Starting phenix.real_space_refine on Thu Mar 5 03:03:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k0n_22604/03_2026/7k0n_22604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k0n_22604/03_2026/7k0n_22604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k0n_22604/03_2026/7k0n_22604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k0n_22604/03_2026/7k0n_22604.map" model { file = "/net/cci-nas-00/data/ceres_data/7k0n_22604/03_2026/7k0n_22604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k0n_22604/03_2026/7k0n_22604.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.103 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 100 5.16 5 C 11952 2.51 5 N 3090 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18470 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3550 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3857 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 473} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1230 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 144} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 476 Classifications: {'peptide': 62} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 59} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 3550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3550 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 22, 'TRANS': 441} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 6, 'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 51 Chain: "F" Number of atoms: 3857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3857 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 473} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 31 Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 36 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 105 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 31 Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 3, 'POV:plan-3': 3} Unresolved non-hydrogen planarities: 36 Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 52 Unusual residues: {'PLP': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 4.12, per 1000 atoms: 0.22 Number of scatterers: 18470 At special positions: 0 Unit cell: (151.755, 115.575, 117.585, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 4 15.00 O 3324 8.00 N 3090 7.00 C 11952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.37 Conformation dependent library (CDL) restraints added in 711.1 milliseconds 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4340 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 14 sheets defined 54.1% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 21 through 41 removed outlier: 3.764A pdb=" N LEU A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 40 " --> pdb=" O ILE A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 114 through 129 removed outlier: 3.579A pdb=" N LYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.572A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.787A pdb=" N ALA A 172 " --> pdb=" O PHE A 168 " (cutoff:3.500A) Proline residue: A 176 - end of helix Processing helix chain 'A' and resid 192 through 202 Processing helix chain 'A' and resid 213 through 231 removed outlier: 3.839A pdb=" N LEU A 217 " --> pdb=" O ASP A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 Processing helix chain 'A' and resid 256 through 268 Processing helix chain 'A' and resid 288 through 294 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 360 through 377 removed outlier: 4.283A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 421 removed outlier: 3.511A pdb=" N ASP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 473 Processing helix chain 'B' and resid 67 through 94 Processing helix chain 'B' and resid 105 through 109 Processing helix chain 'B' and resid 116 through 119 Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.551A pdb=" N ARG B 131 " --> pdb=" O MET B 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP B 134 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.624A pdb=" N GLU B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 228 Processing helix chain 'B' and resid 237 through 250 removed outlier: 3.674A pdb=" N ASN B 242 " --> pdb=" O GLY B 238 " (cutoff:3.500A) Proline residue: B 247 - end of helix Processing helix chain 'B' and resid 263 through 273 Processing helix chain 'B' and resid 284 through 299 Processing helix chain 'B' and resid 326 through 338 Processing helix chain 'B' and resid 358 through 364 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 391 through 401 Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 412 through 427 Processing helix chain 'B' and resid 433 through 456 removed outlier: 3.722A pdb=" N VAL B 439 " --> pdb=" O GLY B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 4.165A pdb=" N GLY B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'C' and resid 9 through 24 Processing helix chain 'C' and resid 30 through 55 Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.843A pdb=" N ILE C 63 " --> pdb=" O HIS C 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 39 Processing helix chain 'D' and resid 44 through 66 Processing helix chain 'D' and resid 84 through 89 Processing helix chain 'D' and resid 90 through 93 Processing helix chain 'D' and resid 96 through 117 Proline residue: D 106 - end of helix Processing helix chain 'D' and resid 120 through 136 Processing helix chain 'D' and resid 137 through 139 No H-bonds generated for 'chain 'D' and resid 137 through 139' Processing helix chain 'D' and resid 146 through 150 Processing helix chain 'H' and resid 21 through 39 Processing helix chain 'H' and resid 44 through 66 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'H' and resid 90 through 93 Processing helix chain 'H' and resid 96 through 117 Proline residue: H 106 - end of helix Processing helix chain 'H' and resid 120 through 136 Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 146 through 150 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 30 through 55 Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.843A pdb=" N ILE G 63 " --> pdb=" O HIS G 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 21 through 41 removed outlier: 3.763A pdb=" N LEU E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 64 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.580A pdb=" N LYS E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.572A pdb=" N LEU E 146 " --> pdb=" O PHE E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 179 removed outlier: 3.787A pdb=" N ALA E 172 " --> pdb=" O PHE E 168 " (cutoff:3.500A) Proline residue: E 176 - end of helix Processing helix chain 'E' and resid 192 through 202 Processing helix chain 'E' and resid 213 through 231 removed outlier: 3.839A pdb=" N LEU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 236 Processing helix chain 'E' and resid 256 through 268 Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 327 through 332 Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 359 Processing helix chain 'E' and resid 360 through 377 removed outlier: 4.282A pdb=" N ALA E 364 " --> pdb=" O PRO E 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 421 removed outlier: 3.510A pdb=" N ASP E 408 " --> pdb=" O SER E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 473 Processing helix chain 'F' and resid 67 through 94 Processing helix chain 'F' and resid 105 through 109 Processing helix chain 'F' and resid 116 through 119 Processing helix chain 'F' and resid 120 through 126 Processing helix chain 'F' and resid 127 through 134 removed outlier: 3.551A pdb=" N ARG F 131 " --> pdb=" O MET F 128 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ASP F 132 " --> pdb=" O ARG F 129 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TRP F 134 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 199 removed outlier: 3.624A pdb=" N GLU F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 228 Processing helix chain 'F' and resid 237 through 250 removed outlier: 3.675A pdb=" N ASN F 242 " --> pdb=" O GLY F 238 " (cutoff:3.500A) Proline residue: F 247 - end of helix Processing helix chain 'F' and resid 263 through 273 Processing helix chain 'F' and resid 284 through 299 Processing helix chain 'F' and resid 326 through 338 Processing helix chain 'F' and resid 358 through 364 Processing helix chain 'F' and resid 366 through 370 Processing helix chain 'F' and resid 391 through 401 Processing helix chain 'F' and resid 402 through 408 Processing helix chain 'F' and resid 412 through 427 Processing helix chain 'F' and resid 433 through 456 removed outlier: 3.722A pdb=" N VAL F 439 " --> pdb=" O GLY F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 489 removed outlier: 4.166A pdb=" N GLY F 480 " --> pdb=" O PRO F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 517 through 536 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.959A pdb=" N ILE A 271 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N SER A 304 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 273 " --> pdb=" O SER A 304 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N ASN A 306 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG A 240 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N PHE A 272 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE A 242 " --> pdb=" O PHE A 272 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU A 274 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL A 244 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 188 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU A 245 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 185 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N PHE A 209 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 187 " --> pdb=" O PHE A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 384 removed outlier: 4.183A pdb=" N THR A 427 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 145 through 146 removed outlier: 6.784A pdb=" N ILE B 171 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 152 removed outlier: 5.343A pdb=" N GLU B 150 " --> pdb=" O THR B 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 163 " --> pdb=" O GLU B 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 6.568A pdb=" N ILE B 310 " --> pdb=" O TYR B 340 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR B 342 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 312 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP B 344 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL B 314 " --> pdb=" O ASP B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 468 through 472 removed outlier: 3.819A pdb=" N VAL B 494 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 94 through 95 Processing sheet with id=AA9, first strand: chain 'E' and resid 160 through 164 removed outlier: 6.959A pdb=" N ILE E 271 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N SER E 304 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU E 273 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N ASN E 306 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG E 240 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N PHE E 272 " --> pdb=" O ARG E 240 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ILE E 242 " --> pdb=" O PHE E 272 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N GLU E 274 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL E 244 " --> pdb=" O GLU E 274 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP E 188 " --> pdb=" O VAL E 243 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N GLU E 245 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 185 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N PHE E 209 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL E 187 " --> pdb=" O PHE E 209 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 383 through 384 removed outlier: 4.184A pdb=" N THR E 427 " --> pdb=" O ARG E 445 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 145 through 146 removed outlier: 6.783A pdb=" N ILE F 171 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 149 through 152 removed outlier: 5.343A pdb=" N GLU F 150 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR F 163 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 231 through 235 removed outlier: 6.570A pdb=" N ILE F 310 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N TYR F 342 " --> pdb=" O ILE F 310 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE F 312 " --> pdb=" O TYR F 342 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ASP F 344 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL F 314 " --> pdb=" O ASP F 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 468 through 472 removed outlier: 3.820A pdb=" N VAL F 494 " --> pdb=" O ARG F 509 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2715 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: 2.80 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5793 1.34 - 1.46: 2665 1.46 - 1.57: 10222 1.57 - 1.69: 4 1.69 - 1.81: 168 Bond restraints: 18852 Sorted by residual: bond pdb=" C29 POV H 903 " pdb="C210 POV H 903 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 bond pdb=" C29 POV D 903 " pdb="C210 POV D 903 " ideal model delta sigma weight residual 1.333 1.522 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" O12 POV B 602 " pdb=" P POV B 602 " ideal model delta sigma weight residual 1.657 1.742 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" O12 POV F 602 " pdb=" P POV F 602 " ideal model delta sigma weight residual 1.657 1.741 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N ASN F 120 " pdb=" CA ASN F 120 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 6.95e+00 ... (remaining 18847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.62: 25381 3.62 - 7.23: 89 7.23 - 10.85: 2 10.85 - 14.47: 0 14.47 - 18.09: 4 Bond angle restraints: 25476 Sorted by residual: angle pdb=" C29 POV D 903 " pdb="C210 POV D 903 " pdb="C211 POV D 903 " ideal model delta sigma weight residual 127.67 109.58 18.09 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C29 POV H 903 " pdb="C210 POV H 903 " pdb="C211 POV H 903 " ideal model delta sigma weight residual 127.67 109.60 18.07 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C28 POV H 903 " pdb=" C29 POV H 903 " pdb="C210 POV H 903 " ideal model delta sigma weight residual 127.79 110.40 17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" C28 POV D 903 " pdb=" C29 POV D 903 " pdb="C210 POV D 903 " ideal model delta sigma weight residual 127.79 110.42 17.37 3.00e+00 1.11e-01 3.35e+01 angle pdb=" N VAL E 450 " pdb=" CA VAL E 450 " pdb=" C VAL E 450 " ideal model delta sigma weight residual 112.80 108.66 4.14 1.15e+00 7.56e-01 1.29e+01 ... (remaining 25471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.97: 10610 22.97 - 45.93: 600 45.93 - 68.90: 62 68.90 - 91.87: 24 91.87 - 114.84: 2 Dihedral angle restraints: 11298 sinusoidal: 4518 harmonic: 6780 Sorted by residual: dihedral pdb=" C5A PLP F 603 " pdb=" O4P PLP F 603 " pdb=" P PLP F 603 " pdb=" O1P PLP F 603 " ideal model delta sinusoidal sigma weight residual 76.43 -168.74 -114.84 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" C5A PLP B 601 " pdb=" O4P PLP B 601 " pdb=" P PLP B 601 " pdb=" O1P PLP B 601 " ideal model delta sinusoidal sigma weight residual 76.43 -168.74 -114.83 1 2.00e+01 2.50e-03 3.41e+01 dihedral pdb=" CA ASN B 133 " pdb=" C ASN B 133 " pdb=" N TRP B 134 " pdb=" CA TRP B 134 " ideal model delta harmonic sigma weight residual -180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 11295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1757 0.029 - 0.058: 651 0.058 - 0.087: 246 0.087 - 0.117: 161 0.117 - 0.146: 31 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CB THR H 52 " pdb=" CA THR H 52 " pdb=" OG1 THR H 52 " pdb=" CG2 THR H 52 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CB THR D 52 " pdb=" CA THR D 52 " pdb=" OG1 THR D 52 " pdb=" CG2 THR D 52 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE E 242 " pdb=" N ILE E 242 " pdb=" C ILE E 242 " pdb=" CB ILE E 242 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.85e-01 ... (remaining 2843 not shown) Planarity restraints: 3224 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV H 903 " 0.080 2.00e-02 2.50e+03 8.01e-02 6.42e+01 pdb=" C29 POV H 903 " -0.082 2.00e-02 2.50e+03 pdb="C210 POV H 903 " -0.079 2.00e-02 2.50e+03 pdb="C211 POV H 903 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 903 " -0.080 2.00e-02 2.50e+03 8.01e-02 6.42e+01 pdb=" C29 POV D 903 " 0.082 2.00e-02 2.50e+03 pdb="C210 POV D 903 " 0.079 2.00e-02 2.50e+03 pdb="C211 POV D 903 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 412 " 0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO B 413 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO B 413 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 413 " 0.030 5.00e-02 4.00e+02 ... (remaining 3221 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3038 2.76 - 3.30: 17050 3.30 - 3.83: 29412 3.83 - 4.37: 35584 4.37 - 4.90: 63009 Nonbonded interactions: 148093 Sorted by model distance: nonbonded pdb=" O TRP E 64 " pdb=" NZ LYS F 338 " model vdw 2.227 3.120 nonbonded pdb=" O VAL H 10 " pdb=" OG1 THR H 74 " model vdw 2.232 3.040 nonbonded pdb=" O VAL D 10 " pdb=" OG1 THR D 74 " model vdw 2.232 3.040 nonbonded pdb=" OH TYR E 178 " pdb=" O VAL E 324 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 178 " pdb=" O VAL A 324 " model vdw 2.243 3.040 ... (remaining 148088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 53 through 543 or resid 602)) selection = (chain 'F' and (resid 53 through 543 or resid 602)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 2.720 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.130 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 : 0.004 0.190 18854 Z= 0.195 Angle : 0.688 18.087 25476 Z= 0.378 Chirality : 0.042 0.146 2846 Planarity : 0.004 0.080 3224 Dihedral : 14.059 114.836 6958 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.32 % Allowed : 0.47 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2324 helix: 1.74 (0.15), residues: 1116 sheet: -0.44 (0.36), residues: 220 loop : -0.76 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 95 TYR 0.020 0.001 TYR A 166 PHE 0.011 0.001 PHE F 239 TRP 0.016 0.001 TRP C 32 HIS 0.008 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00365 (18852) covalent geometry : angle 0.68770 (25476) hydrogen bonds : bond 0.14642 ( 947) hydrogen bonds : angle 5.67409 ( 2715) Misc. bond : bond 0.02956 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 0.646 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 224 average time/residue: 0.1500 time to fit residues: 50.1134 Evaluate side-chains 179 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 GLN H 77 GLN E 469 GLN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136303 restraints weight = 22822.291| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.78 r_work: 0.3648 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18854 Z= 0.201 Angle : 0.596 8.424 25476 Z= 0.316 Chirality : 0.045 0.160 2846 Planarity : 0.005 0.053 3224 Dihedral : 8.078 83.757 2718 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.26 % Allowed : 6.67 % Favored : 92.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.17), residues: 2324 helix: 1.64 (0.15), residues: 1154 sheet: -0.45 (0.36), residues: 220 loop : -0.72 (0.19), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 271 TYR 0.023 0.002 TYR A 166 PHE 0.018 0.002 PHE A 138 TRP 0.017 0.002 TRP G 32 HIS 0.007 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00493 (18852) covalent geometry : angle 0.59597 (25476) hydrogen bonds : bond 0.05412 ( 947) hydrogen bonds : angle 4.62533 ( 2715) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 196 time to evaluate : 0.588 Fit side-chains REVERT: C 50 TYR cc_start: 0.7218 (t80) cc_final: 0.6784 (t80) REVERT: D 87 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8688 (mt-10) REVERT: H 87 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8714 (mt-10) REVERT: G 50 TYR cc_start: 0.7320 (t80) cc_final: 0.6901 (t80) outliers start: 24 outliers final: 13 residues processed: 207 average time/residue: 0.1397 time to fit residues: 43.8089 Evaluate side-chains 199 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 228 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 213 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 103 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.163341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.139964 restraints weight = 22961.049| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.79 r_work: 0.3687 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18854 Z= 0.113 Angle : 0.494 8.583 25476 Z= 0.260 Chirality : 0.041 0.134 2846 Planarity : 0.004 0.052 3224 Dihedral : 7.357 70.662 2718 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.47 % Allowed : 8.40 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2324 helix: 1.86 (0.15), residues: 1154 sheet: -0.42 (0.37), residues: 224 loop : -0.65 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 271 TYR 0.016 0.001 TYR C 27 PHE 0.012 0.001 PHE F 280 TRP 0.014 0.001 TRP C 32 HIS 0.004 0.001 HIS E 24 Details of bonding type rmsd covalent geometry : bond 0.00259 (18852) covalent geometry : angle 0.49444 (25476) hydrogen bonds : bond 0.04222 ( 947) hydrogen bonds : angle 4.32080 ( 2715) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 0.635 Fit side-chains REVERT: A 469 GLN cc_start: 0.7651 (OUTLIER) cc_final: 0.6502 (mp-120) REVERT: B 111 PHE cc_start: 0.8521 (m-80) cc_final: 0.7868 (m-80) REVERT: B 155 ASP cc_start: 0.8402 (t0) cc_final: 0.8181 (t0) REVERT: C 50 TYR cc_start: 0.7192 (t80) cc_final: 0.6857 (t80) REVERT: G 50 TYR cc_start: 0.7302 (t80) cc_final: 0.6956 (t80) REVERT: E 469 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6506 (mp-120) outliers start: 28 outliers final: 22 residues processed: 212 average time/residue: 0.1337 time to fit residues: 43.1133 Evaluate side-chains 206 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 43 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.162505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.139231 restraints weight = 22940.933| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.78 r_work: 0.3675 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18854 Z= 0.128 Angle : 0.501 8.726 25476 Z= 0.263 Chirality : 0.042 0.136 2846 Planarity : 0.004 0.052 3224 Dihedral : 7.071 61.560 2718 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.84 % Allowed : 8.88 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.17), residues: 2324 helix: 1.93 (0.15), residues: 1154 sheet: -0.40 (0.37), residues: 224 loop : -0.65 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 271 TYR 0.018 0.001 TYR C 27 PHE 0.012 0.001 PHE F 280 TRP 0.014 0.001 TRP G 32 HIS 0.005 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00306 (18852) covalent geometry : angle 0.50132 (25476) hydrogen bonds : bond 0.04254 ( 947) hydrogen bonds : angle 4.24520 ( 2715) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.720 Fit side-chains REVERT: A 469 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.6398 (mp-120) REVERT: B 111 PHE cc_start: 0.8492 (m-80) cc_final: 0.7862 (m-80) REVERT: B 155 ASP cc_start: 0.8557 (t0) cc_final: 0.8262 (t0) REVERT: C 50 TYR cc_start: 0.7225 (t80) cc_final: 0.6892 (t80) REVERT: G 50 TYR cc_start: 0.7349 (t80) cc_final: 0.7045 (t80) REVERT: E 356 MET cc_start: 0.8735 (mtp) cc_final: 0.8516 (ttm) REVERT: E 469 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6409 (mp-120) REVERT: F 271 ARG cc_start: 0.8430 (mmt90) cc_final: 0.8012 (mtm110) outliers start: 35 outliers final: 28 residues processed: 201 average time/residue: 0.1454 time to fit residues: 44.4121 Evaluate side-chains 207 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 326 ASP Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.160506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.136920 restraints weight = 22778.767| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.80 r_work: 0.3649 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18854 Z= 0.162 Angle : 0.534 9.342 25476 Z= 0.280 Chirality : 0.043 0.144 2846 Planarity : 0.004 0.052 3224 Dihedral : 6.998 61.560 2718 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.68 % Allowed : 10.82 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2324 helix: 1.83 (0.15), residues: 1158 sheet: -0.35 (0.37), residues: 220 loop : -0.73 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 484 TYR 0.020 0.002 TYR C 27 PHE 0.013 0.002 PHE E 317 TRP 0.014 0.001 TRP G 32 HIS 0.006 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00400 (18852) covalent geometry : angle 0.53365 (25476) hydrogen bonds : bond 0.04716 ( 947) hydrogen bonds : angle 4.28559 ( 2715) Misc. bond : bond 0.00006 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.487 Fit side-chains REVERT: A 469 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6402 (mp-120) REVERT: B 155 ASP cc_start: 0.8672 (t0) cc_final: 0.8342 (t0) REVERT: B 271 ARG cc_start: 0.8395 (mmt90) cc_final: 0.7991 (mtm110) REVERT: C 50 TYR cc_start: 0.7206 (t80) cc_final: 0.6914 (t80) REVERT: G 50 TYR cc_start: 0.7329 (t80) cc_final: 0.7068 (t80) REVERT: E 126 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8117 (mtmt) REVERT: E 469 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.6412 (mp-120) REVERT: F 271 ARG cc_start: 0.8407 (mmt90) cc_final: 0.8006 (mtm110) REVERT: F 333 LEU cc_start: 0.8087 (mp) cc_final: 0.7880 (mp) outliers start: 32 outliers final: 26 residues processed: 203 average time/residue: 0.1534 time to fit residues: 46.6264 Evaluate side-chains 212 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 434 LYS Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.162835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.139387 restraints weight = 22750.841| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.79 r_work: 0.3677 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18854 Z= 0.120 Angle : 0.486 9.259 25476 Z= 0.256 Chirality : 0.041 0.132 2846 Planarity : 0.004 0.052 3224 Dihedral : 6.738 58.805 2718 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.94 % Allowed : 11.08 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.17), residues: 2324 helix: 1.97 (0.15), residues: 1154 sheet: -0.37 (0.38), residues: 224 loop : -0.66 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 484 TYR 0.021 0.001 TYR C 27 PHE 0.012 0.001 PHE F 280 TRP 0.015 0.001 TRP G 32 HIS 0.005 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00284 (18852) covalent geometry : angle 0.48624 (25476) hydrogen bonds : bond 0.04069 ( 947) hydrogen bonds : angle 4.18353 ( 2715) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.724 Fit side-chains REVERT: A 126 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8093 (mtmt) REVERT: A 469 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.6496 (mp-120) REVERT: B 111 PHE cc_start: 0.8475 (m-80) cc_final: 0.7825 (m-80) REVERT: B 155 ASP cc_start: 0.8648 (t0) cc_final: 0.8285 (t0) REVERT: B 271 ARG cc_start: 0.8439 (mmt90) cc_final: 0.8048 (mtm110) REVERT: C 50 TYR cc_start: 0.7214 (t80) cc_final: 0.7003 (t80) REVERT: E 126 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8089 (mtmt) REVERT: E 469 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.6514 (mp-120) REVERT: F 271 ARG cc_start: 0.8454 (mmt90) cc_final: 0.8053 (mtm110) outliers start: 37 outliers final: 27 residues processed: 218 average time/residue: 0.1482 time to fit residues: 48.6985 Evaluate side-chains 210 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 28 MET Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 97 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 108 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 123 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN D 85 HIS H 65 HIS H 85 HIS E 114 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.164604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141223 restraints weight = 23000.583| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.79 r_work: 0.3696 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18854 Z= 0.101 Angle : 0.466 10.887 25476 Z= 0.244 Chirality : 0.040 0.126 2846 Planarity : 0.004 0.050 3224 Dihedral : 6.475 58.387 2718 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.68 % Allowed : 12.03 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.18), residues: 2324 helix: 2.10 (0.15), residues: 1150 sheet: -0.25 (0.38), residues: 222 loop : -0.63 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 233 TYR 0.021 0.001 TYR C 27 PHE 0.011 0.001 PHE B 280 TRP 0.015 0.001 TRP C 32 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00233 (18852) covalent geometry : angle 0.46606 (25476) hydrogen bonds : bond 0.03645 ( 947) hydrogen bonds : angle 4.09103 ( 2715) Misc. bond : bond 0.00004 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.713 Fit side-chains REVERT: A 126 LYS cc_start: 0.8372 (mmtt) cc_final: 0.8094 (mtmt) REVERT: A 469 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.6476 (mp-120) REVERT: B 155 ASP cc_start: 0.8588 (t0) cc_final: 0.8226 (t0) REVERT: B 271 ARG cc_start: 0.8485 (mmt90) cc_final: 0.8049 (mtm110) REVERT: C 50 TYR cc_start: 0.7194 (t80) cc_final: 0.6991 (t80) REVERT: E 126 LYS cc_start: 0.8367 (mmtt) cc_final: 0.8082 (mtmt) REVERT: E 469 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.6482 (mp-120) REVERT: F 271 ARG cc_start: 0.8473 (mmt90) cc_final: 0.8052 (mtm110) REVERT: F 285 MET cc_start: 0.7565 (mmt) cc_final: 0.7094 (mmt) outliers start: 32 outliers final: 24 residues processed: 209 average time/residue: 0.1461 time to fit residues: 46.3339 Evaluate side-chains 209 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 205 SER Chi-restraints excluded: chain F residue 284 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 170 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 127 optimal weight: 0.2980 chunk 78 optimal weight: 0.7980 chunk 32 optimal weight: 0.1980 chunk 61 optimal weight: 0.0570 chunk 212 optimal weight: 3.9990 chunk 66 optimal weight: 0.4980 chunk 126 optimal weight: 2.9990 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN D 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.166067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.142992 restraints weight = 22710.711| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 1.77 r_work: 0.3718 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18854 Z= 0.091 Angle : 0.451 7.185 25476 Z= 0.237 Chirality : 0.040 0.254 2846 Planarity : 0.004 0.050 3224 Dihedral : 6.330 58.754 2718 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.42 % Allowed : 12.50 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.18), residues: 2324 helix: 2.18 (0.15), residues: 1150 sheet: -0.11 (0.38), residues: 218 loop : -0.57 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 233 TYR 0.021 0.001 TYR C 27 PHE 0.018 0.001 PHE B 111 TRP 0.014 0.001 TRP G 32 HIS 0.003 0.001 HIS B 403 Details of bonding type rmsd covalent geometry : bond 0.00201 (18852) covalent geometry : angle 0.45080 (25476) hydrogen bonds : bond 0.03352 ( 947) hydrogen bonds : angle 4.04567 ( 2715) Misc. bond : bond 0.00003 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.649 Fit side-chains REVERT: A 126 LYS cc_start: 0.8354 (mmtt) cc_final: 0.8076 (mtmt) REVERT: A 469 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.6502 (mp-120) REVERT: B 155 ASP cc_start: 0.8548 (t0) cc_final: 0.8225 (t0) REVERT: B 271 ARG cc_start: 0.8460 (mmt90) cc_final: 0.8028 (mtm110) REVERT: E 126 LYS cc_start: 0.8353 (mmtt) cc_final: 0.8063 (mtmt) REVERT: E 469 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6523 (mp-120) REVERT: F 155 ASP cc_start: 0.8519 (t0) cc_final: 0.8178 (t0) REVERT: F 271 ARG cc_start: 0.8468 (mmt90) cc_final: 0.8044 (mtm110) REVERT: F 285 MET cc_start: 0.7497 (mmt) cc_final: 0.7015 (mmt) outliers start: 27 outliers final: 24 residues processed: 211 average time/residue: 0.1452 time to fit residues: 46.9270 Evaluate side-chains 214 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 93 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 230 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN E 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.164606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141270 restraints weight = 22852.263| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 1.79 r_work: 0.3699 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18854 Z= 0.110 Angle : 0.477 7.440 25476 Z= 0.250 Chirality : 0.041 0.233 2846 Planarity : 0.004 0.049 3224 Dihedral : 6.309 58.757 2718 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.79 % Allowed : 12.13 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2324 helix: 2.18 (0.15), residues: 1150 sheet: -0.31 (0.37), residues: 222 loop : -0.59 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 233 TYR 0.022 0.001 TYR C 27 PHE 0.016 0.001 PHE B 111 TRP 0.013 0.001 TRP C 32 HIS 0.004 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00258 (18852) covalent geometry : angle 0.47681 (25476) hydrogen bonds : bond 0.03641 ( 947) hydrogen bonds : angle 4.04521 ( 2715) Misc. bond : bond 0.00002 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 196 time to evaluate : 0.640 Fit side-chains REVERT: A 126 LYS cc_start: 0.8360 (mmtt) cc_final: 0.8088 (mtmt) REVERT: A 469 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.6505 (mp-120) REVERT: B 155 ASP cc_start: 0.8620 (t0) cc_final: 0.8296 (t0) REVERT: B 271 ARG cc_start: 0.8470 (mmt90) cc_final: 0.8050 (mtm110) REVERT: B 333 LEU cc_start: 0.8288 (mm) cc_final: 0.7933 (mp) REVERT: E 126 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8088 (mtmt) REVERT: E 469 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.6521 (mp-120) REVERT: F 155 ASP cc_start: 0.8533 (t0) cc_final: 0.8187 (t0) REVERT: F 271 ARG cc_start: 0.8459 (mmt90) cc_final: 0.8050 (mtm110) REVERT: F 333 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7937 (mp) outliers start: 34 outliers final: 29 residues processed: 218 average time/residue: 0.1458 time to fit residues: 48.3686 Evaluate side-chains 222 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 28 MET Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 157 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 222 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 24 optimal weight: 0.0770 chunk 95 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 141 optimal weight: 10.0000 chunk 61 optimal weight: 0.0870 chunk 228 optimal weight: 0.7980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN E 114 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.165529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.142278 restraints weight = 22799.473| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 1.78 r_work: 0.3714 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 18854 Z= 0.096 Angle : 0.466 8.835 25476 Z= 0.244 Chirality : 0.040 0.232 2846 Planarity : 0.004 0.049 3224 Dihedral : 6.257 59.753 2718 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.73 % Allowed : 12.45 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.18), residues: 2324 helix: 2.22 (0.15), residues: 1150 sheet: -0.28 (0.37), residues: 222 loop : -0.55 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 233 TYR 0.021 0.001 TYR C 27 PHE 0.014 0.001 PHE B 111 TRP 0.014 0.001 TRP C 32 HIS 0.003 0.001 HIS F 403 Details of bonding type rmsd covalent geometry : bond 0.00220 (18852) covalent geometry : angle 0.46603 (25476) hydrogen bonds : bond 0.03439 ( 947) hydrogen bonds : angle 4.00438 ( 2715) Misc. bond : bond 0.00002 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4648 Ramachandran restraints generated. 2324 Oldfield, 0 Emsley, 2324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 0.682 Fit side-chains REVERT: A 126 LYS cc_start: 0.8351 (mmtt) cc_final: 0.8087 (mtmt) REVERT: A 469 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.6505 (mp-120) REVERT: B 155 ASP cc_start: 0.8569 (t0) cc_final: 0.8231 (t0) REVERT: B 271 ARG cc_start: 0.8447 (mmt90) cc_final: 0.8020 (mtm110) REVERT: E 126 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8083 (mtmt) REVERT: E 469 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.6513 (mp-120) REVERT: F 155 ASP cc_start: 0.8476 (t0) cc_final: 0.8136 (t0) REVERT: F 271 ARG cc_start: 0.8457 (mmt90) cc_final: 0.8049 (mtm110) REVERT: F 285 MET cc_start: 0.7559 (mmt) cc_final: 0.7185 (mmt) outliers start: 33 outliers final: 30 residues processed: 216 average time/residue: 0.1427 time to fit residues: 46.9344 Evaluate side-chains 223 residues out of total 2006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 191 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 355 THR Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 VAL Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 36 ILE Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 114 ASN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 162 ILE Chi-restraints excluded: chain E residue 281 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 284 ASN Chi-restraints excluded: chain F residue 355 THR Chi-restraints excluded: chain F residue 410 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 231 optimal weight: 0.0570 chunk 143 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 203 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 135 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 81 optimal weight: 0.0570 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.166446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143305 restraints weight = 22904.425| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.78 r_work: 0.3729 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18854 Z= 0.091 Angle : 0.467 14.090 25476 Z= 0.241 Chirality : 0.040 0.316 2846 Planarity : 0.004 0.048 3224 Dihedral : 6.160 58.918 2718 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.68 % Allowed : 12.45 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.18), residues: 2324 helix: 2.24 (0.15), residues: 1152 sheet: -0.17 (0.38), residues: 218 loop : -0.51 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 233 TYR 0.021 0.001 TYR C 27 PHE 0.012 0.001 PHE B 111 TRP 0.014 0.001 TRP C 32 HIS 0.003 0.001 HIS E 395 Details of bonding type rmsd covalent geometry : bond 0.00203 (18852) covalent geometry : angle 0.46721 (25476) hydrogen bonds : bond 0.03278 ( 947) hydrogen bonds : angle 3.97646 ( 2715) Misc. bond : bond 0.00001 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4664.51 seconds wall clock time: 80 minutes 42.07 seconds (4842.07 seconds total)