Starting phenix.real_space_refine on Wed Jul 30 22:29:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d63_27215/07_2025/8d63_27215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d63_27215/07_2025/8d63_27215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_2025/8d63_27215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_2025/8d63_27215.map" model { file = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_2025/8d63_27215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d63_27215/07_2025/8d63_27215.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 30 5.16 5 C 8375 2.51 5 N 2085 2.21 5 O 2290 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12785 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'LBN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.09, per 1000 atoms: 0.63 Number of scatterers: 12785 At special positions: 0 Unit cell: (92.4, 91.3, 122.1, 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 P 5 15.00 O 2290 8.00 N 2085 7.00 C 8375 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: 3.18 Conformation dependent library (CDL) restraints added in 1.8 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 15 sheets defined 34.9% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'A' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER A 179 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER A 180 " --> pdb=" O HIS A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 201 through 208 Processing helix chain 'A' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 286 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS A 300 " --> pdb=" O ILE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'B' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG B 65 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER B 179 " --> pdb=" O ASP B 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER B 180 " --> pdb=" O HIS B 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 176 through 180' Processing helix chain 'B' and resid 201 through 208 Processing helix chain 'B' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP B 220 " --> pdb=" O ILE B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 286 Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS B 300 " --> pdb=" O ILE B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 317 Processing helix chain 'C' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG C 65 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER C 179 " --> pdb=" O ASP C 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 176 through 180' Processing helix chain 'C' and resid 201 through 208 Processing helix chain 'C' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU C 212 " --> pdb=" O PHE C 208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 286 Processing helix chain 'C' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS C 300 " --> pdb=" O ILE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 317 Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.942A pdb=" N ARG D 65 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER D 179 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER D 180 " --> pdb=" O HIS D 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 176 through 180' Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 286 Processing helix chain 'D' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS D 300 " --> pdb=" O ILE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'E' and resid 61 through 69 removed outlier: 3.943A pdb=" N ARG E 65 " --> pdb=" O THR E 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 180 removed outlier: 3.697A pdb=" N SER E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N SER E 180 " --> pdb=" O HIS E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 176 through 180' Processing helix chain 'E' and resid 201 through 208 Processing helix chain 'E' and resid 208 through 220 removed outlier: 3.730A pdb=" N LEU E 212 " --> pdb=" O PHE E 208 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 252 removed outlier: 3.723A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 286 Processing helix chain 'E' and resid 296 through 300 removed outlier: 3.563A pdb=" N CYS E 300 " --> pdb=" O ILE E 297 " (cutoff:3.500A) 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: 6.381A pdb=" N THR A 32 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY A 25 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR A 44 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP A 13 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL A 12 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP A 144 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL A 14 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N GLN A 146 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N TYR A 148 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 18 " --> pdb=" O TYR A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR B 32 " --> pdb=" O GLY B 25 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY B 25 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR B 44 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASP B 13 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL B 12 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP B 144 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 14 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN B 146 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR B 148 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 18 " --> pdb=" O TYR B 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR C 32 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N GLY C 25 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 44 " --> pdb=" O ASP C 13 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASP C 13 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL C 12 " --> pdb=" O PHE C 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP C 144 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL C 14 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN C 146 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR C 148 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE C 18 " --> pdb=" O TYR C 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR D 32 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY D 25 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR D 44 " --> pdb=" O ASP D 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP D 13 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL D 12 " --> pdb=" O PHE D 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP D 144 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL D 14 " --> pdb=" O ASP D 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN D 146 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N TYR D 148 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE D 18 " --> pdb=" O TYR D 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.381A pdb=" N THR E 32 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLY E 25 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR E 44 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP E 13 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N VAL E 12 " --> pdb=" O PHE E 142 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP E 144 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL E 14 " --> pdb=" O ASP E 144 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N GLN E 146 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR E 148 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE E 18 " --> pdb=" O TYR E 148 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.731A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1845 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: 4.13 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2015 1.31 - 1.43: 3755 1.43 - 1.56: 7223 1.56 - 1.68: 77 1.68 - 1.81: 50 Bond restraints: 13120 Sorted by residual: bond pdb=" C34 LBN C 401 " pdb=" O7 LBN C 401 " ideal model delta sigma weight residual 1.331 1.427 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C34 LBN B 401 " pdb=" O7 LBN B 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C34 LBN E 401 " pdb=" O7 LBN E 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C34 LBN D 401 " pdb=" O7 LBN D 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C34 LBN A 401 " pdb=" O7 LBN A 401 " ideal model delta sigma weight residual 1.331 1.426 -0.095 2.00e-02 2.50e+03 2.25e+01 ... (remaining 13115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 17537 3.20 - 6.40: 228 6.40 - 9.60: 55 9.60 - 12.80: 5 12.80 - 15.99: 5 Bond angle restraints: 17830 Sorted by residual: angle pdb=" N ASN C 60 " pdb=" CA ASN C 60 " pdb=" C ASN C 60 " ideal model delta sigma weight residual 111.07 119.92 -8.85 1.07e+00 8.73e-01 6.84e+01 angle pdb=" N ASN E 60 " pdb=" CA ASN E 60 " pdb=" C ASN E 60 " ideal model delta sigma weight residual 111.07 119.92 -8.85 1.07e+00 8.73e-01 6.84e+01 angle pdb=" N ASN A 60 " pdb=" CA ASN A 60 " pdb=" C ASN A 60 " ideal model delta sigma weight residual 111.07 119.91 -8.84 1.07e+00 8.73e-01 6.83e+01 angle pdb=" N ASN B 60 " pdb=" CA ASN B 60 " pdb=" C ASN B 60 " ideal model delta sigma weight residual 111.07 119.90 -8.83 1.07e+00 8.73e-01 6.80e+01 angle pdb=" N ASN D 60 " pdb=" CA ASN D 60 " pdb=" C ASN D 60 " ideal model delta sigma weight residual 111.07 119.87 -8.80 1.07e+00 8.73e-01 6.77e+01 ... (remaining 17825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.58: 7170 21.58 - 43.15: 435 43.15 - 64.73: 100 64.73 - 86.31: 25 86.31 - 107.88: 20 Dihedral angle restraints: 7750 sinusoidal: 3245 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU D 118 " pdb=" C LEU D 118 " pdb=" N PHE D 119 " pdb=" CA PHE D 119 " ideal model delta harmonic sigma weight residual -180.00 -156.48 -23.52 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA LEU A 118 " pdb=" C LEU A 118 " pdb=" N PHE A 119 " pdb=" CA PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 7747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1518 0.064 - 0.129: 353 0.129 - 0.193: 53 0.193 - 0.257: 21 0.257 - 0.322: 10 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA GLU C 59 " pdb=" N GLU C 59 " pdb=" C GLU C 59 " pdb=" CB GLU C 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLU D 59 " pdb=" N GLU D 59 " pdb=" C GLU D 59 " pdb=" CB GLU D 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CA GLU A 59 " pdb=" N GLU A 59 " pdb=" C GLU A 59 " pdb=" CB GLU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1952 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 50 " 0.033 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO D 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 51 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 50 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO A 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 51 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 50 " 0.033 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO B 51 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 51 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 51 " 0.028 5.00e-02 4.00e+02 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3431 2.81 - 3.33: 10726 3.33 - 3.86: 19914 3.86 - 4.38: 23566 4.38 - 4.90: 42808 Nonbonded interactions: 100445 Sorted by model distance: nonbonded pdb=" O TYR B 248 " pdb=" CD1 ILE B 252 " model vdw 2.290 3.460 nonbonded pdb=" O TYR D 248 " pdb=" CD1 ILE D 252 " model vdw 2.290 3.460 nonbonded pdb=" O TYR E 248 " pdb=" CD1 ILE E 252 " model vdw 2.291 3.460 nonbonded pdb=" O TYR C 248 " pdb=" CD1 ILE C 252 " model vdw 2.291 3.460 nonbonded pdb=" O TYR A 248 " pdb=" CD1 ILE A 252 " model vdw 2.291 3.460 ... (remaining 100440 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 32.630 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 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 : 0.009 0.096 13120 Z= 0.423 Angle : 0.987 15.995 17830 Z= 0.540 Chirality : 0.062 0.322 1955 Planarity : 0.005 0.051 2250 Dihedral : 16.369 107.881 4840 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.69 % Rotamer: Outliers : 0.36 % Allowed : 1.45 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.21), residues: 1525 helix: -0.01 (0.21), residues: 530 sheet: 0.04 (0.25), residues: 490 loop : -1.99 (0.23), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 161 HIS 0.007 0.002 HIS C 177 PHE 0.024 0.003 PHE C 247 TYR 0.011 0.002 TYR A 204 ARG 0.005 0.001 ARG A 123 Details of bonding type rmsd hydrogen bonds : bond 0.15565 ( 580) hydrogen bonds : angle 6.33847 ( 1845) covalent geometry : bond 0.00889 (13120) covalent geometry : angle 0.98660 (17830) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 160 time to evaluate : 1.391 Fit side-chains REVERT: A 163 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7737 (mmt-90) REVERT: A 245 TYR cc_start: 0.8383 (t80) cc_final: 0.8072 (t80) REVERT: C 61 THR cc_start: 0.8940 (m) cc_final: 0.8676 (p) REVERT: C 206 TRP cc_start: 0.7842 (m100) cc_final: 0.7614 (m100) REVERT: D 150 GLU cc_start: 0.7606 (pt0) cc_final: 0.7236 (pt0) REVERT: E 61 THR cc_start: 0.9014 (m) cc_final: 0.8737 (p) REVERT: E 150 GLU cc_start: 0.7678 (pt0) cc_final: 0.7462 (pt0) REVERT: E 174 ARG cc_start: 0.8206 (ttm-80) cc_final: 0.7964 (ttm170) REVERT: E 177 HIS cc_start: 0.6673 (p90) cc_final: 0.6049 (p90) outliers start: 5 outliers final: 0 residues processed: 161 average time/residue: 0.3003 time to fit residues: 66.7583 Evaluate side-chains 114 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 62 GLN A 151 ASN A 251 ASN B 60 ASN B 62 GLN B 251 ASN C 60 ASN C 62 GLN D 60 ASN D 62 GLN E 60 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.147500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.098461 restraints weight = 13112.408| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.14 r_work: 0.2810 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13120 Z= 0.151 Angle : 0.532 5.772 17830 Z= 0.277 Chirality : 0.046 0.142 1955 Planarity : 0.004 0.036 2250 Dihedral : 14.223 112.287 1910 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.44 % Allowed : 4.58 % Favored : 94.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1525 helix: 1.11 (0.22), residues: 535 sheet: 0.12 (0.25), residues: 500 loop : -1.79 (0.24), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 206 HIS 0.003 0.001 HIS E 177 PHE 0.021 0.002 PHE A 247 TYR 0.011 0.001 TYR E 245 ARG 0.004 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.03698 ( 580) hydrogen bonds : angle 4.31335 ( 1845) covalent geometry : bond 0.00373 (13120) covalent geometry : angle 0.53199 (17830) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 1.393 Fit side-chains REVERT: A 163 ARG cc_start: 0.8147 (mmt-90) cc_final: 0.7707 (mmt-90) REVERT: C 61 THR cc_start: 0.8933 (m) cc_final: 0.8259 (p) REVERT: C 163 ARG cc_start: 0.7931 (mmt-90) cc_final: 0.7474 (mmt-90) REVERT: D 150 GLU cc_start: 0.7714 (pt0) cc_final: 0.7439 (pt0) REVERT: E 174 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8268 (ttm170) outliers start: 6 outliers final: 4 residues processed: 130 average time/residue: 0.3009 time to fit residues: 54.3962 Evaluate side-chains 116 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 112 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 116 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN D 251 ASN E 60 ASN E 251 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.142994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.094257 restraints weight = 13429.815| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.14 r_work: 0.2748 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 13120 Z= 0.281 Angle : 0.609 6.682 17830 Z= 0.315 Chirality : 0.049 0.164 1955 Planarity : 0.004 0.038 2250 Dihedral : 13.654 108.722 1910 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.73 % Allowed : 6.84 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.21), residues: 1525 helix: 1.37 (0.22), residues: 540 sheet: 0.01 (0.24), residues: 500 loop : -1.70 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 206 HIS 0.005 0.001 HIS B 177 PHE 0.020 0.002 PHE E 247 TYR 0.013 0.002 TYR B 245 ARG 0.004 0.000 ARG B 190 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 580) hydrogen bonds : angle 4.19237 ( 1845) covalent geometry : bond 0.00715 (13120) covalent geometry : angle 0.60908 (17830) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.492 Fit side-chains REVERT: A 163 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7717 (mmt-90) REVERT: A 245 TYR cc_start: 0.8519 (t80) cc_final: 0.8253 (t80) REVERT: D 150 GLU cc_start: 0.7798 (pt0) cc_final: 0.7549 (pt0) REVERT: D 155 GLU cc_start: 0.6831 (pt0) cc_final: 0.6581 (pt0) REVERT: E 174 ARG cc_start: 0.8567 (ttm-80) cc_final: 0.8219 (ttm170) REVERT: E 245 TYR cc_start: 0.8523 (t80) cc_final: 0.8288 (t80) outliers start: 10 outliers final: 9 residues processed: 128 average time/residue: 0.3277 time to fit residues: 57.1062 Evaluate side-chains 114 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 279 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 0.0040 chunk 136 optimal weight: 5.9990 chunk 135 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 ASN C 251 ASN E 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.146540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.098040 restraints weight = 13225.135| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.15 r_work: 0.2806 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13120 Z= 0.128 Angle : 0.479 5.190 17830 Z= 0.248 Chirality : 0.045 0.143 1955 Planarity : 0.003 0.031 2250 Dihedral : 12.371 107.810 1910 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.58 % Allowed : 7.78 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.22), residues: 1525 helix: 1.92 (0.23), residues: 535 sheet: 0.17 (0.24), residues: 500 loop : -1.59 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 43 HIS 0.002 0.001 HIS E 177 PHE 0.025 0.002 PHE D 247 TYR 0.010 0.001 TYR B 245 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 580) hydrogen bonds : angle 3.85936 ( 1845) covalent geometry : bond 0.00319 (13120) covalent geometry : angle 0.47950 (17830) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 1.356 Fit side-chains REVERT: A 163 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7678 (mmt-90) REVERT: C 163 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.7582 (mmt-90) REVERT: D 77 GLU cc_start: 0.8723 (tt0) cc_final: 0.8460 (tt0) REVERT: D 150 GLU cc_start: 0.7757 (pt0) cc_final: 0.7547 (pt0) REVERT: E 174 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8206 (ttm170) outliers start: 8 outliers final: 7 residues processed: 136 average time/residue: 0.3298 time to fit residues: 61.2572 Evaluate side-chains 121 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 250 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 42 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 ASN C 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.144595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.096098 restraints weight = 13314.642| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.15 r_work: 0.2780 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13120 Z= 0.191 Angle : 0.520 5.287 17830 Z= 0.269 Chirality : 0.047 0.150 1955 Planarity : 0.004 0.036 2250 Dihedral : 12.151 105.888 1910 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.80 % Allowed : 9.02 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1525 helix: 1.93 (0.23), residues: 535 sheet: 0.17 (0.24), residues: 500 loop : -1.52 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 206 HIS 0.004 0.001 HIS B 177 PHE 0.027 0.002 PHE D 247 TYR 0.011 0.001 TYR B 245 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 580) hydrogen bonds : angle 3.87421 ( 1845) covalent geometry : bond 0.00488 (13120) covalent geometry : angle 0.52045 (17830) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.418 Fit side-chains REVERT: C 156 GLU cc_start: 0.7304 (pm20) cc_final: 0.6824 (mm-30) REVERT: D 150 GLU cc_start: 0.7798 (pt0) cc_final: 0.7576 (pt0) REVERT: E 174 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8205 (ttm170) outliers start: 11 outliers final: 9 residues processed: 136 average time/residue: 0.3011 time to fit residues: 56.9790 Evaluate side-chains 125 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 39 optimal weight: 5.9990 chunk 137 optimal weight: 8.9990 chunk 84 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 111 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN B 251 ASN C 251 ASN D 251 ASN E 251 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.147326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.098963 restraints weight = 13431.241| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.17 r_work: 0.2823 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13120 Z= 0.116 Angle : 0.456 5.022 17830 Z= 0.235 Chirality : 0.044 0.137 1955 Planarity : 0.003 0.030 2250 Dihedral : 11.826 104.888 1910 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.95 % Allowed : 9.02 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.22), residues: 1525 helix: 2.21 (0.23), residues: 530 sheet: 0.48 (0.24), residues: 490 loop : -1.46 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 43 HIS 0.002 0.001 HIS D 284 PHE 0.029 0.001 PHE D 247 TYR 0.010 0.001 TYR D 245 ARG 0.002 0.000 ARG E 163 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 580) hydrogen bonds : angle 3.68047 ( 1845) covalent geometry : bond 0.00288 (13120) covalent geometry : angle 0.45650 (17830) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.511 Fit side-chains REVERT: D 77 GLU cc_start: 0.8710 (tt0) cc_final: 0.8441 (tt0) REVERT: D 150 GLU cc_start: 0.7833 (pt0) cc_final: 0.7616 (pt0) REVERT: E 163 ARG cc_start: 0.7990 (mmt180) cc_final: 0.7506 (mmt180) REVERT: E 174 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8219 (ttm170) outliers start: 13 outliers final: 11 residues processed: 141 average time/residue: 0.2992 time to fit residues: 58.5613 Evaluate side-chains 135 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 36 optimal weight: 0.8980 chunk 148 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 117 optimal weight: 0.4980 chunk 59 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 251 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.147521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.099040 restraints weight = 13179.241| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.16 r_work: 0.2817 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13120 Z= 0.121 Angle : 0.461 5.064 17830 Z= 0.238 Chirality : 0.044 0.138 1955 Planarity : 0.003 0.031 2250 Dihedral : 11.504 104.311 1910 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.73 % Allowed : 9.75 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.22), residues: 1525 helix: 2.24 (0.23), residues: 530 sheet: 0.54 (0.24), residues: 490 loop : -1.40 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 43 HIS 0.002 0.001 HIS E 177 PHE 0.032 0.001 PHE D 247 TYR 0.009 0.001 TYR D 245 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 580) hydrogen bonds : angle 3.65029 ( 1845) covalent geometry : bond 0.00302 (13120) covalent geometry : angle 0.46086 (17830) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 1.455 Fit side-chains REVERT: A 60 ASN cc_start: 0.9117 (OUTLIER) cc_final: 0.8908 (m110) REVERT: B 279 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7534 (mm) REVERT: C 156 GLU cc_start: 0.7132 (pm20) cc_final: 0.6658 (mm-30) REVERT: D 77 GLU cc_start: 0.8700 (tt0) cc_final: 0.8427 (tt0) REVERT: D 150 GLU cc_start: 0.7875 (pt0) cc_final: 0.7672 (pt0) REVERT: E 174 ARG cc_start: 0.8502 (ttm-80) cc_final: 0.8205 (ttm170) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.3209 time to fit residues: 58.5505 Evaluate side-chains 125 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 102 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 12 optimal weight: 0.0670 chunk 65 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.147795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.099383 restraints weight = 13313.127| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.17 r_work: 0.2834 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13120 Z= 0.122 Angle : 0.461 5.049 17830 Z= 0.237 Chirality : 0.045 0.138 1955 Planarity : 0.003 0.030 2250 Dihedral : 10.736 102.958 1910 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.87 % Allowed : 9.60 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.22), residues: 1525 helix: 2.27 (0.23), residues: 530 sheet: 0.45 (0.24), residues: 500 loop : -1.26 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 43 HIS 0.002 0.001 HIS C 284 PHE 0.020 0.001 PHE D 247 TYR 0.016 0.001 TYR D 248 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.02834 ( 580) hydrogen bonds : angle 3.61541 ( 1845) covalent geometry : bond 0.00306 (13120) covalent geometry : angle 0.46123 (17830) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.489 Fit side-chains REVERT: B 279 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7549 (mm) REVERT: D 77 GLU cc_start: 0.8739 (tt0) cc_final: 0.8483 (tt0) REVERT: E 174 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8219 (ttm170) outliers start: 12 outliers final: 10 residues processed: 126 average time/residue: 0.3046 time to fit residues: 53.3728 Evaluate side-chains 123 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.143470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.094901 restraints weight = 13362.172| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.16 r_work: 0.2756 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 13120 Z= 0.254 Angle : 0.576 6.190 17830 Z= 0.299 Chirality : 0.049 0.157 1955 Planarity : 0.004 0.036 2250 Dihedral : 10.911 100.070 1910 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.58 % Allowed : 10.11 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.22), residues: 1525 helix: 1.98 (0.23), residues: 535 sheet: 0.40 (0.24), residues: 490 loop : -1.45 (0.25), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 206 HIS 0.005 0.002 HIS B 177 PHE 0.023 0.002 PHE D 247 TYR 0.019 0.002 TYR D 248 ARG 0.003 0.000 ARG E 163 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 580) hydrogen bonds : angle 3.86977 ( 1845) covalent geometry : bond 0.00649 (13120) covalent geometry : angle 0.57582 (17830) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 1.388 Fit side-chains REVERT: A 163 ARG cc_start: 0.7976 (mmt-90) cc_final: 0.7666 (mmp80) REVERT: A 245 TYR cc_start: 0.8545 (t80) cc_final: 0.8262 (t80) REVERT: C 156 GLU cc_start: 0.7327 (pm20) cc_final: 0.6867 (mm-30) REVERT: D 150 GLU cc_start: 0.7754 (pt0) cc_final: 0.7481 (mt-10) REVERT: E 174 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8203 (ttm170) outliers start: 8 outliers final: 7 residues processed: 123 average time/residue: 0.3185 time to fit residues: 53.5341 Evaluate side-chains 119 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 112 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 100 optimal weight: 0.0000 chunk 119 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.150980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.103529 restraints weight = 13089.932| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.05 r_work: 0.2893 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13120 Z= 0.099 Angle : 0.449 4.825 17830 Z= 0.233 Chirality : 0.044 0.133 1955 Planarity : 0.003 0.030 2250 Dihedral : 10.135 100.559 1910 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.65 % Allowed : 9.96 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.22), residues: 1525 helix: 2.25 (0.23), residues: 530 sheet: 0.42 (0.24), residues: 500 loop : -1.23 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 161 HIS 0.002 0.001 HIS E 177 PHE 0.017 0.001 PHE D 247 TYR 0.014 0.001 TYR A 248 ARG 0.002 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.02699 ( 580) hydrogen bonds : angle 3.60102 ( 1845) covalent geometry : bond 0.00238 (13120) covalent geometry : angle 0.44903 (17830) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 1.455 Fit side-chains REVERT: B 279 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7567 (mm) REVERT: D 150 GLU cc_start: 0.7676 (pt0) cc_final: 0.7467 (mt-10) REVERT: E 174 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8245 (ttm170) outliers start: 9 outliers final: 7 residues processed: 129 average time/residue: 0.3126 time to fit residues: 55.5993 Evaluate side-chains 122 residues out of total 1375 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 114 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain C residue 60 ASN Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain E residue 279 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 129 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.144122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.095653 restraints weight = 13353.714| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.18 r_work: 0.2780 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 13120 Z= 0.226 Angle : 0.549 5.527 17830 Z= 0.285 Chirality : 0.048 0.153 1955 Planarity : 0.004 0.034 2250 Dihedral : 10.209 97.959 1910 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.58 % Allowed : 10.25 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.22), residues: 1525 helix: 2.13 (0.23), residues: 530 sheet: 0.44 (0.24), residues: 490 loop : -1.44 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 206 HIS 0.004 0.001 HIS B 177 PHE 0.024 0.002 PHE A 247 TYR 0.018 0.001 TYR A 248 ARG 0.003 0.000 ARG E 163 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 580) hydrogen bonds : angle 3.79730 ( 1845) covalent geometry : bond 0.00579 (13120) covalent geometry : angle 0.54898 (17830) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7164.15 seconds wall clock time: 123 minutes 51.89 seconds (7431.89 seconds total)