc_final: 0.7790 (tp-100) REVERT: G 520 MET cc_start: 0.7415 (tpp) cc_final: 0.7209 (OUTLIER) outliers start: 33 outliers final: 23 residues processed: 239 average time/residue: 2.0302 time to fit residues: 545.5384 Evaluate side-chains 233 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 2.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 180 CYS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 13 PHE Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 180 CYS Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 180 CYS Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain H residue 13 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 40.0000 chunk 135 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 50.0000 chunk 163 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 14596 Z= 0.391 Angle : 1.891 77.539 19848 Z= 0.672 Chirality : 0.037 0.148 2240 Planarity : 0.004 0.040 2468 Dihedral : 12.982 172.615 2340 Min Nonbonded Distance : 1.188 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.71 % Allowed : 15.89 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1864 helix: 0.94 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : 0.02 (0.34), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 304 HIS 0.002 0.001 HIS C 258 PHE 0.019 0.002 PHE E 296 TYR 0.016 0.001 TYR G 545 ARG 0.003 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 221 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: B 202 ASP cc_start: 0.8336 (t0) cc_final: 0.7919 (t0) REVERT: B 361 GLN cc_start: 0.7997 (tt0) cc_final: 0.7762 (tp-100) REVERT: C 202 ASP cc_start: 0.8320 (t0) cc_final: 0.7927 (t0) REVERT: C 361 GLN cc_start: 0.8115 (tt0) cc_final: 0.7736 (tp-100) REVERT: D 69 PHE cc_start: 0.6436 (t80) cc_final: 0.6212 (t80) REVERT: D 102 SER cc_start: 0.7506 (p) cc_final: 0.7239 (m) REVERT: D 115 GLU cc_start: 0.6940 (pm20) cc_final: 0.6718 (pp20) REVERT: E 202 ASP cc_start: 0.8304 (t0) cc_final: 0.7911 (t0) REVERT: E 359 GLN cc_start: 0.8276 (pt0) cc_final: 0.7981 (pt0) REVERT: E 361 GLN cc_start: 0.8114 (tt0) cc_final: 0.7766 (tp-100) REVERT: F 102 SER cc_start: 0.7501 (p) cc_final: 0.7268 (m) REVERT: G 170 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: G 202 ASP cc_start: 0.8287 (t0) cc_final: 0.7892 (t0) REVERT: G 361 GLN cc_start: 0.8039 (tt0) cc_final: 0.7770 (tp-100) REVERT: H 115 GLU cc_start: 0.6846 (pm20) cc_final: 0.6641 (pp20) outliers start: 46 outliers final: 26 residues processed: 249 average time/residue: 1.9261 time to fit residues: 541.6690 Evaluate side-chains 239 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 211 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 PHE Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 235 ILE Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 547 GLN Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 181 optimal weight: 40.0000 chunk 150 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 15 optimal weight: 0.0000 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 overall best weight: 1.0168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.5181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.126 14596 Z= 0.317 Angle : 1.879 77.398 19848 Z= 0.660 Chirality : 0.035 0.143 2240 Planarity : 0.003 0.040 2468 Dihedral : 12.692 177.400 2340 Min Nonbonded Distance : 1.188 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.26 % Allowed : 19.03 % Favored : 78.71 % 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: 1.41 (0.21), residues: 1864 helix: 1.35 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -0.06 (0.34), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 304 HIS 0.001 0.000 HIS G 258 PHE 0.013 0.001 PHE G 166 TYR 0.016 0.001 TYR G 545 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 267 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 239 time to evaluate : 2.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.7386 (p) cc_final: 0.7124 (m) REVERT: B 202 ASP cc_start: 0.8183 (t0) cc_final: 0.7786 (t0) REVERT: C 202 ASP cc_start: 0.8278 (t0) cc_final: 0.7856 (t0) REVERT: C 361 GLN cc_start: 0.8084 (tt0) cc_final: 0.7750 (tp-100) REVERT: D 102 SER cc_start: 0.7477 (p) cc_final: 0.7235 (m) REVERT: E 202 ASP cc_start: 0.8260 (t0) cc_final: 0.7829 (t0) REVERT: E 361 GLN cc_start: 0.8054 (tt0) cc_final: 0.7762 (tp-100) REVERT: F 82 SER cc_start: 0.7580 (t) cc_final: 0.6956 (p) REVERT: F 102 SER cc_start: 0.7465 (p) cc_final: 0.7243 (m) REVERT: G 202 ASP cc_start: 0.8191 (t0) cc_final: 0.7749 (t0) REVERT: H 102 SER cc_start: 0.7395 (p) cc_final: 0.7150 (m) outliers start: 28 outliers final: 18 residues processed: 255 average time/residue: 1.9172 time to fit residues: 552.5216 Evaluate side-chains 225 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 207 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 263 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 547 GLN Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 ILE Chi-restraints excluded: chain G residue 506 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 181 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 14596 Z= 0.393 Angle : 1.891 77.528 19848 Z= 0.671 Chirality : 0.036 0.188 2240 Planarity : 0.003 0.038 2468 Dihedral : 12.914 172.929 2340 Min Nonbonded Distance : 1.188 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.58 % Allowed : 20.73 % Favored : 76.69 % 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: 1.43 (0.21), residues: 1864 helix: 1.34 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : 0.03 (0.33), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 304 HIS 0.004 0.001 HIS E 549 PHE 0.021 0.002 PHE C 166 TYR 0.014 0.001 TYR E 545 ARG 0.004 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 244 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8206 (t0) cc_final: 0.7784 (t0) REVERT: C 202 ASP cc_start: 0.8274 (t0) cc_final: 0.7832 (t0) REVERT: C 361 GLN cc_start: 0.8136 (tt0) cc_final: 0.7835 (tp-100) REVERT: C 543 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8125 (mt-10) REVERT: D 102 SER cc_start: 0.7496 (p) cc_final: 0.7231 (m) REVERT: E 202 ASP cc_start: 0.8276 (t0) cc_final: 0.7787 (t0) REVERT: E 361 GLN cc_start: 0.8108 (tt0) cc_final: 0.7773 (tp-100) REVERT: F 82 SER cc_start: 0.7994 (t) cc_final: 0.7330 (p) REVERT: F 102 SER cc_start: 0.7411 (p) cc_final: 0.7180 (m) REVERT: G 202 ASP cc_start: 0.8284 (t0) cc_final: 0.7895 (t0) REVERT: H 102 SER cc_start: 0.7316 (p) cc_final: 0.7059 (m) outliers start: 32 outliers final: 28 residues processed: 226 average time/residue: 1.9008 time to fit residues: 487.7504 Evaluate side-chains 235 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 290 GLU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 547 GLN Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 271 LEU Chi-restraints excluded: chain G residue 290 GLU Chi-restraints excluded: chain G residue 506 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 142 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 GLN C 359 GLN E 359 GLN G 359 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 14596 Z= 0.335 Angle : 1.882 77.175 19848 Z= 0.663 Chirality : 0.035 0.122 2240 Planarity : 0.003 0.039 2468 Dihedral : 12.739 176.098 2340 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.18 % Allowed : 20.89 % Favored : 76.94 % 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: 1.70 (0.21), residues: 1864 helix: 1.61 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -0.08 (0.32), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 304 HIS 0.003 0.000 HIS E 549 PHE 0.019 0.001 PHE E 166 TYR 0.014 0.001 TYR G 545 ARG 0.002 0.000 ARG E 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 208 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8192 (t0) cc_final: 0.7769 (t0) REVERT: C 202 ASP cc_start: 0.8216 (t0) cc_final: 0.7771 (t0) REVERT: C 361 GLN cc_start: 0.8110 (tt0) cc_final: 0.7791 (tp-100) REVERT: D 66 PHE cc_start: 0.5421 (OUTLIER) cc_final: 0.4882 (p90) REVERT: D 102 SER cc_start: 0.7494 (p) cc_final: 0.7230 (m) REVERT: E 202 ASP cc_start: 0.8247 (t0) cc_final: 0.7797 (t0) REVERT: E 361 GLN cc_start: 0.8080 (tt0) cc_final: 0.7785 (tp-100) REVERT: F 82 SER cc_start: 0.8020 (t) cc_final: 0.7416 (p) REVERT: F 102 SER cc_start: 0.7429 (p) cc_final: 0.7203 (m) REVERT: G 202 ASP cc_start: 0.8263 (t0) cc_final: 0.7804 (t0) REVERT: H 102 SER cc_start: 0.7294 (p) cc_final: 0.7046 (m) outliers start: 27 outliers final: 24 residues processed: 223 average time/residue: 1.8911 time to fit residues: 478.1395 Evaluate side-chains 224 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain D residue 66 PHE Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 547 GLN Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 506 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 178 optimal weight: 30.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 14596 Z= 0.331 Angle : 1.883 77.178 19848 Z= 0.662 Chirality : 0.035 0.181 2240 Planarity : 0.003 0.038 2468 Dihedral : 12.644 176.739 2340 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.18 % Allowed : 21.13 % Favored : 76.69 % 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: 1.85 (0.21), residues: 1864 helix: 1.72 (0.14), residues: 1368 sheet: None (None), residues: 0 loop : -0.07 (0.32), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 304 HIS 0.003 0.000 HIS E 549 PHE 0.019 0.001 PHE E 166 TYR 0.013 0.001 TYR G 545 ARG 0.002 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 203 time to evaluate : 2.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8178 (t0) cc_final: 0.7730 (t0) REVERT: C 202 ASP cc_start: 0.8212 (t0) cc_final: 0.7757 (t0) REVERT: C 361 GLN cc_start: 0.8102 (tt0) cc_final: 0.7815 (tp-100) REVERT: D 102 SER cc_start: 0.7394 (p) cc_final: 0.7129 (m) REVERT: E 202 ASP cc_start: 0.8253 (t0) cc_final: 0.7741 (t0) REVERT: E 361 GLN cc_start: 0.8072 (tt0) cc_final: 0.7786 (tp-100) REVERT: F 82 SER cc_start: 0.8007 (t) cc_final: 0.7419 (p) REVERT: F 102 SER cc_start: 0.7431 (p) cc_final: 0.7194 (m) REVERT: G 202 ASP cc_start: 0.8242 (t0) cc_final: 0.7750 (t0) REVERT: G 531 GLN cc_start: 0.8909 (pt0) cc_final: 0.8677 (tm-30) REVERT: H 102 SER cc_start: 0.7345 (p) cc_final: 0.7081 (m) outliers start: 27 outliers final: 24 residues processed: 220 average time/residue: 1.9032 time to fit residues: 474.5254 Evaluate side-chains 219 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 2.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 271 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 547 GLN Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 506 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 187 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 14596 Z= 0.326 Angle : 1.884 77.060 19848 Z= 0.663 Chirality : 0.034 0.118 2240 Planarity : 0.003 0.039 2468 Dihedral : 12.555 177.814 2340 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.69 % Allowed : 21.85 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.21), residues: 1864 helix: 1.86 (0.14), residues: 1376 sheet: None (None), residues: 0 loop : -0.01 (0.32), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 304 HIS 0.004 0.001 HIS E 549 PHE 0.018 0.001 PHE E 166 TYR 0.012 0.001 TYR G 545 ARG 0.002 0.000 ARG B 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Residue SER 546 is missing expected H atoms. Skipping. Residue THR 6 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue SER 18 is missing expected H atoms. Skipping. Residue LEU 19 is missing expected H atoms. Skipping. Residue LYS 22 is missing expected H atoms. Skipping. Residue THR 27 is missing expected H atoms. Skipping. Residue ILE 28 is missing expected H atoms. Skipping. Residue THR 29 is missing expected H atoms. Skipping. Residue THR 30 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LEU 33 is missing expected H atoms. Skipping. Residue THR 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue MET 37 is missing expected H atoms. Skipping. Residue SER 39 is missing expected H atoms. Skipping. Residue LEU 40 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue LEU 49 is missing expected H atoms. Skipping. Residue MET 52 is missing expected H atoms. Skipping. Residue ILE 53 is missing expected H atoms. Skipping. Residue VAL 56 is missing expected H atoms. Skipping. Residue THR 63 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue THR 71 is missing expected H atoms. Skipping. Residue MET 72 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue MET 77 is missing expected H atoms. Skipping. Residue LYS 78 is missing expected H atoms. Skipping. Residue THR 80 is missing expected H atoms. Skipping. Residue LYS 95 is missing expected H atoms. Skipping. Residue MET 110 is missing expected H atoms. Skipping. Residue THR 118 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue MET 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 131 is missing expected H atoms. Skipping. Residue VAL 137 is missing expected H atoms. Skipping. Residue MET 146 is missing expected H atoms. Skipping. Residue THR 147 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 202 ASP cc_start: 0.8207 (t0) cc_final: 0.7780 (t0) REVERT: C 202 ASP cc_start: 0.8250 (t0) cc_final: 0.7701 (t0) REVERT: C 358 LYS cc_start: 0.8573 (tppt) cc_final: 0.8328 (ttmm) REVERT: C 361 GLN cc_start: 0.8093 (tt0) cc_final: 0.7806 (tp-100) REVERT: D 102 SER cc_start: 0.7374 (p) cc_final: 0.7087 (m) REVERT: E 202 ASP cc_start: 0.8215 (t0) cc_final: 0.7717 (t0) REVERT: E 361 GLN cc_start: 0.8054 (tt0) cc_final: 0.7766 (tp-100) REVERT: F 82 SER cc_start: 0.7994 (t) cc_final: 0.7453 (p) REVERT: F 102 SER cc_start: 0.7470 (p) cc_final: 0.7222 (m) REVERT: G 202 ASP cc_start: 0.8248 (t0) cc_final: 0.7770 (t0) REVERT: H 102 SER cc_start: 0.7334 (p) cc_final: 0.7057 (m) outliers start: 21 outliers final: 20 residues processed: 218 average time/residue: 1.9289 time to fit residues: 477.7061 Evaluate side-chains 210 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 190 time to evaluate : 2.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 506 LEU Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 528 LYS Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain F residue 13 PHE Chi-restraints excluded: chain G residue 122 CYS Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 506 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 153 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 131 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 547 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.190930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.111739 restraints weight = 60026.179| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.39 r_work: 0.3124 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.5978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 14596 Z= 0.503 Angle : 1.914 77.337 19848 Z= 0.690 Chirality : 0.039 0.144 2240 Planarity : 0.004 0.037 2468 Dihedral : 12.952 171.796 2340 Min Nonbonded Distance : 1.189 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.10 % Allowed : 21.94 % Favored : 75.97 % 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: 1.56 (0.20), residues: 1864 helix: 1.48 (0.14), residues: 1380 sheet: None (None), residues: 0 loop : -0.11 (0.32), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 304 HIS 0.003 0.001 HIS B 549 PHE 0.022 0.002 PHE G 296 TYR 0.012 0.002 TYR E 545 ARG 0.004 0.001 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10855.32 seconds wall clock time: 190 minutes 54.92 seconds (11454.92 seconds total)