Starting phenix.real_space_refine on Fri Jul 3 07:25:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngf_49383/07_2026/9ngf_49383_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngf_49383/07_2026/9ngf_49383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ngf_49383/07_2026/9ngf_49383_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngf_49383/07_2026/9ngf_49383_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ngf_49383/07_2026/9ngf_49383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngf_49383/07_2026/9ngf_49383.map" } resolution = 3.4 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 30 5.16 5 Na 5 4.78 5 C 8210 2.51 5 N 2085 2.21 5 O 2255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 12585 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2516 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2560 Chain: "B" Number of atoms: 2516 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2560 Chain: "C" Number of atoms: 2516 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2560 Chain: "D" Number of atoms: 2516 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2560 Chain: "E" Number of atoms: 2516 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Conformer: "B" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} bond proxies already assigned to first conformer: 2560 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 0 Ad-hoc single atom residues: {' NA': 5} Chain breaks: 5 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N APHE A 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 247 " occ=0.50 residue: pdb=" N APHE B 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 247 " occ=0.50 residue: pdb=" N APHE C 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE C 247 " occ=0.50 residue: pdb=" N APHE D 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE D 247 " occ=0.50 residue: pdb=" N APHE E 247 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE E 247 " occ=0.50 Time building chain proxies: 4.31, per 1000 atoms: 0.34 Number of scatterers: 12585 At special positions: 0 Unit cell: (92.008, 91.14, 123.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 Na 5 11.00 O 2255 8.00 N 2085 7.00 C 8210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 811.8 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2920 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 20 sheets defined 38.4% alpha, 40.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 62 through 70 removed outlier: 3.650A pdb=" N TRP A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.652A pdb=" N SER A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 222 through 225 Processing helix chain 'A' and resid 227 through 251 removed outlier: 3.651A pdb=" N ASN A 251 " --> pdb=" O APHE A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 285 Processing helix chain 'A' and resid 296 through 302 removed outlier: 3.680A pdb=" N ARG A 299 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG A 301 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU A 302 " --> pdb=" O ARG A 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 296 through 302' Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'B' and resid 62 through 70 removed outlier: 3.649A pdb=" N TRP B 66 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 176 through 181 removed outlier: 3.652A pdb=" N SER B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 221 Processing helix chain 'B' and resid 222 through 225 Processing helix chain 'B' and resid 227 through 251 removed outlier: 3.650A pdb=" N ASN B 251 " --> pdb=" O APHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 285 Processing helix chain 'B' and resid 296 through 302 removed outlier: 3.680A pdb=" N ARG B 299 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG B 301 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU B 302 " --> pdb=" O ARG B 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 296 through 302' Processing helix chain 'B' and resid 303 through 317 Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.650A pdb=" N TRP C 66 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 176 through 181 removed outlier: 3.652A pdb=" N SER C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 222 through 225 Processing helix chain 'C' and resid 227 through 251 removed outlier: 3.651A pdb=" N ASN C 251 " --> pdb=" O APHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 285 Processing helix chain 'C' and resid 296 through 302 removed outlier: 3.680A pdb=" N ARG C 299 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG C 301 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU C 302 " --> pdb=" O ARG C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 302' Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'D' and resid 62 through 70 removed outlier: 3.650A pdb=" N TRP D 66 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 176 through 181 removed outlier: 3.652A pdb=" N SER D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 222 through 225 Processing helix chain 'D' and resid 227 through 251 removed outlier: 3.650A pdb=" N ASN D 251 " --> pdb=" O APHE D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 285 Processing helix chain 'D' and resid 296 through 302 removed outlier: 3.681A pdb=" N ARG D 299 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG D 301 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU D 302 " --> pdb=" O ARG D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 302' Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'E' and resid 62 through 70 removed outlier: 3.649A pdb=" N TRP E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 176 through 181 removed outlier: 3.652A pdb=" N SER E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 222 through 225 Processing helix chain 'E' and resid 227 through 251 removed outlier: 3.651A pdb=" N ASN E 251 " --> pdb=" O APHE E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 285 Processing helix chain 'E' and resid 296 through 302 removed outlier: 3.680A pdb=" N ARG E 299 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS E 300 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG E 301 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU E 302 " --> pdb=" O ARG E 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 302' Processing helix chain 'E' and resid 303 through 317 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 58 removed outlier: 4.578A pdb=" N SER A 109 " --> pdb=" O VAL A 82 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 58 removed outlier: 3.575A pdb=" N GLY A 108 " --> pdb=" O VAL A 35 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL A 14 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLN A 146 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.801A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.801A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58 removed outlier: 4.578A pdb=" N SER B 109 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.575A pdb=" N GLY B 108 " --> pdb=" O VAL B 35 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL B 14 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLN B 146 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.801A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.801A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 56 through 58 removed outlier: 4.578A pdb=" N SER C 109 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 56 through 58 removed outlier: 3.575A pdb=" N GLY C 108 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL C 14 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLN C 146 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.802A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.802A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 56 through 58 removed outlier: 4.578A pdb=" N SER D 109 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 56 through 58 removed outlier: 3.574A pdb=" N GLY D 108 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL D 14 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLN D 146 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.801A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.801A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 56 through 58 removed outlier: 4.578A pdb=" N SER E 109 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.575A pdb=" N GLY E 108 " --> pdb=" O VAL E 35 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL E 14 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N GLN E 146 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.801A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.801A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 705 hydrogen bonds defined for protein. 2015 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: 2.11 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3971 1.34 - 1.46: 2521 1.46 - 1.57: 6388 1.57 - 1.69: 0 1.69 - 1.81: 50 Bond restraints: 12930 Sorted by residual: bond pdb=" CA ASN E 186 " pdb=" CB ASN E 186 " ideal model delta sigma weight residual 1.531 1.557 -0.027 1.51e-02 4.39e+03 3.09e+00 bond pdb=" CA ASN A 186 " pdb=" CB ASN A 186 " ideal model delta sigma weight residual 1.531 1.557 -0.026 1.51e-02 4.39e+03 2.99e+00 bond pdb=" CA ASN D 186 " pdb=" CB ASN D 186 " ideal model delta sigma weight residual 1.531 1.556 -0.026 1.51e-02 4.39e+03 2.86e+00 bond pdb=" CB ASN E 186 " pdb=" CG ASN E 186 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.86e+00 bond pdb=" CB ASN C 186 " pdb=" CG ASN C 186 " ideal model delta sigma weight residual 1.516 1.550 -0.034 2.50e-02 1.60e+03 1.82e+00 ... (remaining 12925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 16994 1.64 - 3.28: 530 3.28 - 4.92: 61 4.92 - 6.56: 30 6.56 - 8.20: 15 Bond angle restraints: 17630 Sorted by residual: angle pdb=" C ASN E 60 " pdb=" N THR E 61 " pdb=" CA THR E 61 " ideal model delta sigma weight residual 122.61 129.43 -6.82 1.56e+00 4.11e-01 1.91e+01 angle pdb=" C ASN D 60 " pdb=" N THR D 61 " pdb=" CA THR D 61 " ideal model delta sigma weight residual 122.61 129.41 -6.80 1.56e+00 4.11e-01 1.90e+01 angle pdb=" C ASN B 60 " pdb=" N THR B 61 " pdb=" CA THR B 61 " ideal model delta sigma weight residual 122.61 129.41 -6.80 1.56e+00 4.11e-01 1.90e+01 angle pdb=" C ASN A 60 " pdb=" N THR A 61 " pdb=" CA THR A 61 " ideal model delta sigma weight residual 122.61 129.40 -6.79 1.56e+00 4.11e-01 1.90e+01 angle pdb=" C ASN C 60 " pdb=" N THR C 61 " pdb=" CA THR C 61 " ideal model delta sigma weight residual 122.61 129.38 -6.77 1.56e+00 4.11e-01 1.88e+01 ... (remaining 17625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.11: 6546 14.11 - 28.22: 759 28.22 - 42.33: 180 42.33 - 56.45: 50 56.45 - 70.56: 20 Dihedral angle restraints: 7555 sinusoidal: 3030 harmonic: 4525 Sorted by residual: dihedral pdb=" CA ASP D 196 " pdb=" CB ASP D 196 " pdb=" CG ASP D 196 " pdb=" OD1 ASP D 196 " ideal model delta sinusoidal sigma weight residual -30.00 -89.07 59.07 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP A 196 " pdb=" CB ASP A 196 " pdb=" CG ASP A 196 " pdb=" OD1 ASP A 196 " ideal model delta sinusoidal sigma weight residual -30.00 -89.06 59.06 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP E 196 " pdb=" CB ASP E 196 " pdb=" CG ASP E 196 " pdb=" OD1 ASP E 196 " ideal model delta sinusoidal sigma weight residual -30.00 -89.04 59.04 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 7552 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1250 0.040 - 0.079: 454 0.079 - 0.119: 173 0.119 - 0.158: 63 0.158 - 0.198: 15 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA BPHE C 247 " pdb=" N BPHE C 247 " pdb=" C BPHE C 247 " pdb=" CB BPHE C 247 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA BPHE A 247 " pdb=" N BPHE A 247 " pdb=" C BPHE A 247 " pdb=" CB BPHE A 247 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.68e-01 chirality pdb=" CA BPHE E 247 " pdb=" N BPHE E 247 " pdb=" C BPHE E 247 " pdb=" CB BPHE E 247 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 1952 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BPHE D 247 " -0.018 2.00e-02 2.50e+03 1.70e-02 5.06e+00 pdb=" CG BPHE D 247 " 0.039 2.00e-02 2.50e+03 pdb=" CD1BPHE D 247 " -0.009 2.00e-02 2.50e+03 pdb=" CD2BPHE D 247 " -0.003 2.00e-02 2.50e+03 pdb=" CE1BPHE D 247 " -0.002 2.00e-02 2.50e+03 pdb=" CE2BPHE D 247 " -0.007 2.00e-02 2.50e+03 pdb=" CZ BPHE D 247 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BPHE B 247 " 0.018 2.00e-02 2.50e+03 1.70e-02 5.05e+00 pdb=" CG BPHE B 247 " -0.039 2.00e-02 2.50e+03 pdb=" CD1BPHE B 247 " 0.009 2.00e-02 2.50e+03 pdb=" CD2BPHE B 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE1BPHE B 247 " 0.001 2.00e-02 2.50e+03 pdb=" CE2BPHE B 247 " 0.007 2.00e-02 2.50e+03 pdb=" CZ BPHE B 247 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BPHE A 247 " -0.018 2.00e-02 2.50e+03 1.69e-02 5.01e+00 pdb=" CG BPHE A 247 " 0.039 2.00e-02 2.50e+03 pdb=" CD1BPHE A 247 " -0.009 2.00e-02 2.50e+03 pdb=" CD2BPHE A 247 " -0.003 2.00e-02 2.50e+03 pdb=" CE1BPHE A 247 " -0.002 2.00e-02 2.50e+03 pdb=" CE2BPHE A 247 " -0.007 2.00e-02 2.50e+03 pdb=" CZ BPHE A 247 " -0.000 2.00e-02 2.50e+03 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3774 2.83 - 3.35: 10914 3.35 - 3.86: 20616 3.86 - 4.38: 23780 4.38 - 4.90: 41949 Nonbonded interactions: 101033 Sorted by model distance: nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.311 3.040 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.312 3.040 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.312 3.040 nonbonded pdb=" O SER D 221 " pdb=" OG SER D 221 " model vdw 2.312 3.040 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.312 3.040 ... (remaining 101028 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 11 through 246 or resid 248 through 317)) selection = (chain 'B' and (resid 11 through 246 or resid 248 through 317)) selection = (chain 'C' and (resid 11 through 246 or resid 248 through 317)) selection = (chain 'D' and (resid 11 through 246 or resid 248 through 317)) selection = (chain 'E' and (resid 11 through 246 or resid 248 through 317)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.860 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12930 Z= 0.191 Angle : 0.720 8.198 17630 Z= 0.382 Chirality : 0.052 0.198 1955 Planarity : 0.005 0.033 2250 Dihedral : 13.594 70.556 4635 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.65 (0.21), residues: 1540 helix: -0.23 (0.19), residues: 550 sheet: 1.15 (0.26), residues: 475 loop : -2.16 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 123 TYR 0.009 0.001 TYR B 270 PHE 0.017 0.002 PHE B 236 TRP 0.010 0.001 TRP E 220 HIS 0.004 0.002 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (12930) covalent geometry : angle 0.72039 / 0.38 (17630) hydrogen bonds : bond 0.18078 / 12.07 ( 615) hydrogen bonds : angle 7.14861 / 4.96 ( 2015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.494 Fit side-chains REVERT: A 128 LEU cc_start: 0.8667 (mp) cc_final: 0.8454 (mp) REVERT: B 95 PHE cc_start: 0.8170 (m-80) cc_final: 0.7709 (m-80) REVERT: B 270 TYR cc_start: 0.8287 (m-80) cc_final: 0.8005 (m-80) REVERT: D 251 ASN cc_start: 0.8044 (t0) cc_final: 0.7705 (t0) REVERT: E 223 PHE cc_start: 0.8596 (m-80) cc_final: 0.8368 (m-80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0778 time to fit residues: 27.1280 Evaluate side-chains 186 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.0170 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.6620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS A 298 GLN B 251 ASN C 177 HIS C 251 ASN ** C 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN E 177 HIS ** E 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.150436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.125261 restraints weight = 31592.905| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.08 r_work: 0.3136 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12930 Z= 0.111 Angle : 0.523 5.705 17630 Z= 0.278 Chirality : 0.046 0.158 1955 Planarity : 0.004 0.028 2250 Dihedral : 4.320 16.207 1695 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.51 % Allowed : 4.71 % Favored : 94.78 % 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: 0.06 (0.22), residues: 1540 helix: 0.83 (0.21), residues: 580 sheet: 1.28 (0.26), residues: 450 loop : -2.09 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 194 TYR 0.009 0.001 TYR D 248 PHE 0.011 0.001 PHE A 223 TRP 0.007 0.001 TRP C 43 HIS 0.003 0.001 HIS E 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (12930) covalent geometry : angle 0.52269 / 0.28 (17630) hydrogen bonds : bond 0.03998 / 2.61 ( 615) hydrogen bonds : angle 4.65545 / 3.26 ( 2015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 181 time to evaluate : 0.474 Fit side-chains REVERT: B 95 PHE cc_start: 0.7919 (m-80) cc_final: 0.7570 (m-80) REVERT: B 177 HIS cc_start: 0.7029 (p-80) cc_final: 0.6781 (p-80) REVERT: C 177 HIS cc_start: 0.6683 (p-80) cc_final: 0.6482 (p-80) REVERT: C 270 TYR cc_start: 0.8455 (m-80) cc_final: 0.8166 (m-80) REVERT: D 177 HIS cc_start: 0.6620 (p-80) cc_final: 0.6130 (p-80) REVERT: D 251 ASN cc_start: 0.8400 (t0) cc_final: 0.7948 (t0) outliers start: 7 outliers final: 6 residues processed: 182 average time/residue: 0.0892 time to fit residues: 25.7141 Evaluate side-chains 163 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 56 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 124 GLN B 298 GLN C 285 HIS ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN E 177 HIS E 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.145240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.119260 restraints weight = 29247.266| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.92 r_work: 0.3101 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12930 Z= 0.165 Angle : 0.570 6.037 17630 Z= 0.301 Chirality : 0.048 0.166 1955 Planarity : 0.004 0.032 2250 Dihedral : 4.510 17.600 1695 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.59 % Allowed : 6.59 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.23 (0.22), residues: 1540 helix: 1.22 (0.21), residues: 580 sheet: 1.03 (0.25), residues: 450 loop : -1.97 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 255 TYR 0.013 0.002 TYR D 248 PHE 0.012 0.002 PHE B 236 TRP 0.008 0.001 TRP D 161 HIS 0.005 0.001 HIS E 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (12930) covalent geometry : angle 0.57023 / 0.30 (17630) hydrogen bonds : bond 0.04551 / 2.94 ( 615) hydrogen bonds : angle 4.58218 / 3.20 ( 2015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.451 Fit side-chains REVERT: A 137 ASN cc_start: 0.7933 (t0) cc_final: 0.7691 (t0) REVERT: A 140 LEU cc_start: 0.8562 (tp) cc_final: 0.8317 (tt) REVERT: B 177 HIS cc_start: 0.7297 (p-80) cc_final: 0.7025 (p-80) REVERT: B 255 ARG cc_start: 0.7166 (mmp-170) cc_final: 0.6830 (mmm-85) REVERT: C 205 LEU cc_start: 0.8792 (tp) cc_final: 0.8548 (tp) REVERT: D 155 GLU cc_start: 0.7061 (mm-30) cc_final: 0.6806 (mm-30) REVERT: D 177 HIS cc_start: 0.6937 (p-80) cc_final: 0.6333 (p-80) REVERT: D 205 LEU cc_start: 0.8748 (tp) cc_final: 0.8527 (tp) REVERT: D 251 ASN cc_start: 0.8531 (t0) cc_final: 0.8106 (t0) REVERT: D 255 ARG cc_start: 0.7312 (mmp-170) cc_final: 0.6963 (mmm-85) REVERT: E 140 LEU cc_start: 0.8417 (tp) cc_final: 0.8195 (tt) REVERT: E 255 ARG cc_start: 0.7093 (mmp-170) cc_final: 0.6876 (mmm-85) outliers start: 22 outliers final: 21 residues processed: 188 average time/residue: 0.1157 time to fit residues: 31.1406 Evaluate side-chains 188 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 167 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 297 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 chunk 130 optimal weight: 0.0040 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 0.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 42 GLN B 251 ASN C 177 HIS C 285 HIS D 42 GLN D 285 HIS E 42 GLN E 177 HIS E 285 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.151473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.126381 restraints weight = 32465.401| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.04 r_work: 0.3160 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2992 r_free = 0.2992 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12930 Z= 0.095 Angle : 0.477 5.420 17630 Z= 0.251 Chirality : 0.045 0.141 1955 Planarity : 0.004 0.029 2250 Dihedral : 3.973 15.184 1695 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.94 % Allowed : 8.55 % Favored : 90.51 % 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: 0.52 (0.22), residues: 1540 helix: 1.51 (0.22), residues: 580 sheet: 1.07 (0.25), residues: 455 loop : -1.79 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 99 TYR 0.008 0.001 TYR D 245 PHE 0.010 0.001 PHE E 95 TRP 0.008 0.001 TRP D 43 HIS 0.002 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (12930) covalent geometry : angle 0.47667 / 0.25 (17630) hydrogen bonds : bond 0.03172 / 2.07 ( 615) hydrogen bonds : angle 4.05864 / 2.84 ( 2015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 172 time to evaluate : 0.498 Fit side-chains REVERT: A 137 ASN cc_start: 0.7865 (t0) cc_final: 0.7621 (t0) REVERT: B 84 SER cc_start: 0.8552 (m) cc_final: 0.8239 (p) REVERT: B 177 HIS cc_start: 0.7289 (p-80) cc_final: 0.7016 (p-80) REVERT: B 205 LEU cc_start: 0.8699 (tp) cc_final: 0.8439 (tp) REVERT: C 177 HIS cc_start: 0.6726 (p-80) cc_final: 0.6184 (p-80) REVERT: C 270 TYR cc_start: 0.8522 (m-80) cc_final: 0.8242 (m-80) REVERT: D 177 HIS cc_start: 0.6902 (p-80) cc_final: 0.6300 (p-80) REVERT: D 251 ASN cc_start: 0.8513 (t0) cc_final: 0.8147 (t0) outliers start: 13 outliers final: 10 residues processed: 174 average time/residue: 0.0859 time to fit residues: 23.8243 Evaluate side-chains 168 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 56 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 121 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN C 42 GLN C 285 HIS D 251 ASN ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 HIS E 251 ASN E 285 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.140158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.114261 restraints weight = 30799.046| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.04 r_work: 0.3002 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 12930 Z= 0.285 Angle : 0.697 7.406 17630 Z= 0.368 Chirality : 0.052 0.189 1955 Planarity : 0.005 0.040 2250 Dihedral : 5.022 19.950 1695 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.88 % Allowed : 9.28 % Favored : 88.84 % 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 (0.22), residues: 1540 helix: 1.48 (0.22), residues: 550 sheet: 0.67 (0.25), residues: 470 loop : -2.01 (0.25), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 255 TYR 0.026 0.002 TYR E 248 PHE 0.018 0.003 PHE E 95 TRP 0.013 0.002 TRP E 220 HIS 0.005 0.002 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00690 / 0.28 (12930) covalent geometry : angle 0.69715 / 0.37 (17630) hydrogen bonds : bond 0.05641 / 3.64 ( 615) hydrogen bonds : angle 4.80514 / 3.35 ( 2015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.353 Fit side-chains REVERT: A 137 ASN cc_start: 0.8162 (t0) cc_final: 0.7880 (t0) REVERT: A 140 LEU cc_start: 0.8621 (tp) cc_final: 0.8399 (tt) REVERT: A 255 ARG cc_start: 0.7271 (mmp-170) cc_final: 0.6980 (mmm-85) REVERT: B 255 ARG cc_start: 0.7353 (mmp-170) cc_final: 0.6940 (mmm-85) REVERT: C 177 HIS cc_start: 0.7036 (p-80) cc_final: 0.6557 (p-80) REVERT: C 251 ASN cc_start: 0.8695 (t0) cc_final: 0.8454 (t0) REVERT: D 177 HIS cc_start: 0.7152 (p-80) cc_final: 0.6278 (p-80) REVERT: D 251 ASN cc_start: 0.8647 (t0) cc_final: 0.8159 (t0) REVERT: D 255 ARG cc_start: 0.7392 (mmp-170) cc_final: 0.7046 (mmm-85) REVERT: E 255 ARG cc_start: 0.7278 (mmp-170) cc_final: 0.6969 (mmm-85) outliers start: 26 outliers final: 23 residues processed: 186 average time/residue: 0.1222 time to fit residues: 31.6731 Evaluate side-chains 186 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 54 optimal weight: 0.0570 chunk 40 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 251 ASN D 251 ASN D 285 HIS E 177 HIS E 251 ASN E 285 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.147280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.121451 restraints weight = 26453.716| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.04 r_work: 0.3139 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12930 Z= 0.106 Angle : 0.503 5.647 17630 Z= 0.265 Chirality : 0.046 0.145 1955 Planarity : 0.004 0.035 2250 Dihedral : 4.249 16.608 1695 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.38 % Allowed : 9.78 % Favored : 88.84 % 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: 0.52 (0.22), residues: 1540 helix: 1.96 (0.22), residues: 550 sheet: 0.58 (0.24), residues: 500 loop : -1.84 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 99 TYR 0.015 0.001 TYR E 248 PHE 0.011 0.001 PHE E 95 TRP 0.008 0.001 TRP C 43 HIS 0.003 0.001 HIS E 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (12930) covalent geometry : angle 0.50263 / 0.26 (17630) hydrogen bonds : bond 0.03526 / 2.29 ( 615) hydrogen bonds : angle 4.21334 / 2.96 ( 2015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 0.459 Fit side-chains REVERT: A 137 ASN cc_start: 0.7867 (t0) cc_final: 0.7570 (t0) REVERT: A 140 LEU cc_start: 0.8596 (tp) cc_final: 0.8353 (tt) REVERT: B 255 ARG cc_start: 0.7202 (mmp-170) cc_final: 0.6893 (mmm-85) REVERT: C 270 TYR cc_start: 0.8478 (m-80) cc_final: 0.8169 (m-80) REVERT: D 177 HIS cc_start: 0.7050 (p-80) cc_final: 0.6314 (p-80) REVERT: D 251 ASN cc_start: 0.8582 (t0) cc_final: 0.8190 (t0) REVERT: D 255 ARG cc_start: 0.7327 (mmp-170) cc_final: 0.6966 (mmm-85) REVERT: E 255 ARG cc_start: 0.7106 (mmp-170) cc_final: 0.6871 (mmm-85) outliers start: 19 outliers final: 16 residues processed: 173 average time/residue: 0.1138 time to fit residues: 28.0206 Evaluate side-chains 180 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 219 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 45 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 6 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 HIS ** D 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 HIS E 251 ASN E 285 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.143807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117306 restraints weight = 31465.479| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.14 r_work: 0.3078 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12930 Z= 0.160 Angle : 0.557 6.106 17630 Z= 0.292 Chirality : 0.048 0.162 1955 Planarity : 0.004 0.037 2250 Dihedral : 4.481 17.702 1695 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 1.67 % Allowed : 10.58 % Favored : 87.75 % 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: 0.42 (0.22), residues: 1540 helix: 1.91 (0.22), residues: 550 sheet: 0.52 (0.24), residues: 495 loop : -1.90 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 163 TYR 0.017 0.001 TYR E 248 PHE 0.016 0.002 PHE E 95 TRP 0.007 0.001 TRP E 206 HIS 0.004 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (12930) covalent geometry : angle 0.55695 / 0.29 (17630) hydrogen bonds : bond 0.04277 / 2.76 ( 615) hydrogen bonds : angle 4.39131 / 3.07 ( 2015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.454 Fit side-chains REVERT: A 137 ASN cc_start: 0.8078 (t0) cc_final: 0.7792 (t0) REVERT: A 140 LEU cc_start: 0.8642 (tp) cc_final: 0.8421 (tt) REVERT: B 255 ARG cc_start: 0.7335 (mmp-170) cc_final: 0.7014 (mmm-85) REVERT: D 177 HIS cc_start: 0.7175 (p-80) cc_final: 0.6262 (p-80) REVERT: D 251 ASN cc_start: 0.8626 (t0) cc_final: 0.8262 (t0) REVERT: D 255 ARG cc_start: 0.7463 (mmp-170) cc_final: 0.7091 (mmm-85) REVERT: E 255 ARG cc_start: 0.7231 (mmp-170) cc_final: 0.6928 (mmm-85) outliers start: 23 outliers final: 21 residues processed: 176 average time/residue: 0.1101 time to fit residues: 27.5984 Evaluate side-chains 176 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 155 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 113 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 HIS E 177 HIS E 251 ASN E 285 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.142890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117515 restraints weight = 24664.213| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.10 r_work: 0.3067 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12930 Z= 0.175 Angle : 0.578 6.140 17630 Z= 0.304 Chirality : 0.048 0.163 1955 Planarity : 0.004 0.037 2250 Dihedral : 4.615 17.819 1695 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.67 % Allowed : 10.94 % Favored : 87.39 % 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: 0.30 (0.22), residues: 1540 helix: 1.85 (0.22), residues: 550 sheet: 0.31 (0.24), residues: 500 loop : -1.87 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 255 TYR 0.016 0.002 TYR E 248 PHE 0.016 0.002 PHE E 95 TRP 0.008 0.001 TRP E 206 HIS 0.004 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 (12930) covalent geometry : angle 0.57810 / 0.30 (17630) hydrogen bonds : bond 0.04477 / 2.89 ( 615) hydrogen bonds : angle 4.44840 / 3.11 ( 2015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 0.344 Fit side-chains REVERT: A 137 ASN cc_start: 0.8007 (t0) cc_final: 0.7704 (t0) REVERT: A 140 LEU cc_start: 0.8602 (tp) cc_final: 0.8373 (tt) REVERT: B 255 ARG cc_start: 0.7329 (mmp-170) cc_final: 0.7026 (mmm-85) REVERT: D 177 HIS cc_start: 0.7212 (p-80) cc_final: 0.6440 (p-80) REVERT: D 251 ASN cc_start: 0.8652 (t0) cc_final: 0.8263 (t0) REVERT: D 255 ARG cc_start: 0.7415 (mmp-170) cc_final: 0.6943 (mmm-85) REVERT: E 255 ARG cc_start: 0.7260 (mmp-170) cc_final: 0.6913 (mmm-85) outliers start: 23 outliers final: 22 residues processed: 174 average time/residue: 0.1084 time to fit residues: 26.7020 Evaluate side-chains 174 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 101 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 134 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 HIS E 177 HIS E 251 ASN E 285 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.144448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.117291 restraints weight = 28742.502| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.38 r_work: 0.3033 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12930 Z= 0.148 Angle : 0.546 5.949 17630 Z= 0.287 Chirality : 0.047 0.155 1955 Planarity : 0.004 0.036 2250 Dihedral : 4.478 17.172 1695 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.74 % Allowed : 10.94 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.43 (0.22), residues: 1540 helix: 1.94 (0.22), residues: 550 sheet: 0.62 (0.25), residues: 470 loop : -1.93 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 163 TYR 0.015 0.001 TYR E 248 PHE 0.015 0.002 PHE E 95 TRP 0.006 0.001 TRP C 161 HIS 0.004 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (12930) covalent geometry : angle 0.54600 / 0.29 (17630) hydrogen bonds : bond 0.04111 / 2.66 ( 615) hydrogen bonds : angle 4.33044 / 3.04 ( 2015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.402 Fit side-chains REVERT: A 137 ASN cc_start: 0.7879 (t0) cc_final: 0.7573 (t0) REVERT: A 140 LEU cc_start: 0.8605 (tp) cc_final: 0.8381 (tt) REVERT: B 255 ARG cc_start: 0.7316 (mmp-170) cc_final: 0.6996 (mmm-85) REVERT: D 177 HIS cc_start: 0.7219 (p-80) cc_final: 0.6427 (p-80) REVERT: D 251 ASN cc_start: 0.8547 (t0) cc_final: 0.8157 (t0) REVERT: D 255 ARG cc_start: 0.7379 (mmp-170) cc_final: 0.7021 (mmm-85) REVERT: E 255 ARG cc_start: 0.7150 (mmp-170) cc_final: 0.6870 (mmm-85) outliers start: 24 outliers final: 24 residues processed: 171 average time/residue: 0.1128 time to fit residues: 27.2970 Evaluate side-chains 176 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 219 SER Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 8.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 135 optimal weight: 0.0040 chunk 61 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 177 HIS E 177 HIS E 251 ASN E 285 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.148015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.120008 restraints weight = 32819.072| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.34 r_work: 0.3100 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12930 Z= 0.103 Angle : 0.499 8.223 17630 Z= 0.261 Chirality : 0.046 0.143 1955 Planarity : 0.004 0.034 2250 Dihedral : 4.153 15.811 1695 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.45 % Allowed : 11.45 % Favored : 87.10 % 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: 0.58 (0.22), residues: 1540 helix: 2.06 (0.22), residues: 550 sheet: 0.50 (0.24), residues: 500 loop : -1.74 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 163 TYR 0.012 0.001 TYR E 248 PHE 0.012 0.001 PHE E 95 TRP 0.008 0.001 TRP C 43 HIS 0.003 0.001 HIS C 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (12930) covalent geometry : angle 0.49872 / 0.26 (17630) hydrogen bonds : bond 0.03359 / 2.18 ( 615) hydrogen bonds : angle 4.06111 / 2.85 ( 2015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 163 time to evaluate : 0.471 Fit side-chains REVERT: A 137 ASN cc_start: 0.7719 (t0) cc_final: 0.7408 (t0) REVERT: A 140 LEU cc_start: 0.8585 (tp) cc_final: 0.8343 (tt) REVERT: B 255 ARG cc_start: 0.7242 (mmp-170) cc_final: 0.6920 (mmm-85) REVERT: C 177 HIS cc_start: 0.6832 (p-80) cc_final: 0.6153 (p-80) REVERT: C 270 TYR cc_start: 0.8447 (m-80) cc_final: 0.8151 (m-80) REVERT: D 177 HIS cc_start: 0.7161 (p-80) cc_final: 0.6240 (p-80) REVERT: D 251 ASN cc_start: 0.8432 (t0) cc_final: 0.8083 (t0) REVERT: D 255 ARG cc_start: 0.7352 (mmp-170) cc_final: 0.6963 (mmm-85) REVERT: E 255 ARG cc_start: 0.7065 (mmp-170) cc_final: 0.6822 (mmm-85) outliers start: 20 outliers final: 19 residues processed: 177 average time/residue: 0.1131 time to fit residues: 28.3065 Evaluate side-chains 181 residues out of total 1370 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 93 MET Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 93 MET Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 256 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 118 optimal weight: 0.0060 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 177 HIS E 251 ASN E 285 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.146224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.118534 restraints weight = 30556.969| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.32 r_work: 0.3056 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12930 Z= 0.121 Angle : 0.518 8.301 17630 Z= 0.270 Chirality : 0.046 0.151 1955 Planarity : 0.004 0.035 2250 Dihedral : 4.208 16.017 1695 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.59 % Allowed : 11.38 % Favored : 87.03 % 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: 0.60 (0.22), residues: 1540 helix: 2.08 (0.22), residues: 550 sheet: 0.51 (0.24), residues: 500 loop : -1.75 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 163 TYR 0.014 0.001 TYR E 248 PHE 0.012 0.001 PHE E 223 TRP 0.006 0.001 TRP C 43 HIS 0.003 0.001 HIS E 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (12930) covalent geometry : angle 0.51752 / 0.27 (17630) hydrogen bonds : bond 0.03659 / 2.37 ( 615) hydrogen bonds : angle 4.13271 / 2.90 ( 2015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.30 seconds wall clock time: 48 minutes 16.80 seconds (2896.80 seconds total)