Starting phenix.real_space_refine on Sun Jul 5 07:33:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwe_44970/07_2026/9bwe_44970.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwe_44970/07_2026/9bwe_44970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bwe_44970/07_2026/9bwe_44970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwe_44970/07_2026/9bwe_44970.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwe_44970/07_2026/9bwe_44970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwe_44970/07_2026/9bwe_44970.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 14615 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9550 2.51 5 N 2320 2.21 5 O 2645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14615 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "C" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "D" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "E" Number of atoms: 2822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2822 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 16, 'TRANS': 329} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 81 Unusual residues: {'PIO': 7, 'PX4': 1} Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'PIO:plan-2': 3, 'PIO:plan-1': 4, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 68 Unusual residues: {'PIO': 6, 'PX4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 266 Unresolved non-hydrogen angles: 382 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'PIO:plan-2': 3, 'PIO:plan-1': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 60 Unusual residues: {'PIO': 5, 'PX4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'PIO:plan-2': 3, 'PIO:plan-1': 2, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 76 Unusual residues: {'PIO': 7, 'PX4': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 306 Unresolved non-hydrogen angles: 440 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'PIO:plan-2': 3, 'PIO:plan-1': 4, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 32 Chain: "E" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 65 Unusual residues: {'PIO': 5, 'PX4': 1} Inner-chain residues flagged as termini: ['pdbres="GLY E 504 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 226 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'PIO:plan-1': 2, 'PIO:plan-2': 3, 'PX4:plan-2': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 3.41, per 1000 atoms: 0.23 Number of scatterers: 14615 At special positions: 0 Unit cell: (97.44, 98.28, 128.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2645 8.00 N 2320 7.00 C 9550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS E 198 " - pdb=" SG CYS E 209 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 38 " " NAG G 1 " - " ASN B 38 " " NAG H 1 " - " ASN C 38 " " NAG I 1 " - " ASN D 38 " " NAG J 1 " - " ASN E 38 " Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 719.4 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3340 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 25 sheets defined 40.1% alpha, 40.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 10 through 18 removed outlier: 4.179A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.942A pdb=" N MET A 89 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE A 93 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 220 through 228 removed outlier: 3.761A pdb=" N TYR A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 239 Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.105A pdb=" N THR A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 309 removed outlier: 3.749A pdb=" N PHE A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 401 removed outlier: 3.515A pdb=" N ARG A 391 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 401 " --> pdb=" O THR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 416 removed outlier: 3.680A pdb=" N PHE A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.750A pdb=" N LEU A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 18 removed outlier: 4.180A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.942A pdb=" N MET B 89 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE B 93 " --> pdb=" O LEU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 147 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.761A pdb=" N TYR B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 239 Processing helix chain 'B' and resid 240 through 243 Processing helix chain 'B' and resid 248 through 270 removed outlier: 4.105A pdb=" N THR B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 309 removed outlier: 3.750A pdb=" N PHE B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 401 removed outlier: 3.515A pdb=" N ARG B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 395 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 416 removed outlier: 3.680A pdb=" N PHE B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.749A pdb=" N LEU B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 18 removed outlier: 4.179A pdb=" N LEU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP C 15 " --> pdb=" O SER C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 74 Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.941A pdb=" N MET C 89 " --> pdb=" O ASP C 86 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE C 93 " --> pdb=" O LEU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 220 through 228 removed outlier: 3.760A pdb=" N TYR C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 248 through 270 removed outlier: 4.105A pdb=" N THR C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR C 265 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 309 removed outlier: 3.749A pdb=" N PHE C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG C 309 " --> pdb=" O ASN C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 401 removed outlier: 3.515A pdb=" N ARG C 391 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 395 " --> pdb=" O ARG C 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA C 401 " --> pdb=" O THR C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 removed outlier: 3.680A pdb=" N PHE C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.750A pdb=" N LEU C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 18 removed outlier: 4.179A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP D 15 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 74 Processing helix chain 'D' and resid 86 through 93 removed outlier: 3.941A pdb=" N MET D 89 " --> pdb=" O ASP D 86 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE D 93 " --> pdb=" O LEU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 147 Processing helix chain 'D' and resid 220 through 228 removed outlier: 3.760A pdb=" N TYR D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 239 Processing helix chain 'D' and resid 240 through 243 Processing helix chain 'D' and resid 248 through 270 removed outlier: 4.104A pdb=" N THR D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR D 265 " --> pdb=" O LEU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 309 removed outlier: 3.749A pdb=" N PHE D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG D 309 " --> pdb=" O ASN D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 401 removed outlier: 3.515A pdb=" N ARG D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE D 395 " --> pdb=" O ARG D 391 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP D 396 " --> pdb=" O ALA D 392 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 401 " --> pdb=" O THR D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 416 removed outlier: 3.680A pdb=" N PHE D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 removed outlier: 3.750A pdb=" N LEU D 421 " --> pdb=" O ILE D 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 18 removed outlier: 4.179A pdb=" N LEU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 74 Processing helix chain 'E' and resid 86 through 93 removed outlier: 3.942A pdb=" N MET E 89 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE E 93 " --> pdb=" O LEU E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 147 Processing helix chain 'E' and resid 220 through 228 removed outlier: 3.760A pdb=" N TYR E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 239 Processing helix chain 'E' and resid 240 through 243 Processing helix chain 'E' and resid 248 through 270 removed outlier: 4.105A pdb=" N THR E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR E 265 " --> pdb=" O LEU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 removed outlier: 3.749A pdb=" N PHE E 306 " --> pdb=" O ALA E 302 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG E 309 " --> pdb=" O ASN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 removed outlier: 3.515A pdb=" N ARG E 391 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP E 396 " --> pdb=" O ALA E 392 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 416 removed outlier: 3.680A pdb=" N PHE E 410 " --> pdb=" O ALA E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.751A pdb=" N LEU E 421 " --> pdb=" O ILE E 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 85 removed outlier: 3.728A pdb=" N LEU A 118 " --> pdb=" O LEU A 85 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN A 125 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 107 removed outlier: 6.862A pdb=" N THR A 135 " --> pdb=" O LYS A 104 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA A 106 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR A 133 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP A 57 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER A 50 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG A 59 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE A 48 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN A 61 " --> pdb=" O ASN A 46 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN A 69 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN A 38 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 Processing sheet with id=AA4, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.524A pdb=" N GLU A 211 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 194 " --> pdb=" O ARG A 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 85 removed outlier: 3.728A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 107 removed outlier: 6.862A pdb=" N THR B 135 " --> pdb=" O LYS B 104 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA B 106 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR B 133 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 57 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER B 50 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG B 59 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE B 48 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN B 61 " --> pdb=" O ASN B 46 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 100 Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.524A pdb=" N GLU B 211 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP B 194 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AB2, first strand: chain 'C' and resid 82 through 85 removed outlier: 3.728A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 107 removed outlier: 6.862A pdb=" N THR C 135 " --> pdb=" O LYS C 104 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA C 106 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR C 133 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP C 57 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER C 50 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG C 59 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE C 48 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN C 61 " --> pdb=" O ASN C 46 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN C 69 " --> pdb=" O ASN C 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN C 38 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 98 through 100 Processing sheet with id=AB5, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.524A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP C 194 " --> pdb=" O ARG C 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 202 Processing sheet with id=AB7, first strand: chain 'D' and resid 82 through 85 removed outlier: 3.728A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 107 removed outlier: 6.862A pdb=" N THR D 135 " --> pdb=" O LYS D 104 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ALA D 106 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR D 133 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP D 57 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER D 50 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG D 59 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE D 48 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ASN D 61 " --> pdb=" O ASN D 46 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 98 through 100 Processing sheet with id=AC1, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.525A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP D 194 " --> pdb=" O ARG D 213 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AC3, first strand: chain 'E' and resid 82 through 85 removed outlier: 3.728A pdb=" N LEU E 118 " --> pdb=" O LEU E 85 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 103 through 107 removed outlier: 6.862A pdb=" N THR E 135 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ALA E 106 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR E 133 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP E 57 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER E 50 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ARG E 59 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE E 48 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASN E 61 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN E 69 " --> pdb=" O ASN E 38 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN E 38 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 98 through 100 Processing sheet with id=AC6, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.525A pdb=" N GLU E 211 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP E 194 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 201 through 202 790 hydrogen bonds defined for protein. 2280 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: 2.08 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2285 1.31 - 1.44: 4168 1.44 - 1.57: 8272 1.57 - 1.70: 50 1.70 - 1.83: 165 Bond restraints: 14940 Sorted by residual: bond pdb=" C9 PX4 A 508 " pdb=" O5 PX4 A 508 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C9 PX4 D 508 " pdb=" O5 PX4 D 508 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C9 PX4 E 503 " pdb=" O5 PX4 E 503 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C9 PX4 C 508 " pdb=" O5 PX4 C 508 " ideal model delta sigma weight residual 1.327 1.466 -0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" C9 PX4 B 508 " pdb=" O5 PX4 B 508 " ideal model delta sigma weight residual 1.327 1.465 -0.138 2.00e-02 2.50e+03 4.78e+01 ... (remaining 14935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 18885 1.97 - 3.94: 1047 3.94 - 5.91: 153 5.91 - 7.88: 50 7.88 - 9.85: 20 Bond angle restraints: 20155 Sorted by residual: angle pdb=" N ASP C 172 " pdb=" CA ASP C 172 " pdb=" C ASP C 172 " ideal model delta sigma weight residual 113.28 103.79 9.49 1.22e+00 6.72e-01 6.05e+01 angle pdb=" N ASP B 172 " pdb=" CA ASP B 172 " pdb=" C ASP B 172 " ideal model delta sigma weight residual 113.28 103.79 9.49 1.22e+00 6.72e-01 6.05e+01 angle pdb=" N ASP E 172 " pdb=" CA ASP E 172 " pdb=" C ASP E 172 " ideal model delta sigma weight residual 113.28 103.79 9.49 1.22e+00 6.72e-01 6.05e+01 angle pdb=" N ASP D 172 " pdb=" CA ASP D 172 " pdb=" C ASP D 172 " ideal model delta sigma weight residual 113.28 103.79 9.49 1.22e+00 6.72e-01 6.05e+01 angle pdb=" N ASP A 172 " pdb=" CA ASP A 172 " pdb=" C ASP A 172 " ideal model delta sigma weight residual 113.28 103.82 9.46 1.22e+00 6.72e-01 6.01e+01 ... (remaining 20150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 8150 17.31 - 34.63: 669 34.63 - 51.94: 181 51.94 - 69.26: 30 69.26 - 86.57: 20 Dihedral angle restraints: 9050 sinusoidal: 3915 harmonic: 5135 Sorted by residual: dihedral pdb=" CA ASP E 390 " pdb=" CB ASP E 390 " pdb=" CG ASP E 390 " pdb=" OD1 ASP E 390 " ideal model delta sinusoidal sigma weight residual -30.00 -87.22 57.22 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP D 390 " pdb=" CB ASP D 390 " pdb=" CG ASP D 390 " pdb=" OD1 ASP D 390 " ideal model delta sinusoidal sigma weight residual -30.00 -87.20 57.20 1 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CA ASP C 390 " pdb=" CB ASP C 390 " pdb=" CG ASP C 390 " pdb=" OD1 ASP C 390 " ideal model delta sinusoidal sigma weight residual -30.00 -87.19 57.19 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 9047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1723 0.057 - 0.114: 429 0.114 - 0.171: 74 0.171 - 0.228: 14 0.228 - 0.286: 5 Chirality restraints: 2245 Sorted by residual: chirality pdb=" CA ILE C 426 " pdb=" N ILE C 426 " pdb=" C ILE C 426 " pdb=" CB ILE C 426 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ILE A 426 " pdb=" N ILE A 426 " pdb=" C ILE A 426 " pdb=" CB ILE A 426 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ILE E 426 " pdb=" N ILE E 426 " pdb=" C ILE E 426 " pdb=" CB ILE E 426 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2242 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 87 " 0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" C PRO B 87 " -0.059 2.00e-02 2.50e+03 pdb=" O PRO B 87 " 0.022 2.00e-02 2.50e+03 pdb=" N SER B 88 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO D 87 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C PRO D 87 " 0.059 2.00e-02 2.50e+03 pdb=" O PRO D 87 " -0.022 2.00e-02 2.50e+03 pdb=" N SER D 88 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 87 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.15e+01 pdb=" C PRO E 87 " 0.059 2.00e-02 2.50e+03 pdb=" O PRO E 87 " -0.022 2.00e-02 2.50e+03 pdb=" N SER E 88 " -0.020 2.00e-02 2.50e+03 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 55 2.50 - 3.10: 9817 3.10 - 3.70: 21872 3.70 - 4.30: 32112 4.30 - 4.90: 53932 Nonbonded interactions: 117788 Sorted by model distance: nonbonded pdb=" NH2 ARG A 422 " pdb=" CD2 HIS A 423 " model vdw 1.898 3.340 nonbonded pdb=" NH2 ARG B 422 " pdb=" CD2 HIS B 423 " model vdw 1.898 3.340 nonbonded pdb=" NH2 ARG C 422 " pdb=" CD2 HIS C 423 " model vdw 1.898 3.340 nonbonded pdb=" NH2 ARG D 422 " pdb=" CD2 HIS D 423 " model vdw 1.898 3.340 nonbonded pdb=" NH2 ARG E 422 " pdb=" CD2 HIS E 423 " model vdw 1.898 3.340 ... (remaining 117783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 8 through 427) selection = (chain 'B' and resid 8 through 427) selection = (chain 'C' and resid 8 through 427) selection = (chain 'D' and resid 8 through 427) selection = (chain 'E' and resid 8 through 427) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.190 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 0.008 0.139 14955 Z= 0.398 Angle : 1.023 9.848 20195 Z= 0.564 Chirality : 0.055 0.286 2245 Planarity : 0.007 0.048 2510 Dihedral : 14.466 86.570 5695 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.32 % Allowed : 0.32 % Favored : 99.36 % 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: -2.05 (0.19), residues: 1710 helix: -1.76 (0.17), residues: 605 sheet: -0.70 (0.28), residues: 375 loop : -1.15 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 271 TYR 0.047 0.003 TYR E 279 PHE 0.021 0.002 PHE D 145 TRP 0.010 0.001 TRP C 170 HIS 0.002 0.001 HIS E 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00752 / 0.40 (14940) covalent geometry : angle 1.01914 / 0.56 (20155) SS BOND : bond 0.00522 / 0.28 ( 5) SS BOND : angle 4.25180 / 2.19 ( 10) hydrogen bonds : bond 0.14457 / 9.19 ( 645) hydrogen bonds : angle 7.11132 / 4.76 ( 2280) link_BETA1-4 : bond 0.00443 / 0.24 ( 5) link_BETA1-4 : angle 1.23296 / 0.69 ( 15) link_NAG-ASN : bond 0.00270 / 0.15 ( 5) link_NAG-ASN : angle 0.61684 / 0.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.458 Fit side-chains REVERT: C 121 PHE cc_start: 0.8608 (m-80) cc_final: 0.8163 (m-80) REVERT: E 163 MET cc_start: 0.8197 (mmm) cc_final: 0.7914 (mmm) REVERT: E 287 MET cc_start: 0.7320 (mmm) cc_final: 0.7061 (mmm) outliers start: 5 outliers final: 0 residues processed: 168 average time/residue: 0.0862 time to fit residues: 23.9682 Evaluate side-chains 129 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 61 ASN B 46 ASN B 61 ASN B 226 GLN B 427 HIS C 46 ASN C 61 ASN C 226 GLN C 427 HIS D 46 ASN D 61 ASN D 226 GLN E 46 ASN E 61 ASN E 266 GLN E 427 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.100966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.079977 restraints weight = 31343.330| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.83 r_work: 0.3122 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14955 Z= 0.131 Angle : 0.575 8.897 20195 Z= 0.291 Chirality : 0.041 0.132 2245 Planarity : 0.004 0.037 2510 Dihedral : 6.987 57.042 2295 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.51 % Allowed : 7.07 % Favored : 92.42 % 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: -0.64 (0.20), residues: 1710 helix: -0.09 (0.21), residues: 580 sheet: -0.39 (0.27), residues: 390 loop : -0.53 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 252 TYR 0.019 0.001 TYR B 301 PHE 0.011 0.001 PHE E 99 TRP 0.009 0.001 TRP B 170 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (14940) covalent geometry : angle 0.57293 / 0.29 (20155) SS BOND : bond 0.00055 / 0.03 ( 5) SS BOND : angle 1.46534 / 0.76 ( 10) hydrogen bonds : bond 0.04414 / 2.95 ( 645) hydrogen bonds : angle 4.79845 / 3.22 ( 2280) link_BETA1-4 : bond 0.00320 / 0.18 ( 5) link_BETA1-4 : angle 1.25053 / 0.73 ( 15) link_NAG-ASN : bond 0.00077 / 0.04 ( 5) link_NAG-ASN : angle 0.66712 / 0.40 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.631 Fit side-chains REVERT: A 89 MET cc_start: 0.7519 (pmm) cc_final: 0.7304 (pmm) REVERT: B 56 MET cc_start: 0.8973 (mmt) cc_final: 0.8517 (mmt) REVERT: B 89 MET cc_start: 0.7428 (pmm) cc_final: 0.7165 (pmm) REVERT: C 121 PHE cc_start: 0.8659 (m-80) cc_final: 0.8317 (m-80) REVERT: C 226 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8818 (tt0) outliers start: 8 outliers final: 7 residues processed: 152 average time/residue: 0.0810 time to fit residues: 20.5820 Evaluate side-chains 142 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 226 GLN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 296 SER Chi-restraints excluded: chain E residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 153 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 159 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS B 266 GLN C 423 HIS D 266 GLN E 423 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.100278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.079046 restraints weight = 31723.978| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.86 r_work: 0.3097 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14955 Z= 0.122 Angle : 0.533 8.268 20195 Z= 0.266 Chirality : 0.041 0.147 2245 Planarity : 0.003 0.032 2510 Dihedral : 6.437 55.836 2295 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.13 % Allowed : 10.38 % Favored : 89.49 % 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: -0.32 (0.20), residues: 1710 helix: 0.45 (0.22), residues: 580 sheet: -0.31 (0.26), residues: 390 loop : -0.55 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 271 TYR 0.020 0.002 TYR B 301 PHE 0.014 0.001 PHE D 121 TRP 0.008 0.001 TRP A 170 HIS 0.001 0.000 HIS A 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (14940) covalent geometry : angle 0.53137 / 0.27 (20155) SS BOND : bond 0.00066 / 0.03 ( 5) SS BOND : angle 1.26771 / 0.65 ( 10) hydrogen bonds : bond 0.03908 / 2.62 ( 645) hydrogen bonds : angle 4.29525 / 2.89 ( 2280) link_BETA1-4 : bond 0.00190 / 0.10 ( 5) link_BETA1-4 : angle 1.22310 / 0.74 ( 15) link_NAG-ASN : bond 0.00020 / 0.01 ( 5) link_NAG-ASN : angle 0.62260 / 0.38 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 132 time to evaluate : 0.567 Fit side-chains REVERT: A 89 MET cc_start: 0.7540 (pmm) cc_final: 0.7277 (pmm) REVERT: B 56 MET cc_start: 0.8957 (mmt) cc_final: 0.8542 (mmt) REVERT: B 89 MET cc_start: 0.7561 (pmm) cc_final: 0.7272 (pmm) REVERT: C 97 ASP cc_start: 0.8869 (p0) cc_final: 0.8593 (p0) REVERT: C 121 PHE cc_start: 0.8627 (m-80) cc_final: 0.8341 (m-80) REVERT: E 56 MET cc_start: 0.8855 (mmt) cc_final: 0.8644 (mmt) outliers start: 2 outliers final: 1 residues processed: 133 average time/residue: 0.0857 time to fit residues: 18.8716 Evaluate side-chains 126 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 50 optimal weight: 0.5980 chunk 68 optimal weight: 0.0020 chunk 24 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 84 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS B 423 HIS C 423 HIS C 427 HIS D 423 HIS D 427 HIS E 423 HIS E 427 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.100153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.079087 restraints weight = 31091.092| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.81 r_work: 0.3106 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14955 Z= 0.106 Angle : 0.506 8.418 20195 Z= 0.252 Chirality : 0.040 0.131 2245 Planarity : 0.003 0.030 2510 Dihedral : 5.917 53.466 2295 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.83 % Allowed : 10.70 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.20), residues: 1710 helix: 0.73 (0.22), residues: 575 sheet: -0.37 (0.26), residues: 395 loop : -0.60 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 271 TYR 0.020 0.001 TYR E 301 PHE 0.012 0.001 PHE D 121 TRP 0.007 0.001 TRP A 170 HIS 0.001 0.000 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (14940) covalent geometry : angle 0.50511 / 0.25 (20155) SS BOND : bond 0.00099 / 0.05 ( 5) SS BOND : angle 0.97208 / 0.50 ( 10) hydrogen bonds : bond 0.03537 / 2.39 ( 645) hydrogen bonds : angle 3.96699 / 2.67 ( 2280) link_BETA1-4 : bond 0.00269 / 0.15 ( 5) link_BETA1-4 : angle 1.20201 / 0.72 ( 15) link_NAG-ASN : bond 0.00029 / 0.02 ( 5) link_NAG-ASN : angle 0.55109 / 0.33 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.463 Fit side-chains REVERT: A 89 MET cc_start: 0.7559 (pmm) cc_final: 0.7265 (pmm) REVERT: A 427 HIS cc_start: 0.7244 (m90) cc_final: 0.7025 (m90) REVERT: B 56 MET cc_start: 0.8952 (mmt) cc_final: 0.8535 (mmt) REVERT: C 121 PHE cc_start: 0.8579 (m-80) cc_final: 0.8239 (m-80) outliers start: 13 outliers final: 7 residues processed: 148 average time/residue: 0.0813 time to fit residues: 20.1523 Evaluate side-chains 130 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain E residue 55 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 94 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 ASN A 423 HIS B 203 ASN B 423 HIS C 203 ASN C 423 HIS D 203 ASN D 423 HIS E 203 ASN E 266 GLN E 423 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.096190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.074561 restraints weight = 31734.274| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.91 r_work: 0.3002 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14955 Z= 0.177 Angle : 0.566 8.939 20195 Z= 0.280 Chirality : 0.042 0.125 2245 Planarity : 0.003 0.030 2510 Dihedral : 5.908 52.150 2295 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.02 % Allowed : 11.34 % Favored : 87.64 % 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: -0.24 (0.20), residues: 1710 helix: 0.82 (0.22), residues: 575 sheet: -0.44 (0.26), residues: 395 loop : -0.68 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 29 TYR 0.022 0.002 TYR D 301 PHE 0.016 0.001 PHE D 99 TRP 0.009 0.001 TRP D 170 HIS 0.001 0.000 HIS C 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (14940) covalent geometry : angle 0.56412 / 0.28 (20155) SS BOND : bond 0.00208 / 0.11 ( 5) SS BOND : angle 1.24382 / 0.64 ( 10) hydrogen bonds : bond 0.03923 / 2.66 ( 645) hydrogen bonds : angle 4.06785 / 2.75 ( 2280) link_BETA1-4 : bond 0.00087 / 0.05 ( 5) link_BETA1-4 : angle 1.24699 / 0.76 ( 15) link_NAG-ASN : bond 0.00203 / 0.11 ( 5) link_NAG-ASN : angle 0.99832 / 0.57 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.394 Fit side-chains REVERT: B 56 MET cc_start: 0.8890 (mmt) cc_final: 0.8567 (mmt) REVERT: C 56 MET cc_start: 0.9101 (mmt) cc_final: 0.8630 (mmt) REVERT: C 121 PHE cc_start: 0.8578 (m-80) cc_final: 0.8253 (m-80) REVERT: D 246 MET cc_start: 0.7800 (ptm) cc_final: 0.7496 (ptt) outliers start: 16 outliers final: 15 residues processed: 127 average time/residue: 0.0877 time to fit residues: 18.4029 Evaluate side-chains 124 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 296 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 36 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 156 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS C 423 HIS D 423 HIS E 423 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.076853 restraints weight = 31693.263| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 3.85 r_work: 0.3057 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14955 Z= 0.103 Angle : 0.506 7.569 20195 Z= 0.251 Chirality : 0.040 0.140 2245 Planarity : 0.003 0.030 2510 Dihedral : 5.508 46.263 2295 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.15 % Allowed : 11.91 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.20), residues: 1710 helix: 1.01 (0.22), residues: 570 sheet: -0.39 (0.26), residues: 395 loop : -0.65 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 252 TYR 0.018 0.001 TYR E 301 PHE 0.013 0.001 PHE D 121 TRP 0.006 0.001 TRP D 170 HIS 0.002 0.000 HIS B 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (14940) covalent geometry : angle 0.50493 / 0.25 (20155) SS BOND : bond 0.00072 / 0.04 ( 5) SS BOND : angle 0.70392 / 0.36 ( 10) hydrogen bonds : bond 0.03492 / 2.36 ( 645) hydrogen bonds : angle 3.80877 / 2.56 ( 2280) link_BETA1-4 : bond 0.00254 / 0.14 ( 5) link_BETA1-4 : angle 1.16376 / 0.69 ( 15) link_NAG-ASN : bond 0.00061 / 0.03 ( 5) link_NAG-ASN : angle 0.49246 / 0.28 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.411 Fit side-chains REVERT: A 427 HIS cc_start: 0.7322 (m90) cc_final: 0.7104 (m90) REVERT: B 56 MET cc_start: 0.8943 (mmt) cc_final: 0.8548 (mmt) REVERT: C 56 MET cc_start: 0.9148 (mmt) cc_final: 0.8664 (mmt) REVERT: C 97 ASP cc_start: 0.8979 (p0) cc_final: 0.8677 (p0) REVERT: C 121 PHE cc_start: 0.8573 (m-80) cc_final: 0.8282 (m-80) REVERT: C 140 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8622 (mtm) REVERT: C 226 GLN cc_start: 0.9161 (tt0) cc_final: 0.8948 (tt0) REVERT: D 103 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: D 246 MET cc_start: 0.7603 (ptm) cc_final: 0.7314 (ptt) REVERT: E 140 MET cc_start: 0.8240 (mtm) cc_final: 0.7922 (mtm) outliers start: 18 outliers final: 9 residues processed: 141 average time/residue: 0.0859 time to fit residues: 19.9206 Evaluate side-chains 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 37 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 137 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 128 optimal weight: 0.2980 chunk 131 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS B 423 HIS C 423 HIS D 423 HIS E 423 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.096093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.074565 restraints weight = 31676.646| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.87 r_work: 0.2995 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14955 Z= 0.164 Angle : 0.550 8.190 20195 Z= 0.272 Chirality : 0.042 0.132 2245 Planarity : 0.003 0.030 2510 Dihedral : 5.582 41.138 2295 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.46 % Allowed : 12.61 % Favored : 85.92 % 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: -0.19 (0.20), residues: 1710 helix: 0.93 (0.22), residues: 575 sheet: -0.44 (0.26), residues: 395 loop : -0.69 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 29 TYR 0.021 0.002 TYR D 301 PHE 0.015 0.001 PHE D 99 TRP 0.006 0.001 TRP B 170 HIS 0.001 0.000 HIS A 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (14940) covalent geometry : angle 0.54846 / 0.27 (20155) SS BOND : bond 0.00211 / 0.11 ( 5) SS BOND : angle 1.08241 / 0.56 ( 10) hydrogen bonds : bond 0.03766 / 2.55 ( 645) hydrogen bonds : angle 3.92803 / 2.65 ( 2280) link_BETA1-4 : bond 0.00179 / 0.10 ( 5) link_BETA1-4 : angle 1.31908 / 0.81 ( 15) link_NAG-ASN : bond 0.00213 / 0.11 ( 5) link_NAG-ASN : angle 0.97346 / 0.55 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.373 Fit side-chains REVERT: A 427 HIS cc_start: 0.7347 (m90) cc_final: 0.7134 (m90) REVERT: B 56 MET cc_start: 0.8888 (mmt) cc_final: 0.8536 (mmt) REVERT: B 163 MET cc_start: 0.8292 (mmm) cc_final: 0.7961 (mmm) REVERT: C 56 MET cc_start: 0.9089 (mmt) cc_final: 0.8649 (mmt) REVERT: C 121 PHE cc_start: 0.8547 (m-80) cc_final: 0.8262 (m-80) REVERT: C 140 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8878 (mtt) REVERT: C 226 GLN cc_start: 0.9145 (tt0) cc_final: 0.8790 (tt0) REVERT: C 246 MET cc_start: 0.7838 (ptm) cc_final: 0.7586 (ptt) REVERT: D 103 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: D 246 MET cc_start: 0.7772 (ptm) cc_final: 0.7511 (ptt) REVERT: E 56 MET cc_start: 0.8833 (mmt) cc_final: 0.8469 (mmt) outliers start: 23 outliers final: 16 residues processed: 138 average time/residue: 0.0824 time to fit residues: 18.8068 Evaluate side-chains 129 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 255 LEU Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 296 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 86 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 160 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS B 423 HIS C 423 HIS E 423 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.097830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.076619 restraints weight = 31072.193| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.87 r_work: 0.3038 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14955 Z= 0.110 Angle : 0.524 7.607 20195 Z= 0.257 Chirality : 0.041 0.140 2245 Planarity : 0.003 0.029 2510 Dihedral : 5.332 34.038 2295 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.02 % Allowed : 13.38 % Favored : 85.61 % 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: -0.15 (0.20), residues: 1710 helix: 0.97 (0.22), residues: 575 sheet: -0.40 (0.26), residues: 395 loop : -0.69 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 252 TYR 0.019 0.001 TYR D 301 PHE 0.011 0.001 PHE D 99 TRP 0.005 0.001 TRP C 68 HIS 0.002 0.000 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (14940) covalent geometry : angle 0.52254 / 0.26 (20155) SS BOND : bond 0.00106 / 0.06 ( 5) SS BOND : angle 0.70174 / 0.36 ( 10) hydrogen bonds : bond 0.03507 / 2.38 ( 645) hydrogen bonds : angle 3.76247 / 2.53 ( 2280) link_BETA1-4 : bond 0.00255 / 0.14 ( 5) link_BETA1-4 : angle 1.19615 / 0.72 ( 15) link_NAG-ASN : bond 0.00016 / 0.01 ( 5) link_NAG-ASN : angle 0.57893 / 0.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.510 Fit side-chains REVERT: A 427 HIS cc_start: 0.7361 (m90) cc_final: 0.7137 (m90) REVERT: B 56 MET cc_start: 0.8931 (mmt) cc_final: 0.8580 (mmt) REVERT: B 163 MET cc_start: 0.8318 (mmm) cc_final: 0.7813 (mmm) REVERT: C 56 MET cc_start: 0.9130 (mmt) cc_final: 0.8708 (mmt) REVERT: C 121 PHE cc_start: 0.8543 (m-80) cc_final: 0.8340 (m-80) REVERT: C 140 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8902 (mtt) REVERT: C 226 GLN cc_start: 0.9163 (tt0) cc_final: 0.8807 (tt0) REVERT: C 246 MET cc_start: 0.7810 (ptm) cc_final: 0.7593 (ptt) REVERT: D 103 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: D 150 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7818 (mm-40) REVERT: D 246 MET cc_start: 0.7759 (ptm) cc_final: 0.7507 (ptt) REVERT: E 56 MET cc_start: 0.8874 (mmt) cc_final: 0.8468 (mmt) outliers start: 16 outliers final: 11 residues processed: 137 average time/residue: 0.0859 time to fit residues: 19.6197 Evaluate side-chains 129 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 147 MET Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 159 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS B 423 HIS C 423 HIS D 423 HIS E 423 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.095835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.074366 restraints weight = 31836.843| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.90 r_work: 0.2992 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14955 Z= 0.162 Angle : 0.553 7.767 20195 Z= 0.272 Chirality : 0.042 0.130 2245 Planarity : 0.003 0.029 2510 Dihedral : 5.463 30.875 2295 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.21 % Allowed : 13.76 % Favored : 85.03 % 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: -0.21 (0.20), residues: 1710 helix: 0.95 (0.22), residues: 575 sheet: -0.46 (0.26), residues: 395 loop : -0.73 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 29 TYR 0.021 0.001 TYR C 301 PHE 0.014 0.001 PHE D 121 TRP 0.010 0.001 TRP B 239 HIS 0.002 0.000 HIS A 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (14940) covalent geometry : angle 0.55172 / 0.27 (20155) SS BOND : bond 0.00186 / 0.10 ( 5) SS BOND : angle 0.99706 / 0.51 ( 10) hydrogen bonds : bond 0.03698 / 2.50 ( 645) hydrogen bonds : angle 3.87648 / 2.61 ( 2280) link_BETA1-4 : bond 0.00147 / 0.08 ( 5) link_BETA1-4 : angle 1.30265 / 0.79 ( 15) link_NAG-ASN : bond 0.00216 / 0.12 ( 5) link_NAG-ASN : angle 1.00156 / 0.56 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.546 Fit side-chains REVERT: A 89 MET cc_start: 0.7901 (pmm) cc_final: 0.7602 (ppp) REVERT: A 427 HIS cc_start: 0.7401 (m90) cc_final: 0.7168 (m90) REVERT: B 56 MET cc_start: 0.8862 (mmt) cc_final: 0.8542 (mmt) REVERT: B 163 MET cc_start: 0.8316 (mmm) cc_final: 0.8090 (mmm) REVERT: C 56 MET cc_start: 0.9097 (mmt) cc_final: 0.8685 (mmt) REVERT: C 121 PHE cc_start: 0.8523 (m-80) cc_final: 0.8241 (m-80) REVERT: C 140 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8934 (mtt) REVERT: C 226 GLN cc_start: 0.9134 (tt0) cc_final: 0.8732 (tt0) REVERT: C 246 MET cc_start: 0.8008 (ptm) cc_final: 0.7785 (ptt) REVERT: D 103 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8302 (tm-30) REVERT: D 246 MET cc_start: 0.7837 (ptm) cc_final: 0.7578 (ptt) outliers start: 19 outliers final: 15 residues processed: 131 average time/residue: 0.0833 time to fit residues: 18.2744 Evaluate side-chains 127 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 423 HIS Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 257 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 6.9990 chunk 164 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 152 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 423 HIS ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 HIS C 423 HIS D 423 HIS E 423 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.075792 restraints weight = 31555.148| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.89 r_work: 0.3022 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14955 Z= 0.112 Angle : 0.533 8.165 20195 Z= 0.261 Chirality : 0.041 0.139 2245 Planarity : 0.003 0.029 2510 Dihedral : 5.334 30.922 2295 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Rotamer: Outliers : 1.21 % Allowed : 13.82 % Favored : 84.97 % 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: -0.16 (0.20), residues: 1710 helix: 1.00 (0.22), residues: 575 sheet: -0.44 (0.26), residues: 395 loop : -0.70 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 422 TYR 0.019 0.001 TYR D 301 PHE 0.011 0.001 PHE D 99 TRP 0.006 0.001 TRP B 239 HIS 0.004 0.000 HIS D 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (14940) covalent geometry : angle 0.53220 / 0.26 (20155) SS BOND : bond 0.00108 / 0.06 ( 5) SS BOND : angle 0.69822 / 0.36 ( 10) hydrogen bonds : bond 0.03515 / 2.38 ( 645) hydrogen bonds : angle 3.79506 / 2.55 ( 2280) link_BETA1-4 : bond 0.00185 / 0.10 ( 5) link_BETA1-4 : angle 1.24790 / 0.75 ( 15) link_NAG-ASN : bond 0.00069 / 0.04 ( 5) link_NAG-ASN : angle 0.68191 / 0.38 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.587 Fit side-chains REVERT: A 89 MET cc_start: 0.7944 (pmm) cc_final: 0.7587 (ppp) REVERT: A 163 MET cc_start: 0.8154 (mmm) cc_final: 0.7833 (mmm) REVERT: B 56 MET cc_start: 0.8887 (mmt) cc_final: 0.8578 (mmt) REVERT: B 163 MET cc_start: 0.8325 (mmm) cc_final: 0.7978 (mmm) REVERT: C 56 MET cc_start: 0.9104 (mmt) cc_final: 0.8670 (mmt) REVERT: C 121 PHE cc_start: 0.8513 (m-80) cc_final: 0.8309 (m-80) REVERT: C 140 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8910 (mtt) REVERT: C 226 GLN cc_start: 0.9168 (tt0) cc_final: 0.8768 (tt0) REVERT: C 246 MET cc_start: 0.7996 (ptm) cc_final: 0.7778 (ptt) REVERT: D 103 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: D 150 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7903 (mm-40) REVERT: D 246 MET cc_start: 0.7776 (ptm) cc_final: 0.7538 (ptt) outliers start: 19 outliers final: 17 residues processed: 135 average time/residue: 0.0783 time to fit residues: 17.8492 Evaluate side-chains 134 residues out of total 1570 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 423 HIS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 423 HIS Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 144 ASN Chi-restraints excluded: chain D residue 147 MET Chi-restraints excluded: chain D residue 423 HIS Chi-restraints excluded: chain E residue 41 CYS Chi-restraints excluded: chain E residue 144 ASN Chi-restraints excluded: chain E residue 257 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 46 optimal weight: 5.9990 chunk 115 optimal weight: 0.3980 chunk 57 optimal weight: 5.9990 chunk 152 optimal weight: 0.3980 chunk 159 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 423 HIS A 427 HIS ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 423 HIS C 423 HIS D 423 HIS E 423 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.096454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.075133 restraints weight = 31664.878| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.86 r_work: 0.3011 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14955 Z= 0.141 Angle : 0.548 8.222 20195 Z= 0.266 Chirality : 0.041 0.135 2245 Planarity : 0.003 0.028 2510 Dihedral : 5.350 31.769 2295 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.34 % Allowed : 13.89 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.19 (0.20), residues: 1710 helix: 0.94 (0.22), residues: 580 sheet: -0.43 (0.26), residues: 395 loop : -0.72 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 422 TYR 0.020 0.001 TYR D 301 PHE 0.013 0.001 PHE D 121 TRP 0.007 0.001 TRP B 239 HIS 0.005 0.001 HIS D 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (14940) covalent geometry : angle 0.54652 / 0.27 (20155) SS BOND : bond 0.00146 / 0.08 ( 5) SS BOND : angle 0.85806 / 0.44 ( 10) hydrogen bonds : bond 0.03551 / 2.40 ( 645) hydrogen bonds : angle 3.83789 / 2.59 ( 2280) link_BETA1-4 : bond 0.00170 / 0.09 ( 5) link_BETA1-4 : angle 1.26412 / 0.77 ( 15) link_NAG-ASN : bond 0.00154 / 0.09 ( 5) link_NAG-ASN : angle 0.82746 / 0.46 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2538.29 seconds wall clock time: 44 minutes 38.65 seconds (2678.65 seconds total)