Starting phenix.real_space_refine on Thu Feb 5 19:48:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wz7_66384/02_2026/9wz7_66384.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wz7_66384/02_2026/9wz7_66384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9wz7_66384/02_2026/9wz7_66384.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wz7_66384/02_2026/9wz7_66384.map" model { file = "/net/cci-nas-00/data/ceres_data/9wz7_66384/02_2026/9wz7_66384.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wz7_66384/02_2026/9wz7_66384.cif" } resolution = 2.66 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= 0.004 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 12432 2.51 5 N 3402 2.21 5 O 3640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19558 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "M" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 1397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1397 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 5, 'TRANS': 169} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.95, per 1000 atoms: 0.20 Number of scatterers: 19558 At special positions: 0 Unit cell: (138.55, 143.65, 111.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3640 8.00 N 3402 7.00 C 12432 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: 1.69 Conformation dependent library (CDL) restraints added in 790.7 milliseconds 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4648 Finding SS restraints... Secondary structure from input PDB file: 196 helices and 0 sheets defined 85.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 3 through 14 removed outlier: 3.841A pdb=" N ALA A 7 " --> pdb=" O ARG A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 61 through 77 Processing helix chain 'A' and resid 78 through 90 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 99 through 107 Processing helix chain 'A' and resid 109 through 118 removed outlier: 4.005A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.506A pdb=" N ALA A 149 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 166 through 175 removed outlier: 3.510A pdb=" N VAL A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 14 removed outlier: 3.992A pdb=" N ALA B 7 " --> pdb=" O ARG B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 27 removed outlier: 4.055A pdb=" N LYS B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 48 through 60 removed outlier: 3.609A pdb=" N ASP B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 77 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 99 through 107 removed outlier: 3.655A pdb=" N VAL B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 118 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 135 through 144 Processing helix chain 'B' and resid 145 through 150 Proline residue: B 148 - end of helix No H-bonds generated for 'chain 'B' and resid 145 through 150' Processing helix chain 'B' and resid 151 through 166 Processing helix chain 'B' and resid 166 through 175 removed outlier: 3.533A pdb=" N VAL B 170 " --> pdb=" O GLN B 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 14 removed outlier: 4.133A pdb=" N ALA C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 3.507A pdb=" N LYS C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 48 through 60 removed outlier: 3.611A pdb=" N ASP C 54 " --> pdb=" O LEU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 77 Processing helix chain 'C' and resid 78 through 90 removed outlier: 3.677A pdb=" N ALA C 82 " --> pdb=" O LEU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 99 through 107 Processing helix chain 'C' and resid 109 through 118 removed outlier: 4.267A pdb=" N LEU C 113 " --> pdb=" O ASN C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 132 Processing helix chain 'C' and resid 135 through 145 removed outlier: 3.520A pdb=" N SER C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 151 through 166 Processing helix chain 'C' and resid 166 through 175 removed outlier: 3.541A pdb=" N VAL C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 removed outlier: 4.053A pdb=" N ALA D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 27 removed outlier: 3.580A pdb=" N LYS D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 61 through 77 Processing helix chain 'D' and resid 78 through 90 removed outlier: 3.827A pdb=" N ALA D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 99 through 107 Processing helix chain 'D' and resid 109 through 118 removed outlier: 3.805A pdb=" N LEU D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 135 through 144 Processing helix chain 'D' and resid 145 through 150 Proline residue: D 148 - end of helix No H-bonds generated for 'chain 'D' and resid 145 through 150' Processing helix chain 'D' and resid 151 through 166 Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.549A pdb=" N VAL D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 14 removed outlier: 4.147A pdb=" N ALA E 7 " --> pdb=" O ARG E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 48 through 60 removed outlier: 3.533A pdb=" N ASP E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 77 Processing helix chain 'E' and resid 78 through 90 removed outlier: 3.845A pdb=" N ALA E 82 " --> pdb=" O LEU E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 99 through 107 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.714A pdb=" N LEU E 113 " --> pdb=" O ASN E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 135 through 145 Processing helix chain 'E' and resid 146 through 150 Processing helix chain 'E' and resid 151 through 166 Processing helix chain 'E' and resid 166 through 175 Processing helix chain 'F' and resid 3 through 14 removed outlier: 4.006A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 27 removed outlier: 3.557A pdb=" N LYS F 21 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 48 through 60 removed outlier: 3.502A pdb=" N ASP F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 77 Processing helix chain 'F' and resid 78 through 90 removed outlier: 3.531A pdb=" N ALA F 82 " --> pdb=" O LEU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 99 Processing helix chain 'F' and resid 99 through 107 Processing helix chain 'F' and resid 109 through 118 removed outlier: 4.223A pdb=" N LEU F 113 " --> pdb=" O ASN F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 132 Processing helix chain 'F' and resid 135 through 145 Processing helix chain 'F' and resid 146 through 150 Processing helix chain 'F' and resid 151 through 166 Processing helix chain 'F' and resid 166 through 175 removed outlier: 3.569A pdb=" N VAL F 170 " --> pdb=" O GLN F 166 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 14 removed outlier: 3.978A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 48 through 60 removed outlier: 3.603A pdb=" N ASP G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 77 Processing helix chain 'G' and resid 78 through 90 removed outlier: 3.542A pdb=" N ALA G 82 " --> pdb=" O LEU G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 99 Processing helix chain 'G' and resid 99 through 107 removed outlier: 3.538A pdb=" N VAL G 107 " --> pdb=" O LEU G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 4.190A pdb=" N LEU G 113 " --> pdb=" O ASN G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 135 through 144 Processing helix chain 'G' and resid 145 through 150 Proline residue: G 148 - end of helix No H-bonds generated for 'chain 'G' and resid 145 through 150' Processing helix chain 'G' and resid 151 through 166 Processing helix chain 'G' and resid 166 through 175 removed outlier: 3.508A pdb=" N VAL G 170 " --> pdb=" O GLN G 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 14 removed outlier: 4.210A pdb=" N ALA H 7 " --> pdb=" O ARG H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 27 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 48 through 60 removed outlier: 3.661A pdb=" N ASP H 54 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 77 Processing helix chain 'H' and resid 78 through 90 removed outlier: 3.521A pdb=" N ALA H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 99 through 107 removed outlier: 3.907A pdb=" N VAL H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 118 removed outlier: 4.257A pdb=" N LEU H 113 " --> pdb=" O ASN H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 132 Processing helix chain 'H' and resid 135 through 145 removed outlier: 3.526A pdb=" N SER H 145 " --> pdb=" O ARG H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 150 Processing helix chain 'H' and resid 151 through 166 Processing helix chain 'H' and resid 166 through 175 removed outlier: 3.561A pdb=" N VAL H 170 " --> pdb=" O GLN H 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 14 removed outlier: 3.908A pdb=" N ALA I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN I 14 " --> pdb=" O ASP I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 27 removed outlier: 3.543A pdb=" N LYS I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 48 through 60 Processing helix chain 'I' and resid 61 through 77 Processing helix chain 'I' and resid 78 through 90 removed outlier: 3.516A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 94 through 99 Processing helix chain 'I' and resid 99 through 107 removed outlier: 3.539A pdb=" N VAL I 107 " --> pdb=" O LEU I 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 109 through 118 removed outlier: 3.900A pdb=" N LEU I 113 " --> pdb=" O ASN I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 132 Processing helix chain 'I' and resid 135 through 145 Processing helix chain 'I' and resid 146 through 150 Processing helix chain 'I' and resid 151 through 166 Processing helix chain 'I' and resid 166 through 175 removed outlier: 3.924A pdb=" N VAL I 170 " --> pdb=" O GLN I 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 3 through 14 removed outlier: 4.232A pdb=" N ALA J 7 " --> pdb=" O ARG J 3 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN J 14 " --> pdb=" O ASP J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 27 removed outlier: 3.601A pdb=" N LYS J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 48 through 60 removed outlier: 3.636A pdb=" N ASP J 54 " --> pdb=" O LEU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'J' and resid 78 through 90 removed outlier: 3.632A pdb=" N ALA J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 99 Processing helix chain 'J' and resid 99 through 107 Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.859A pdb=" N LEU J 113 " --> pdb=" O ASN J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 132 Processing helix chain 'J' and resid 135 through 145 removed outlier: 3.529A pdb=" N SER J 145 " --> pdb=" O ARG J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 150 Processing helix chain 'J' and resid 151 through 166 Processing helix chain 'J' and resid 166 through 175 removed outlier: 3.579A pdb=" N VAL J 170 " --> pdb=" O GLN J 166 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 removed outlier: 3.904A pdb=" N ALA K 7 " --> pdb=" O ARG K 3 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN K 14 " --> pdb=" O ASP K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 16 through 27 removed outlier: 3.884A pdb=" N LYS K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 61 through 77 Processing helix chain 'K' and resid 78 through 90 removed outlier: 3.513A pdb=" N ALA K 82 " --> pdb=" O LEU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 94 through 99 Processing helix chain 'K' and resid 99 through 107 Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.869A pdb=" N LEU K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 132 Processing helix chain 'K' and resid 135 through 144 Processing helix chain 'K' and resid 145 through 150 Proline residue: K 148 - end of helix No H-bonds generated for 'chain 'K' and resid 145 through 150' Processing helix chain 'K' and resid 151 through 166 Processing helix chain 'K' and resid 166 through 175 removed outlier: 3.517A pdb=" N VAL K 170 " --> pdb=" O GLN K 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 14 removed outlier: 3.990A pdb=" N ALA L 7 " --> pdb=" O ARG L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 16 through 27 removed outlier: 3.776A pdb=" N LYS L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 48 through 60 removed outlier: 3.561A pdb=" N ASP L 54 " --> pdb=" O LEU L 50 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 Processing helix chain 'L' and resid 78 through 90 Processing helix chain 'L' and resid 94 through 99 Processing helix chain 'L' and resid 99 through 107 Processing helix chain 'L' and resid 109 through 118 removed outlier: 3.962A pdb=" N LEU L 113 " --> pdb=" O ASN L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 132 Processing helix chain 'L' and resid 135 through 144 Processing helix chain 'L' and resid 145 through 150 Proline residue: L 148 - end of helix No H-bonds generated for 'chain 'L' and resid 145 through 150' Processing helix chain 'L' and resid 151 through 166 Processing helix chain 'L' and resid 166 through 175 removed outlier: 3.573A pdb=" N VAL L 170 " --> pdb=" O GLN L 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 14 removed outlier: 3.855A pdb=" N ALA M 7 " --> pdb=" O ARG M 3 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 40 through 45 Processing helix chain 'M' and resid 48 through 60 Processing helix chain 'M' and resid 61 through 77 Processing helix chain 'M' and resid 78 through 90 Processing helix chain 'M' and resid 94 through 99 Processing helix chain 'M' and resid 99 through 107 removed outlier: 3.805A pdb=" N VAL M 107 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 118 removed outlier: 4.084A pdb=" N LEU M 113 " --> pdb=" O ASN M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 123 through 133 removed outlier: 3.721A pdb=" N GLU M 133 " --> pdb=" O ALA M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 145 removed outlier: 3.505A pdb=" N SER M 145 " --> pdb=" O ARG M 141 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 150 Processing helix chain 'M' and resid 151 through 166 Processing helix chain 'M' and resid 166 through 175 removed outlier: 3.507A pdb=" N VAL M 170 " --> pdb=" O GLN M 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 14 removed outlier: 3.863A pdb=" N ALA N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 40 through 45 Processing helix chain 'N' and resid 48 through 60 removed outlier: 3.579A pdb=" N ASP N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 Processing helix chain 'N' and resid 78 through 90 removed outlier: 3.711A pdb=" N ALA N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Processing helix chain 'N' and resid 94 through 99 Processing helix chain 'N' and resid 99 through 107 Processing helix chain 'N' and resid 109 through 118 removed outlier: 3.829A pdb=" N LEU N 113 " --> pdb=" O ASN N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 132 Processing helix chain 'N' and resid 135 through 145 Processing helix chain 'N' and resid 146 through 150 Processing helix chain 'N' and resid 151 through 166 Processing helix chain 'N' and resid 166 through 175 1230 hydrogen bonds defined for protein. 3639 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: 2.96 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6537 1.34 - 1.46: 4191 1.46 - 1.58: 9012 1.58 - 1.70: 0 1.70 - 1.81: 154 Bond restraints: 19894 Sorted by residual: bond pdb=" C THR A 147 " pdb=" N PRO A 148 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.28e-02 6.10e+03 4.23e+00 bond pdb=" CA GLN I 166 " pdb=" CB GLN I 166 " ideal model delta sigma weight residual 1.524 1.549 -0.025 1.46e-02 4.69e+03 2.86e+00 bond pdb=" CB ASP D 172 " pdb=" CG ASP D 172 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.46e-01 bond pdb=" CA ARG E 3 " pdb=" C ARG E 3 " ideal model delta sigma weight residual 1.525 1.538 -0.013 1.40e-02 5.10e+03 8.50e-01 bond pdb=" N GLY C 119 " pdb=" CA GLY C 119 " ideal model delta sigma weight residual 1.449 1.462 -0.013 1.45e-02 4.76e+03 8.25e-01 ... (remaining 19889 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 26339 1.23 - 2.46: 441 2.46 - 3.69: 63 3.69 - 4.92: 41 4.92 - 6.15: 10 Bond angle restraints: 26894 Sorted by residual: angle pdb=" N THR G 147 " pdb=" CA THR G 147 " pdb=" C THR G 147 " ideal model delta sigma weight residual 109.81 115.17 -5.36 2.21e+00 2.05e-01 5.88e+00 angle pdb=" N THR K 147 " pdb=" CA THR K 147 " pdb=" C THR K 147 " ideal model delta sigma weight residual 109.81 115.09 -5.28 2.21e+00 2.05e-01 5.71e+00 angle pdb=" CA LYS E 120 " pdb=" CB LYS E 120 " pdb=" CG LYS E 120 " ideal model delta sigma weight residual 114.10 118.64 -4.54 2.00e+00 2.50e-01 5.15e+00 angle pdb=" N ILE B 104 " pdb=" CA ILE B 104 " pdb=" C ILE B 104 " ideal model delta sigma weight residual 112.50 109.47 3.03 1.39e+00 5.18e-01 4.74e+00 angle pdb=" N GLU L 174 " pdb=" CA GLU L 174 " pdb=" CB GLU L 174 " ideal model delta sigma weight residual 110.28 113.57 -3.29 1.55e+00 4.16e-01 4.52e+00 ... (remaining 26889 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 11160 17.84 - 35.68: 800 35.68 - 53.52: 113 53.52 - 71.36: 39 71.36 - 89.21: 12 Dihedral angle restraints: 12124 sinusoidal: 4956 harmonic: 7168 Sorted by residual: dihedral pdb=" CA ASP B 51 " pdb=" CB ASP B 51 " pdb=" CG ASP B 51 " pdb=" OD1 ASP B 51 " ideal model delta sinusoidal sigma weight residual -30.00 -87.75 57.75 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CG ARG M 33 " pdb=" CD ARG M 33 " pdb=" NE ARG M 33 " pdb=" CZ ARG M 33 " ideal model delta sinusoidal sigma weight residual 180.00 135.52 44.48 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG H 33 " pdb=" CD ARG H 33 " pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " ideal model delta sinusoidal sigma weight residual 180.00 136.07 43.93 2 1.50e+01 4.44e-03 1.03e+01 ... (remaining 12121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2193 0.029 - 0.057: 593 0.057 - 0.086: 151 0.086 - 0.114: 87 0.114 - 0.143: 28 Chirality restraints: 3052 Sorted by residual: chirality pdb=" CA THR F 147 " pdb=" N THR F 147 " pdb=" C THR F 147 " pdb=" CB THR F 147 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA THR A 147 " pdb=" N THR A 147 " pdb=" C THR A 147 " pdb=" CB THR A 147 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA THR H 147 " pdb=" N THR H 147 " pdb=" C THR H 147 " pdb=" CB THR H 147 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.65e-01 ... (remaining 3049 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 147 " 0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO G 148 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO G 148 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 148 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR K 147 " -0.028 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO K 148 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO K 148 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO K 148 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 30 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO E 31 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO E 31 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 31 " 0.015 5.00e-02 4.00e+02 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 267 2.69 - 3.24: 18783 3.24 - 3.80: 29546 3.80 - 4.35: 38205 4.35 - 4.90: 65525 Nonbonded interactions: 152326 Sorted by model distance: nonbonded pdb=" OG1 THR A 123 " pdb=" OE1 GLN A 126 " model vdw 2.141 3.040 nonbonded pdb=" NE2 GLN D 79 " pdb=" O GLY G 35 " model vdw 2.218 3.120 nonbonded pdb=" NH1 ARG A 33 " pdb=" OE2 GLU M 164 " model vdw 2.267 3.120 nonbonded pdb=" NE2 GLN A 98 " pdb=" OD1 ASP M 115 " model vdw 2.291 3.120 nonbonded pdb=" OG1 THR H 123 " pdb=" OE1 GLN H 126 " model vdw 2.292 3.040 ... (remaining 152321 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.060 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 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 : 0.002 0.028 19894 Z= 0.099 Angle : 0.441 6.152 26894 Z= 0.238 Chirality : 0.034 0.143 3052 Planarity : 0.003 0.041 3444 Dihedral : 12.686 89.206 7476 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 2.10 (0.18), residues: 2422 helix: 2.00 (0.13), residues: 1848 sheet: None (None), residues: 0 loop : -0.62 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 3 TYR 0.008 0.001 TYR D 168 PHE 0.012 0.001 PHE I 59 TRP 0.004 0.000 TRP G 152 HIS 0.003 0.000 HIS M 90 Details of bonding type rmsd covalent geometry : bond 0.00209 (19894) covalent geometry : angle 0.44116 (26894) hydrogen bonds : bond 0.16602 ( 1230) hydrogen bonds : angle 4.78345 ( 3639) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.7903 (p0) cc_final: 0.7662 (p0) REVERT: A 51 ASP cc_start: 0.8478 (m-30) cc_final: 0.8113 (m-30) REVERT: A 115 ASP cc_start: 0.8976 (t70) cc_final: 0.8702 (OUTLIER) REVERT: A 172 ASP cc_start: 0.9189 (t0) cc_final: 0.8916 (t0) REVERT: B 13 GLU cc_start: 0.8231 (tt0) cc_final: 0.8004 (pt0) REVERT: B 51 ASP cc_start: 0.8465 (m-30) cc_final: 0.8224 (m-30) REVERT: B 171 GLU cc_start: 0.8029 (pp20) cc_final: 0.7794 (pp20) REVERT: B 172 ASP cc_start: 0.9162 (t0) cc_final: 0.8909 (t0) REVERT: C 171 GLU cc_start: 0.8004 (pp20) cc_final: 0.7717 (pp20) REVERT: C 172 ASP cc_start: 0.9134 (t70) cc_final: 0.8807 (OUTLIER) REVERT: D 10 ASP cc_start: 0.8123 (m-30) cc_final: 0.7877 (m-30) REVERT: D 51 ASP cc_start: 0.8373 (m-30) cc_final: 0.7979 (m-30) REVERT: E 51 ASP cc_start: 0.8650 (m-30) cc_final: 0.8199 (m-30) REVERT: E 139 LYS cc_start: 0.8911 (mttt) cc_final: 0.8597 (mttp) REVERT: E 168 TYR cc_start: 0.8344 (p90) cc_final: 0.7954 (p90) REVERT: E 172 ASP cc_start: 0.9256 (t0) cc_final: 0.9040 (t0) REVERT: F 1 MET cc_start: 0.6112 (ttp) cc_final: 0.5681 (ttm) REVERT: F 48 ASP cc_start: 0.6992 (p0) cc_final: 0.6279 (p0) REVERT: F 51 ASP cc_start: 0.8339 (m-30) cc_final: 0.7765 (m-30) REVERT: F 115 ASP cc_start: 0.8908 (t70) cc_final: 0.8697 (t0) REVERT: G 51 ASP cc_start: 0.8271 (m-30) cc_final: 0.8042 (m-30) REVERT: G 75 ASP cc_start: 0.8007 (t0) cc_final: 0.7754 (t0) REVERT: H 48 ASP cc_start: 0.8168 (p0) cc_final: 0.7955 (p0) REVERT: I 75 ASP cc_start: 0.8277 (t0) cc_final: 0.8067 (t0) REVERT: J 51 ASP cc_start: 0.8536 (m-30) cc_final: 0.8228 (m-30) REVERT: K 13 GLU cc_start: 0.8265 (tt0) cc_final: 0.7922 (pt0) REVERT: K 51 ASP cc_start: 0.8251 (m-30) cc_final: 0.7684 (m-30) REVERT: K 115 ASP cc_start: 0.8926 (t70) cc_final: 0.8708 (t0) REVERT: L 139 LYS cc_start: 0.9011 (mttp) cc_final: 0.8779 (mttp) REVERT: L 172 ASP cc_start: 0.9059 (t70) cc_final: 0.8859 (t0) REVERT: M 48 ASP cc_start: 0.7575 (p0) cc_final: 0.7325 (p0) REVERT: M 51 ASP cc_start: 0.8316 (m-30) cc_final: 0.8063 (m-30) REVERT: M 172 ASP cc_start: 0.9175 (t70) cc_final: 0.8741 (t0) REVERT: N 1 MET cc_start: 0.6787 (ttm) cc_final: 0.6581 (ttm) REVERT: N 111 GLU cc_start: 0.8485 (mp0) cc_final: 0.8245 (mp0) REVERT: N 171 GLU cc_start: 0.8078 (pp20) cc_final: 0.7834 (pp20) REVERT: N 172 ASP cc_start: 0.9093 (t70) cc_final: 0.8734 (t0) outliers start: 0 outliers final: 4 residues processed: 614 average time/residue: 0.7522 time to fit residues: 505.1661 Evaluate side-chains 498 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 496 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 172 ASP Chi-restraints excluded: chain N residue 115 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.0040 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 7.9990 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN C 86 GLN C 166 GLN D 98 GLN D 166 GLN E 84 GLN E 86 GLN F 84 GLN F 128 GLN G 128 GLN I 91 GLN K 128 GLN L 14 ASN L 128 GLN L 166 GLN M 128 GLN N 86 GLN N 166 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.080677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.064126 restraints weight = 39668.479| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 3.05 r_work: 0.2698 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 19894 Z= 0.115 Angle : 0.491 7.611 26894 Z= 0.255 Chirality : 0.035 0.147 3052 Planarity : 0.004 0.039 3444 Dihedral : 4.156 115.186 2692 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.21 % Allowed : 12.97 % Favored : 85.81 % 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: 2.19 (0.18), residues: 2422 helix: 2.02 (0.13), residues: 1876 sheet: None (None), residues: 0 loop : -0.56 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 3 TYR 0.015 0.001 TYR F 168 PHE 0.010 0.001 PHE I 59 TRP 0.004 0.000 TRP A 152 HIS 0.004 0.001 HIS M 90 Details of bonding type rmsd covalent geometry : bond 0.00272 (19894) covalent geometry : angle 0.49126 (26894) hydrogen bonds : bond 0.03347 ( 1230) hydrogen bonds : angle 3.55228 ( 3639) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 537 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 ASP cc_start: 0.7967 (p0) cc_final: 0.7493 (p0) REVERT: A 51 ASP cc_start: 0.8775 (m-30) cc_final: 0.8422 (m-30) REVERT: A 115 ASP cc_start: 0.9185 (t70) cc_final: 0.8911 (OUTLIER) REVERT: A 171 GLU cc_start: 0.8090 (pp20) cc_final: 0.7749 (pp20) REVERT: A 172 ASP cc_start: 0.9230 (t0) cc_final: 0.9025 (t0) REVERT: A 175 ARG cc_start: 0.6423 (tpm170) cc_final: 0.5929 (mmp-170) REVERT: B 51 ASP cc_start: 0.8740 (m-30) cc_final: 0.8442 (m-30) REVERT: B 171 GLU cc_start: 0.8175 (pp20) cc_final: 0.7853 (pp20) REVERT: B 172 ASP cc_start: 0.9214 (t0) cc_final: 0.8937 (t0) REVERT: C 26 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8816 (tttm) REVERT: C 172 ASP cc_start: 0.9185 (t70) cc_final: 0.8855 (t0) REVERT: D 48 ASP cc_start: 0.7893 (p0) cc_final: 0.7061 (p0) REVERT: D 51 ASP cc_start: 0.8710 (m-30) cc_final: 0.8323 (m-30) REVERT: D 138 SER cc_start: 0.9271 (m) cc_final: 0.8973 (p) REVERT: D 172 ASP cc_start: 0.9319 (t0) cc_final: 0.9006 (t0) REVERT: E 6 ASP cc_start: 0.8414 (m-30) cc_final: 0.8056 (m-30) REVERT: E 48 ASP cc_start: 0.7886 (p0) cc_final: 0.7309 (p0) REVERT: E 51 ASP cc_start: 0.8901 (m-30) cc_final: 0.8507 (m-30) REVERT: E 120 LYS cc_start: 0.6280 (mptt) cc_final: 0.5981 (mptt) REVERT: E 172 ASP cc_start: 0.9249 (t0) cc_final: 0.8940 (t0) REVERT: F 115 ASP cc_start: 0.9165 (t70) cc_final: 0.8963 (t0) REVERT: G 75 ASP cc_start: 0.8541 (t0) cc_final: 0.8288 (t0) REVERT: H 6 ASP cc_start: 0.8379 (m-30) cc_final: 0.8001 (m-30) REVERT: I 18 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8065 (tm-30) REVERT: I 26 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8168 (mptp) REVERT: I 48 ASP cc_start: 0.7817 (p0) cc_final: 0.7139 (p0) REVERT: I 51 ASP cc_start: 0.8609 (m-30) cc_final: 0.8277 (m-30) REVERT: I 133 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8827 (mm-30) REVERT: J 48 ASP cc_start: 0.7953 (p0) cc_final: 0.7191 (p0) REVERT: J 51 ASP cc_start: 0.8804 (m-30) cc_final: 0.8426 (m-30) REVERT: J 91 GLN cc_start: 0.7574 (tp40) cc_final: 0.7147 (mp10) REVERT: K 48 ASP cc_start: 0.7828 (p0) cc_final: 0.6962 (p0) REVERT: K 51 ASP cc_start: 0.8605 (m-30) cc_final: 0.8053 (m-30) REVERT: K 115 ASP cc_start: 0.9172 (t70) cc_final: 0.8970 (t0) REVERT: L 139 LYS cc_start: 0.8927 (mttp) cc_final: 0.8633 (mttm) REVERT: L 172 ASP cc_start: 0.9152 (t70) cc_final: 0.8931 (t0) REVERT: M 6 ASP cc_start: 0.8412 (m-30) cc_final: 0.7853 (m-30) REVERT: M 10 ASP cc_start: 0.8364 (m-30) cc_final: 0.8005 (m-30) REVERT: M 48 ASP cc_start: 0.7883 (p0) cc_final: 0.7528 (p0) REVERT: M 51 ASP cc_start: 0.8712 (m-30) cc_final: 0.8366 (m-30) REVERT: M 172 ASP cc_start: 0.9227 (t70) cc_final: 0.8829 (t0) REVERT: N 111 GLU cc_start: 0.8838 (mp0) cc_final: 0.8578 (mp0) REVERT: N 171 GLU cc_start: 0.8186 (pp20) cc_final: 0.7908 (pp20) REVERT: N 172 ASP cc_start: 0.9136 (t70) cc_final: 0.8741 (t0) outliers start: 25 outliers final: 7 residues processed: 546 average time/residue: 0.6959 time to fit residues: 419.1092 Evaluate side-chains 488 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 481 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain N residue 115 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 51 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 188 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 200 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN D 98 GLN D 166 GLN F 84 GLN F 166 GLN H 91 GLN I 91 GLN K 14 ASN K 84 GLN K 128 GLN L 166 GLN M 128 GLN N 166 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.077764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.061145 restraints weight = 40161.772| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.02 r_work: 0.2625 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 19894 Z= 0.186 Angle : 0.544 7.296 26894 Z= 0.281 Chirality : 0.037 0.152 3052 Planarity : 0.004 0.042 3444 Dihedral : 3.926 93.443 2690 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.46 % Allowed : 15.94 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.18), residues: 2422 helix: 2.08 (0.13), residues: 1876 sheet: None (None), residues: 0 loop : -0.67 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 33 TYR 0.008 0.001 TYR L 64 PHE 0.024 0.002 PHE M 59 TRP 0.004 0.001 TRP J 112 HIS 0.003 0.001 HIS M 90 Details of bonding type rmsd covalent geometry : bond 0.00453 (19894) covalent geometry : angle 0.54351 (26894) hydrogen bonds : bond 0.04373 ( 1230) hydrogen bonds : angle 3.42632 ( 3639) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 512 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.7738 (p0) cc_final: 0.7312 (p0) REVERT: A 51 ASP cc_start: 0.8823 (m-30) cc_final: 0.8409 (m-30) REVERT: A 80 GLU cc_start: 0.4530 (mp0) cc_final: 0.4006 (mt-10) REVERT: A 115 ASP cc_start: 0.9188 (t70) cc_final: 0.8922 (OUTLIER) REVERT: A 171 GLU cc_start: 0.8049 (pp20) cc_final: 0.7776 (pp20) REVERT: A 172 ASP cc_start: 0.9240 (t0) cc_final: 0.9022 (t0) REVERT: A 175 ARG cc_start: 0.6489 (tpm170) cc_final: 0.6197 (mmp-170) REVERT: B 51 ASP cc_start: 0.8830 (m-30) cc_final: 0.8561 (m-30) REVERT: B 80 GLU cc_start: 0.4677 (pm20) cc_final: 0.4163 (pm20) REVERT: B 171 GLU cc_start: 0.8119 (pp20) cc_final: 0.7846 (pp20) REVERT: B 172 ASP cc_start: 0.9221 (t0) cc_final: 0.8934 (t0) REVERT: B 175 ARG cc_start: 0.6293 (tpm170) cc_final: 0.6044 (mmp-170) REVERT: C 81 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7946 (mtm) REVERT: C 172 ASP cc_start: 0.9191 (t70) cc_final: 0.8864 (OUTLIER) REVERT: D 19 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8335 (mt-10) REVERT: D 48 ASP cc_start: 0.7886 (p0) cc_final: 0.7116 (p0) REVERT: D 51 ASP cc_start: 0.8731 (m-30) cc_final: 0.8409 (m-30) REVERT: D 138 SER cc_start: 0.9349 (m) cc_final: 0.9097 (p) REVERT: D 172 ASP cc_start: 0.9319 (t0) cc_final: 0.9061 (t0) REVERT: E 48 ASP cc_start: 0.7976 (p0) cc_final: 0.7398 (p0) REVERT: E 51 ASP cc_start: 0.8962 (m-30) cc_final: 0.8548 (m-30) REVERT: E 172 ASP cc_start: 0.9257 (t0) cc_final: 0.8979 (t0) REVERT: F 80 GLU cc_start: 0.4728 (mp0) cc_final: 0.4336 (mp0) REVERT: F 115 ASP cc_start: 0.9208 (t70) cc_final: 0.8988 (t0) REVERT: F 174 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8599 (mm-30) REVERT: G 75 ASP cc_start: 0.8586 (t0) cc_final: 0.8330 (t0) REVERT: G 172 ASP cc_start: 0.9032 (t0) cc_final: 0.8786 (t0) REVERT: I 18 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8131 (tm-30) REVERT: I 26 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8107 (mptp) REVERT: I 48 ASP cc_start: 0.7903 (p0) cc_final: 0.7283 (p0) REVERT: I 51 ASP cc_start: 0.8633 (m-30) cc_final: 0.8304 (m-30) REVERT: J 48 ASP cc_start: 0.7952 (p0) cc_final: 0.7216 (p0) REVERT: J 51 ASP cc_start: 0.8794 (m-30) cc_final: 0.8414 (m-30) REVERT: K 48 ASP cc_start: 0.7650 (p0) cc_final: 0.6823 (p0) REVERT: K 51 ASP cc_start: 0.8595 (m-30) cc_final: 0.8075 (m-30) REVERT: L 6 ASP cc_start: 0.8431 (m-30) cc_final: 0.8059 (m-30) REVERT: L 10 ASP cc_start: 0.8293 (m-30) cc_final: 0.8010 (m-30) REVERT: L 139 LYS cc_start: 0.8954 (mttp) cc_final: 0.8644 (mttm) REVERT: L 172 ASP cc_start: 0.9175 (t70) cc_final: 0.8940 (t0) REVERT: M 10 ASP cc_start: 0.8383 (m-30) cc_final: 0.8122 (m-30) REVERT: M 48 ASP cc_start: 0.8094 (p0) cc_final: 0.7775 (p0) REVERT: M 51 ASP cc_start: 0.8753 (m-30) cc_final: 0.8449 (m-30) REVERT: M 172 ASP cc_start: 0.9239 (t70) cc_final: 0.8854 (t0) REVERT: N 48 ASP cc_start: 0.7946 (p0) cc_final: 0.7282 (p0) REVERT: N 51 ASP cc_start: 0.8910 (m-30) cc_final: 0.8539 (m-30) REVERT: N 62 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: N 111 GLU cc_start: 0.8815 (mp0) cc_final: 0.8504 (mp0) REVERT: N 172 ASP cc_start: 0.9136 (t70) cc_final: 0.8897 (t0) outliers start: 30 outliers final: 11 residues processed: 521 average time/residue: 0.7033 time to fit residues: 403.4598 Evaluate side-chains 474 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 462 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain L residue 86 GLN Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain N residue 62 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 150 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 235 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN D 98 GLN D 166 GLN F 84 GLN F 128 GLN F 166 GLN I 91 GLN J 14 ASN K 128 GLN L 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.078924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.062343 restraints weight = 39870.576| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.03 r_work: 0.2658 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19894 Z= 0.132 Angle : 0.499 6.562 26894 Z= 0.261 Chirality : 0.035 0.139 3052 Planarity : 0.004 0.041 3444 Dihedral : 3.389 16.239 2688 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.60 % Allowed : 16.76 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.18), residues: 2422 helix: 2.23 (0.13), residues: 1862 sheet: None (None), residues: 0 loop : -0.84 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 3 TYR 0.006 0.001 TYR F 64 PHE 0.014 0.001 PHE M 59 TRP 0.004 0.000 TRP J 112 HIS 0.003 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00320 (19894) covalent geometry : angle 0.49912 (26894) hydrogen bonds : bond 0.03441 ( 1230) hydrogen bonds : angle 3.31566 ( 3639) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 503 time to evaluate : 0.816 Fit side-chains REVERT: A 48 ASP cc_start: 0.7643 (p0) cc_final: 0.7213 (p0) REVERT: A 51 ASP cc_start: 0.8809 (m-30) cc_final: 0.8362 (m-30) REVERT: A 80 GLU cc_start: 0.4612 (mp0) cc_final: 0.4144 (mp0) REVERT: A 115 ASP cc_start: 0.9195 (t70) cc_final: 0.8933 (OUTLIER) REVERT: A 171 GLU cc_start: 0.8119 (pp20) cc_final: 0.7778 (pp20) REVERT: A 172 ASP cc_start: 0.9259 (t0) cc_final: 0.9027 (t0) REVERT: B 47 MET cc_start: 0.8770 (mtm) cc_final: 0.8355 (ptp) REVERT: B 51 ASP cc_start: 0.8864 (m-30) cc_final: 0.8583 (m-30) REVERT: B 62 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: B 80 GLU cc_start: 0.4501 (pm20) cc_final: 0.3899 (pm20) REVERT: B 172 ASP cc_start: 0.9216 (t0) cc_final: 0.8958 (t0) REVERT: C 75 ASP cc_start: 0.8559 (t0) cc_final: 0.8331 (t0) REVERT: C 81 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.7912 (mtm) REVERT: C 172 ASP cc_start: 0.9193 (t70) cc_final: 0.8833 (t0) REVERT: D 48 ASP cc_start: 0.7778 (p0) cc_final: 0.6915 (p0) REVERT: D 51 ASP cc_start: 0.8735 (m-30) cc_final: 0.8295 (m-30) REVERT: D 138 SER cc_start: 0.9342 (m) cc_final: 0.9083 (p) REVERT: D 172 ASP cc_start: 0.9351 (t0) cc_final: 0.9007 (t0) REVERT: E 1 MET cc_start: 0.7032 (ttm) cc_final: 0.3044 (ptt) REVERT: E 48 ASP cc_start: 0.7873 (p0) cc_final: 0.7303 (p0) REVERT: E 51 ASP cc_start: 0.8925 (m-30) cc_final: 0.8515 (m-30) REVERT: E 172 ASP cc_start: 0.9253 (t0) cc_final: 0.8913 (t0) REVERT: F 48 ASP cc_start: 0.7961 (p0) cc_final: 0.7213 (p0) REVERT: F 51 ASP cc_start: 0.8774 (m-30) cc_final: 0.8230 (m-30) REVERT: F 115 ASP cc_start: 0.9207 (t70) cc_final: 0.8992 (t0) REVERT: F 174 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8645 (mm-30) REVERT: G 75 ASP cc_start: 0.8554 (t0) cc_final: 0.8284 (t0) REVERT: G 172 ASP cc_start: 0.9054 (t0) cc_final: 0.8805 (t0) REVERT: I 18 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8072 (tm-30) REVERT: I 26 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8059 (mptp) REVERT: I 48 ASP cc_start: 0.7932 (p0) cc_final: 0.7357 (p0) REVERT: I 51 ASP cc_start: 0.8635 (m-30) cc_final: 0.8295 (m-30) REVERT: I 81 MET cc_start: 0.8783 (mpp) cc_final: 0.8315 (mmp) REVERT: I 133 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8782 (mm-30) REVERT: J 48 ASP cc_start: 0.7940 (p0) cc_final: 0.7263 (p0) REVERT: J 51 ASP cc_start: 0.8787 (m-30) cc_final: 0.8412 (m-30) REVERT: J 128 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8939 (mm-40) REVERT: K 48 ASP cc_start: 0.7571 (p0) cc_final: 0.6763 (p0) REVERT: K 51 ASP cc_start: 0.8579 (m-30) cc_final: 0.8047 (m-30) REVERT: L 139 LYS cc_start: 0.8941 (mttp) cc_final: 0.8624 (mttm) REVERT: L 172 ASP cc_start: 0.9182 (t70) cc_final: 0.8906 (t0) REVERT: M 6 ASP cc_start: 0.8388 (m-30) cc_final: 0.8047 (m-30) REVERT: M 10 ASP cc_start: 0.8379 (m-30) cc_final: 0.8045 (m-30) REVERT: M 48 ASP cc_start: 0.8054 (p0) cc_final: 0.7492 (p0) REVERT: M 51 ASP cc_start: 0.8744 (m-30) cc_final: 0.8354 (m-30) REVERT: M 172 ASP cc_start: 0.9218 (t70) cc_final: 0.8824 (t0) REVERT: N 48 ASP cc_start: 0.7898 (p0) cc_final: 0.7216 (p0) REVERT: N 51 ASP cc_start: 0.8923 (m-30) cc_final: 0.8603 (m-30) REVERT: N 62 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: N 111 GLU cc_start: 0.8789 (mp0) cc_final: 0.8461 (mp0) REVERT: N 171 GLU cc_start: 0.8128 (pp20) cc_final: 0.7837 (pp20) REVERT: N 172 ASP cc_start: 0.9153 (t70) cc_final: 0.8720 (t0) outliers start: 33 outliers final: 14 residues processed: 518 average time/residue: 0.7533 time to fit residues: 430.7204 Evaluate side-chains 488 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 471 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain N residue 62 GLU Chi-restraints excluded: chain N residue 115 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 135 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 157 optimal weight: 0.0770 chunk 131 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 224 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN C 128 GLN C 166 GLN D 128 GLN D 166 GLN F 84 GLN G 128 GLN I 128 GLN J 14 ASN K 84 GLN K 128 GLN L 166 GLN M 128 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.063037 restraints weight = 39609.685| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.03 r_work: 0.2675 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19894 Z= 0.116 Angle : 0.497 7.758 26894 Z= 0.257 Chirality : 0.034 0.145 3052 Planarity : 0.004 0.040 3444 Dihedral : 3.278 15.168 2688 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.17 % Allowed : 18.46 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.18), residues: 2422 helix: 2.32 (0.13), residues: 1862 sheet: None (None), residues: 0 loop : -0.84 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 175 TYR 0.013 0.001 TYR F 168 PHE 0.012 0.001 PHE M 59 TRP 0.005 0.000 TRP J 112 HIS 0.002 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00279 (19894) covalent geometry : angle 0.49739 (26894) hydrogen bonds : bond 0.03059 ( 1230) hydrogen bonds : angle 3.23789 ( 3639) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 495 time to evaluate : 0.823 Fit side-chains REVERT: A 48 ASP cc_start: 0.7593 (p0) cc_final: 0.7182 (p0) REVERT: A 51 ASP cc_start: 0.8827 (m-30) cc_final: 0.8390 (m-30) REVERT: A 80 GLU cc_start: 0.4544 (mp0) cc_final: 0.4230 (mp0) REVERT: A 115 ASP cc_start: 0.9201 (t70) cc_final: 0.8939 (OUTLIER) REVERT: A 171 GLU cc_start: 0.8047 (pp20) cc_final: 0.7823 (pp20) REVERT: B 47 MET cc_start: 0.8755 (mtm) cc_final: 0.8338 (ptp) REVERT: B 51 ASP cc_start: 0.8887 (m-30) cc_final: 0.8636 (m-30) REVERT: B 80 GLU cc_start: 0.4454 (pm20) cc_final: 0.3987 (pm20) REVERT: B 172 ASP cc_start: 0.9230 (t0) cc_final: 0.8961 (t0) REVERT: C 81 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7903 (mtm) REVERT: C 172 ASP cc_start: 0.9192 (t70) cc_final: 0.8826 (t0) REVERT: D 48 ASP cc_start: 0.7619 (p0) cc_final: 0.6792 (p0) REVERT: D 51 ASP cc_start: 0.8688 (m-30) cc_final: 0.8296 (m-30) REVERT: D 138 SER cc_start: 0.9283 (m) cc_final: 0.9007 (p) REVERT: D 172 ASP cc_start: 0.9352 (t0) cc_final: 0.9028 (t0) REVERT: E 1 MET cc_start: 0.6866 (ttm) cc_final: 0.2717 (ptt) REVERT: E 48 ASP cc_start: 0.7764 (p0) cc_final: 0.7248 (p0) REVERT: E 51 ASP cc_start: 0.8902 (m-30) cc_final: 0.8502 (m-30) REVERT: E 172 ASP cc_start: 0.9248 (t0) cc_final: 0.8900 (t0) REVERT: F 48 ASP cc_start: 0.7926 (p0) cc_final: 0.7093 (p0) REVERT: F 51 ASP cc_start: 0.8763 (m-30) cc_final: 0.8099 (m-30) REVERT: F 115 ASP cc_start: 0.9199 (t70) cc_final: 0.8990 (t0) REVERT: F 171 GLU cc_start: 0.8129 (pp20) cc_final: 0.7910 (pp20) REVERT: F 174 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8623 (mm-30) REVERT: G 172 ASP cc_start: 0.9065 (t0) cc_final: 0.8777 (t0) REVERT: I 18 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8044 (tm-30) REVERT: I 26 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8115 (mptp) REVERT: I 48 ASP cc_start: 0.7835 (p0) cc_final: 0.7455 (p0) REVERT: I 51 ASP cc_start: 0.8591 (m-30) cc_final: 0.8256 (m-30) REVERT: I 81 MET cc_start: 0.8757 (mpp) cc_final: 0.8308 (mmp) REVERT: J 48 ASP cc_start: 0.7898 (p0) cc_final: 0.7245 (p0) REVERT: J 51 ASP cc_start: 0.8776 (m-30) cc_final: 0.8404 (m-30) REVERT: J 128 GLN cc_start: 0.9163 (mm-40) cc_final: 0.8950 (mm-40) REVERT: K 48 ASP cc_start: 0.7509 (p0) cc_final: 0.6725 (p0) REVERT: K 51 ASP cc_start: 0.8579 (m-30) cc_final: 0.8035 (m-30) REVERT: L 75 ASP cc_start: 0.8783 (t70) cc_final: 0.8486 (t0) REVERT: L 139 LYS cc_start: 0.8936 (mttp) cc_final: 0.8625 (mttm) REVERT: L 172 ASP cc_start: 0.9174 (t70) cc_final: 0.8883 (t0) REVERT: M 6 ASP cc_start: 0.8401 (m-30) cc_final: 0.7899 (m-30) REVERT: M 10 ASP cc_start: 0.8360 (m-30) cc_final: 0.7972 (m-30) REVERT: M 48 ASP cc_start: 0.8043 (p0) cc_final: 0.7551 (p0) REVERT: M 51 ASP cc_start: 0.8730 (m-30) cc_final: 0.8372 (m-30) REVERT: M 172 ASP cc_start: 0.9236 (t70) cc_final: 0.8833 (t0) REVERT: N 48 ASP cc_start: 0.7813 (p0) cc_final: 0.7116 (p0) REVERT: N 51 ASP cc_start: 0.8908 (m-30) cc_final: 0.8583 (m-30) REVERT: N 111 GLU cc_start: 0.8754 (mp0) cc_final: 0.8430 (mp0) REVERT: N 171 GLU cc_start: 0.8108 (pp20) cc_final: 0.7784 (pp20) REVERT: N 172 ASP cc_start: 0.9140 (t70) cc_final: 0.8706 (t0) outliers start: 24 outliers final: 13 residues processed: 504 average time/residue: 0.7119 time to fit residues: 396.8342 Evaluate side-chains 482 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 468 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 147 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 172 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 205 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 20 optimal weight: 0.0050 overall best weight: 4.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN D 166 GLN E 128 GLN F 84 GLN F 128 GLN H 14 ASN K 84 GLN K 128 GLN L 166 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.060386 restraints weight = 39863.286| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.00 r_work: 0.2621 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 19894 Z= 0.207 Angle : 0.571 8.347 26894 Z= 0.295 Chirality : 0.037 0.143 3052 Planarity : 0.004 0.040 3444 Dihedral : 3.593 18.699 2688 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.85 % Allowed : 18.76 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.18), residues: 2422 helix: 2.35 (0.13), residues: 1848 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 33 TYR 0.008 0.001 TYR D 60 PHE 0.024 0.002 PHE I 59 TRP 0.006 0.000 TRP J 112 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00506 (19894) covalent geometry : angle 0.57127 (26894) hydrogen bonds : bond 0.04441 ( 1230) hydrogen bonds : angle 3.37597 ( 3639) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 470 time to evaluate : 0.910 Fit side-chains REVERT: A 48 ASP cc_start: 0.7666 (p0) cc_final: 0.7199 (p0) REVERT: A 51 ASP cc_start: 0.8766 (m-30) cc_final: 0.8324 (m-30) REVERT: A 80 GLU cc_start: 0.4543 (mp0) cc_final: 0.3783 (mt-10) REVERT: A 115 ASP cc_start: 0.9203 (t70) cc_final: 0.8938 (OUTLIER) REVERT: A 171 GLU cc_start: 0.8106 (pp20) cc_final: 0.7881 (pp20) REVERT: B 62 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: B 80 GLU cc_start: 0.4693 (pm20) cc_final: 0.3699 (pm20) REVERT: B 172 ASP cc_start: 0.9224 (t0) cc_final: 0.8968 (t0) REVERT: C 81 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7943 (mtm) REVERT: C 172 ASP cc_start: 0.9196 (t70) cc_final: 0.8850 (t0) REVERT: D 48 ASP cc_start: 0.7738 (p0) cc_final: 0.6887 (p0) REVERT: D 51 ASP cc_start: 0.8733 (m-30) cc_final: 0.8310 (m-30) REVERT: D 172 ASP cc_start: 0.9368 (t0) cc_final: 0.9035 (t0) REVERT: E 1 MET cc_start: 0.7309 (ttm) cc_final: 0.3195 (ptt) REVERT: E 48 ASP cc_start: 0.7914 (p0) cc_final: 0.7397 (p0) REVERT: E 51 ASP cc_start: 0.8961 (m-30) cc_final: 0.8629 (m-30) REVERT: E 172 ASP cc_start: 0.9257 (t0) cc_final: 0.8957 (t0) REVERT: F 48 ASP cc_start: 0.7971 (p0) cc_final: 0.7179 (p0) REVERT: F 51 ASP cc_start: 0.8749 (m-30) cc_final: 0.8172 (m-30) REVERT: F 80 GLU cc_start: 0.4862 (mp0) cc_final: 0.4447 (mp0) REVERT: F 115 ASP cc_start: 0.9209 (t70) cc_final: 0.8996 (t0) REVERT: F 174 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8649 (mm-30) REVERT: G 172 ASP cc_start: 0.9036 (t0) cc_final: 0.8737 (t0) REVERT: I 18 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8100 (tm-30) REVERT: I 26 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8068 (mptp) REVERT: I 48 ASP cc_start: 0.7886 (p0) cc_final: 0.7344 (p0) REVERT: I 51 ASP cc_start: 0.8624 (m-30) cc_final: 0.8274 (m-30) REVERT: J 3 ARG cc_start: 0.1732 (mmt180) cc_final: 0.1416 (mmt180) REVERT: J 48 ASP cc_start: 0.7991 (p0) cc_final: 0.7368 (p0) REVERT: J 51 ASP cc_start: 0.8792 (m-30) cc_final: 0.8350 (m-30) REVERT: J 128 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8951 (mm-40) REVERT: K 48 ASP cc_start: 0.7596 (p0) cc_final: 0.6804 (p0) REVERT: K 51 ASP cc_start: 0.8590 (m-30) cc_final: 0.8092 (m-30) REVERT: L 10 ASP cc_start: 0.8265 (m-30) cc_final: 0.8056 (m-30) REVERT: L 97 ASP cc_start: 0.8853 (m-30) cc_final: 0.8581 (m-30) REVERT: L 172 ASP cc_start: 0.9159 (t70) cc_final: 0.8896 (t0) REVERT: M 48 ASP cc_start: 0.8099 (p0) cc_final: 0.7550 (p0) REVERT: M 51 ASP cc_start: 0.8739 (m-30) cc_final: 0.8322 (m-30) REVERT: M 172 ASP cc_start: 0.9250 (t70) cc_final: 0.8881 (t0) REVERT: N 48 ASP cc_start: 0.7897 (p0) cc_final: 0.7238 (p0) REVERT: N 51 ASP cc_start: 0.8887 (m-30) cc_final: 0.8508 (m-30) REVERT: N 172 ASP cc_start: 0.9161 (t70) cc_final: 0.8825 (t0) outliers start: 38 outliers final: 20 residues processed: 489 average time/residue: 0.6710 time to fit residues: 364.5060 Evaluate side-chains 478 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 456 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 167 SER Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 167 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 27 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 156 optimal weight: 0.0040 chunk 189 optimal weight: 6.9990 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN D 166 GLN F 14 ASN F 84 GLN F 166 GLN G 14 ASN G 166 GLN J 14 ASN J 166 GLN K 84 GLN K 128 GLN L 166 GLN M 128 GLN N 166 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.060987 restraints weight = 40087.553| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.04 r_work: 0.2627 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19894 Z= 0.173 Angle : 0.559 8.868 26894 Z= 0.289 Chirality : 0.036 0.158 3052 Planarity : 0.004 0.041 3444 Dihedral : 3.560 19.972 2688 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.60 % Allowed : 20.02 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.18), residues: 2422 helix: 2.36 (0.13), residues: 1848 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 33 TYR 0.007 0.001 TYR D 60 PHE 0.018 0.002 PHE M 59 TRP 0.005 0.000 TRP J 112 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00424 (19894) covalent geometry : angle 0.55865 (26894) hydrogen bonds : bond 0.03901 ( 1230) hydrogen bonds : angle 3.33653 ( 3639) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 486 time to evaluate : 0.783 Fit side-chains REVERT: A 48 ASP cc_start: 0.7675 (p0) cc_final: 0.7217 (p0) REVERT: A 51 ASP cc_start: 0.8770 (m-30) cc_final: 0.8330 (m-30) REVERT: A 80 GLU cc_start: 0.4427 (mp0) cc_final: 0.3669 (mp0) REVERT: A 115 ASP cc_start: 0.9209 (t70) cc_final: 0.8941 (OUTLIER) REVERT: A 171 GLU cc_start: 0.8141 (pp20) cc_final: 0.7915 (pp20) REVERT: B 47 MET cc_start: 0.8764 (mtm) cc_final: 0.8416 (ptp) REVERT: B 51 ASP cc_start: 0.8813 (m-30) cc_final: 0.8584 (m-30) REVERT: B 62 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: B 80 GLU cc_start: 0.4671 (pm20) cc_final: 0.4237 (pm20) REVERT: B 171 GLU cc_start: 0.8166 (pp20) cc_final: 0.7915 (pp20) REVERT: B 172 ASP cc_start: 0.9220 (t0) cc_final: 0.8920 (t0) REVERT: C 81 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7957 (mtm) REVERT: C 172 ASP cc_start: 0.9197 (t70) cc_final: 0.8860 (t0) REVERT: D 48 ASP cc_start: 0.7680 (p0) cc_final: 0.6874 (p0) REVERT: D 51 ASP cc_start: 0.8731 (m-30) cc_final: 0.8318 (m-30) REVERT: D 172 ASP cc_start: 0.9370 (t0) cc_final: 0.9048 (t0) REVERT: E 1 MET cc_start: 0.7168 (ttm) cc_final: 0.3099 (ptt) REVERT: E 48 ASP cc_start: 0.7897 (p0) cc_final: 0.7359 (p0) REVERT: E 51 ASP cc_start: 0.8959 (m-30) cc_final: 0.8551 (m-30) REVERT: E 172 ASP cc_start: 0.9239 (t0) cc_final: 0.8961 (t0) REVERT: F 48 ASP cc_start: 0.7983 (p0) cc_final: 0.7193 (p0) REVERT: F 51 ASP cc_start: 0.8748 (m-30) cc_final: 0.8180 (m-30) REVERT: F 80 GLU cc_start: 0.4812 (mp0) cc_final: 0.4495 (mp0) REVERT: F 115 ASP cc_start: 0.9208 (t70) cc_final: 0.8997 (t0) REVERT: F 171 GLU cc_start: 0.8191 (pp20) cc_final: 0.7947 (pp20) REVERT: F 174 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8688 (mm-30) REVERT: G 172 ASP cc_start: 0.9047 (t0) cc_final: 0.8742 (t0) REVERT: I 18 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8065 (tm-30) REVERT: I 26 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8099 (mptp) REVERT: I 48 ASP cc_start: 0.7947 (p0) cc_final: 0.7405 (p0) REVERT: I 51 ASP cc_start: 0.8668 (m-30) cc_final: 0.8306 (m-30) REVERT: J 3 ARG cc_start: 0.1975 (mmt180) cc_final: 0.1680 (mmt180) REVERT: J 48 ASP cc_start: 0.7962 (p0) cc_final: 0.7326 (p0) REVERT: J 51 ASP cc_start: 0.8789 (m-30) cc_final: 0.8344 (m-30) REVERT: K 48 ASP cc_start: 0.7571 (p0) cc_final: 0.6747 (p0) REVERT: K 51 ASP cc_start: 0.8591 (m-30) cc_final: 0.8079 (m-30) REVERT: L 75 ASP cc_start: 0.8812 (t70) cc_final: 0.8449 (t0) REVERT: L 166 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7740 (pt0) REVERT: L 172 ASP cc_start: 0.9179 (t70) cc_final: 0.8894 (t0) REVERT: M 48 ASP cc_start: 0.8122 (p0) cc_final: 0.7559 (p0) REVERT: M 51 ASP cc_start: 0.8749 (m-30) cc_final: 0.8295 (m-30) REVERT: M 172 ASP cc_start: 0.9255 (t70) cc_final: 0.8892 (t0) REVERT: N 48 ASP cc_start: 0.7911 (p0) cc_final: 0.7299 (p0) REVERT: N 51 ASP cc_start: 0.8892 (m-30) cc_final: 0.8518 (m-30) REVERT: N 111 GLU cc_start: 0.8788 (mp0) cc_final: 0.8517 (mp0) REVERT: N 172 ASP cc_start: 0.9171 (t70) cc_final: 0.8877 (t0) outliers start: 33 outliers final: 20 residues processed: 501 average time/residue: 0.6451 time to fit residues: 358.1367 Evaluate side-chains 499 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 476 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 115 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain J residue 14 ASN Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 166 GLN Chi-restraints excluded: chain N residue 167 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 236 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN C 166 GLN D 166 GLN F 84 GLN F 166 GLN G 166 GLN K 84 GLN K 128 GLN L 166 GLN N 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.077436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.060712 restraints weight = 39999.027| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 3.00 r_work: 0.2579 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19894 Z= 0.136 Angle : 0.560 11.190 26894 Z= 0.290 Chirality : 0.035 0.139 3052 Planarity : 0.004 0.040 3444 Dihedral : 3.446 19.131 2688 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.60 % Allowed : 21.28 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.18), residues: 2422 helix: 2.41 (0.13), residues: 1848 sheet: None (None), residues: 0 loop : -0.80 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 175 TYR 0.006 0.001 TYR F 64 PHE 0.012 0.001 PHE M 59 TRP 0.005 0.000 TRP J 112 HIS 0.003 0.001 HIS M 90 Details of bonding type rmsd covalent geometry : bond 0.00330 (19894) covalent geometry : angle 0.56044 (26894) hydrogen bonds : bond 0.03288 ( 1230) hydrogen bonds : angle 3.26304 ( 3639) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 508 time to evaluate : 0.653 Fit side-chains REVERT: A 48 ASP cc_start: 0.7701 (p0) cc_final: 0.7258 (p0) REVERT: A 51 ASP cc_start: 0.8819 (m-30) cc_final: 0.8378 (m-30) REVERT: A 80 GLU cc_start: 0.4653 (mp0) cc_final: 0.4146 (mp0) REVERT: A 115 ASP cc_start: 0.9190 (t70) cc_final: 0.8921 (OUTLIER) REVERT: A 171 GLU cc_start: 0.8138 (pp20) cc_final: 0.7929 (pp20) REVERT: B 47 MET cc_start: 0.8762 (mtm) cc_final: 0.8447 (ptp) REVERT: B 171 GLU cc_start: 0.8174 (pp20) cc_final: 0.7928 (pp20) REVERT: B 172 ASP cc_start: 0.9209 (t0) cc_final: 0.8915 (t0) REVERT: C 81 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7921 (mtm) REVERT: C 172 ASP cc_start: 0.9218 (t70) cc_final: 0.8879 (t0) REVERT: D 48 ASP cc_start: 0.7598 (p0) cc_final: 0.6749 (p0) REVERT: D 51 ASP cc_start: 0.8713 (m-30) cc_final: 0.8312 (m-30) REVERT: D 172 ASP cc_start: 0.9380 (t0) cc_final: 0.9052 (t0) REVERT: E 1 MET cc_start: 0.7265 (ttm) cc_final: 0.3286 (ptt) REVERT: E 48 ASP cc_start: 0.7840 (p0) cc_final: 0.7336 (p0) REVERT: E 51 ASP cc_start: 0.8963 (m-30) cc_final: 0.8550 (m-30) REVERT: E 172 ASP cc_start: 0.9204 (t0) cc_final: 0.8842 (t0) REVERT: F 13 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8380 (mt-10) REVERT: F 48 ASP cc_start: 0.7942 (p0) cc_final: 0.7155 (p0) REVERT: F 51 ASP cc_start: 0.8760 (m-30) cc_final: 0.8188 (m-30) REVERT: F 80 GLU cc_start: 0.4596 (mp0) cc_final: 0.4265 (pm20) REVERT: F 115 ASP cc_start: 0.9213 (t70) cc_final: 0.9007 (t0) REVERT: G 166 GLN cc_start: 0.7836 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: G 172 ASP cc_start: 0.9067 (t0) cc_final: 0.8754 (t0) REVERT: I 18 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8106 (tm-30) REVERT: I 26 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8144 (mptp) REVERT: I 48 ASP cc_start: 0.7884 (p0) cc_final: 0.7365 (p0) REVERT: I 51 ASP cc_start: 0.8665 (m-30) cc_final: 0.8310 (m-30) REVERT: I 111 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8697 (pt0) REVERT: J 3 ARG cc_start: 0.1850 (mmt180) cc_final: 0.1598 (mmt180) REVERT: J 19 GLU cc_start: 0.8580 (mt-10) cc_final: 0.7963 (mt-10) REVERT: J 48 ASP cc_start: 0.7978 (p0) cc_final: 0.7196 (p0) REVERT: J 51 ASP cc_start: 0.8811 (m-30) cc_final: 0.8394 (m-30) REVERT: J 81 MET cc_start: 0.8905 (mmm) cc_final: 0.8566 (mpp) REVERT: J 111 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7790 (pt0) REVERT: J 171 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8110 (pp20) REVERT: K 26 LYS cc_start: 0.9170 (ttmm) cc_final: 0.8907 (mttm) REVERT: K 48 ASP cc_start: 0.7502 (p0) cc_final: 0.6712 (p0) REVERT: K 51 ASP cc_start: 0.8621 (m-30) cc_final: 0.8096 (m-30) REVERT: L 172 ASP cc_start: 0.9185 (t70) cc_final: 0.8893 (t0) REVERT: M 48 ASP cc_start: 0.8095 (p0) cc_final: 0.7544 (p0) REVERT: M 51 ASP cc_start: 0.8735 (m-30) cc_final: 0.8287 (m-30) REVERT: M 172 ASP cc_start: 0.9270 (t70) cc_final: 0.8899 (t0) REVERT: N 48 ASP cc_start: 0.7863 (p0) cc_final: 0.7259 (p0) REVERT: N 51 ASP cc_start: 0.8940 (m-30) cc_final: 0.8561 (m-30) REVERT: N 111 GLU cc_start: 0.8786 (mp0) cc_final: 0.8513 (mp0) REVERT: N 171 GLU cc_start: 0.8143 (pp20) cc_final: 0.7868 (pp20) REVERT: N 172 ASP cc_start: 0.9162 (t70) cc_final: 0.8706 (t0) outliers start: 33 outliers final: 18 residues processed: 524 average time/residue: 0.6809 time to fit residues: 394.2913 Evaluate side-chains 489 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 468 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain I residue 162 LEU Chi-restraints excluded: chain J residue 111 GLU Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain K residue 167 SER Chi-restraints excluded: chain L residue 147 THR Chi-restraints excluded: chain L residue 167 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 86 optimal weight: 0.7980 chunk 94 optimal weight: 0.2980 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 126 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 201 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN F 14 ASN F 84 GLN F 166 GLN G 128 GLN G 166 GLN J 14 ASN K 84 GLN K 91 GLN K 128 GLN L 128 GLN N 166 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.079615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.062891 restraints weight = 39391.892| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.00 r_work: 0.2635 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19894 Z= 0.115 Angle : 0.568 10.417 26894 Z= 0.294 Chirality : 0.034 0.149 3052 Planarity : 0.004 0.040 3444 Dihedral : 3.236 17.043 2688 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.12 % Allowed : 22.98 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.18), residues: 2422 helix: 2.46 (0.13), residues: 1848 sheet: None (None), residues: 0 loop : -0.73 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 3 TYR 0.012 0.001 TYR F 168 PHE 0.009 0.001 PHE N 23 TRP 0.005 0.000 TRP J 112 HIS 0.003 0.000 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00275 (19894) covalent geometry : angle 0.56814 (26894) hydrogen bonds : bond 0.02454 ( 1230) hydrogen bonds : angle 3.20237 ( 3639) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 501 time to evaluate : 0.617 Fit side-chains REVERT: A 48 ASP cc_start: 0.7609 (p0) cc_final: 0.7204 (p0) REVERT: A 51 ASP cc_start: 0.8833 (m-30) cc_final: 0.8381 (m-30) REVERT: A 80 GLU cc_start: 0.4395 (mp0) cc_final: 0.4113 (pm20) REVERT: A 115 ASP cc_start: 0.9194 (t70) cc_final: 0.8939 (OUTLIER) REVERT: A 168 TYR cc_start: 0.8354 (p90) cc_final: 0.8116 (p90) REVERT: A 171 GLU cc_start: 0.8159 (pp20) cc_final: 0.7947 (pp20) REVERT: B 80 GLU cc_start: 0.4693 (pm20) cc_final: 0.4360 (pm20) REVERT: C 172 ASP cc_start: 0.9205 (t70) cc_final: 0.8856 (t0) REVERT: D 48 ASP cc_start: 0.7533 (p0) cc_final: 0.6762 (p0) REVERT: D 51 ASP cc_start: 0.8690 (m-30) cc_final: 0.8300 (m-30) REVERT: D 172 ASP cc_start: 0.9355 (t0) cc_final: 0.9034 (t0) REVERT: E 1 MET cc_start: 0.7266 (ttm) cc_final: 0.3510 (ptt) REVERT: E 48 ASP cc_start: 0.7646 (p0) cc_final: 0.7166 (p0) REVERT: E 51 ASP cc_start: 0.8880 (m-30) cc_final: 0.8482 (m-30) REVERT: E 172 ASP cc_start: 0.9164 (t0) cc_final: 0.8788 (t0) REVERT: F 48 ASP cc_start: 0.7796 (p0) cc_final: 0.7044 (p0) REVERT: F 51 ASP cc_start: 0.8784 (m-30) cc_final: 0.8282 (m-30) REVERT: F 115 ASP cc_start: 0.9193 (t70) cc_final: 0.8981 (t0) REVERT: F 174 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8707 (mm-30) REVERT: G 172 ASP cc_start: 0.9048 (t0) cc_final: 0.8731 (t0) REVERT: H 47 MET cc_start: 0.8568 (ptp) cc_final: 0.8200 (ptp) REVERT: I 18 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8050 (tm-30) REVERT: I 26 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8130 (mptp) REVERT: I 48 ASP cc_start: 0.7892 (p0) cc_final: 0.7571 (p0) REVERT: I 51 ASP cc_start: 0.8630 (m-30) cc_final: 0.8308 (m-30) REVERT: J 3 ARG cc_start: 0.1522 (mmt180) cc_final: 0.1213 (mmt180) REVERT: J 19 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8169 (mt-10) REVERT: J 48 ASP cc_start: 0.7866 (p0) cc_final: 0.7270 (p0) REVERT: J 51 ASP cc_start: 0.8770 (m-30) cc_final: 0.8484 (m-30) REVERT: J 81 MET cc_start: 0.8883 (mmm) cc_final: 0.8527 (mpp) REVERT: K 26 LYS cc_start: 0.9188 (ttmm) cc_final: 0.8934 (mttm) REVERT: K 48 ASP cc_start: 0.7342 (p0) cc_final: 0.6587 (p0) REVERT: K 51 ASP cc_start: 0.8561 (m-30) cc_final: 0.8012 (m-30) REVERT: K 171 GLU cc_start: 0.8460 (pp20) cc_final: 0.7888 (pp20) REVERT: L 172 ASP cc_start: 0.9180 (t70) cc_final: 0.8875 (t0) REVERT: M 48 ASP cc_start: 0.8048 (p0) cc_final: 0.7528 (p0) REVERT: M 51 ASP cc_start: 0.8655 (m-30) cc_final: 0.8300 (m-30) REVERT: M 172 ASP cc_start: 0.9266 (t70) cc_final: 0.8883 (t0) REVERT: N 48 ASP cc_start: 0.7778 (p0) cc_final: 0.7163 (p0) REVERT: N 51 ASP cc_start: 0.8947 (m-30) cc_final: 0.8636 (m-30) REVERT: N 111 GLU cc_start: 0.8778 (mp0) cc_final: 0.8437 (mp0) REVERT: N 171 GLU cc_start: 0.8169 (pp20) cc_final: 0.7878 (pp20) REVERT: N 172 ASP cc_start: 0.9154 (t70) cc_final: 0.8698 (t0) outliers start: 23 outliers final: 9 residues processed: 511 average time/residue: 0.6116 time to fit residues: 346.2871 Evaluate side-chains 496 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 487 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain K residue 55 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 1 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 233 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 0.0040 chunk 65 optimal weight: 9.9990 overall best weight: 4.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 166 GLN D 128 GLN D 166 GLN F 84 GLN F 128 GLN F 166 GLN I 128 GLN J 91 GLN K 84 GLN K 91 GLN K 128 GLN L 91 GLN M 128 GLN N 98 GLN N 166 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.059359 restraints weight = 40159.756| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.02 r_work: 0.2546 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19894 Z= 0.197 Angle : 0.640 9.974 26894 Z= 0.330 Chirality : 0.037 0.143 3052 Planarity : 0.004 0.039 3444 Dihedral : 3.618 22.928 2688 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.92 % Allowed : 23.23 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.18), residues: 2422 helix: 2.44 (0.13), residues: 1848 sheet: None (None), residues: 0 loop : -0.83 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 3 TYR 0.025 0.001 TYR D 168 PHE 0.021 0.002 PHE I 59 TRP 0.006 0.000 TRP J 112 HIS 0.005 0.001 HIS M 90 Details of bonding type rmsd covalent geometry : bond 0.00484 (19894) covalent geometry : angle 0.64027 (26894) hydrogen bonds : bond 0.04226 ( 1230) hydrogen bonds : angle 3.33564 ( 3639) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4844 Ramachandran restraints generated. 2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 472 time to evaluate : 0.637 Fit side-chains REVERT: A 48 ASP cc_start: 0.7748 (p0) cc_final: 0.7294 (p0) REVERT: A 51 ASP cc_start: 0.8770 (m-30) cc_final: 0.8354 (m-30) REVERT: A 80 GLU cc_start: 0.4476 (mp0) cc_final: 0.3742 (mt-10) REVERT: A 115 ASP cc_start: 0.9216 (t70) cc_final: 0.8953 (OUTLIER) REVERT: B 80 GLU cc_start: 0.4703 (pm20) cc_final: 0.3794 (pm20) REVERT: B 172 ASP cc_start: 0.9226 (t0) cc_final: 0.8987 (t0) REVERT: C 172 ASP cc_start: 0.9209 (t70) cc_final: 0.8872 (t0) REVERT: D 48 ASP cc_start: 0.7769 (p0) cc_final: 0.6978 (p0) REVERT: D 51 ASP cc_start: 0.8750 (m-30) cc_final: 0.8338 (m-30) REVERT: D 172 ASP cc_start: 0.9380 (t0) cc_final: 0.9053 (t0) REVERT: E 1 MET cc_start: 0.7323 (ttm) cc_final: 0.3343 (ptt) REVERT: E 48 ASP cc_start: 0.7914 (p0) cc_final: 0.7412 (p0) REVERT: E 51 ASP cc_start: 0.8970 (m-30) cc_final: 0.8645 (m-30) REVERT: E 172 ASP cc_start: 0.9230 (t0) cc_final: 0.8933 (t0) REVERT: F 13 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8392 (mt-10) REVERT: F 47 MET cc_start: 0.8602 (ptp) cc_final: 0.8179 (ptp) REVERT: F 48 ASP cc_start: 0.7953 (p0) cc_final: 0.7083 (p0) REVERT: F 51 ASP cc_start: 0.8753 (m-30) cc_final: 0.8200 (m-30) REVERT: F 80 GLU cc_start: 0.4543 (mp0) cc_final: 0.3979 (pm20) REVERT: F 115 ASP cc_start: 0.9220 (t70) cc_final: 0.9018 (t0) REVERT: G 1 MET cc_start: 0.5532 (tmm) cc_final: 0.2931 (tmm) REVERT: G 172 ASP cc_start: 0.9068 (t0) cc_final: 0.8764 (t0) REVERT: I 18 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8151 (tm-30) REVERT: I 26 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8147 (mptp) REVERT: I 48 ASP cc_start: 0.7909 (p0) cc_final: 0.7407 (p0) REVERT: I 51 ASP cc_start: 0.8654 (m-30) cc_final: 0.8299 (m-30) REVERT: I 111 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8710 (pt0) REVERT: I 133 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8944 (mm-30) REVERT: J 3 ARG cc_start: 0.1963 (mmt180) cc_final: 0.1698 (mmt180) REVERT: J 48 ASP cc_start: 0.7989 (p0) cc_final: 0.7341 (p0) REVERT: J 51 ASP cc_start: 0.8884 (m-30) cc_final: 0.8431 (m-30) REVERT: J 54 ASP cc_start: 0.8672 (t70) cc_final: 0.8460 (t0) REVERT: K 48 ASP cc_start: 0.7597 (p0) cc_final: 0.6784 (p0) REVERT: K 51 ASP cc_start: 0.8612 (m-30) cc_final: 0.8109 (m-30) REVERT: L 97 ASP cc_start: 0.8812 (m-30) cc_final: 0.8596 (m-30) REVERT: L 172 ASP cc_start: 0.9195 (t70) cc_final: 0.8902 (t0) REVERT: M 48 ASP cc_start: 0.8162 (p0) cc_final: 0.7615 (p0) REVERT: M 51 ASP cc_start: 0.8768 (m-30) cc_final: 0.8341 (m-30) REVERT: M 172 ASP cc_start: 0.9258 (t70) cc_final: 0.8900 (t0) REVERT: N 48 ASP cc_start: 0.7874 (p0) cc_final: 0.7244 (p0) REVERT: N 51 ASP cc_start: 0.8917 (m-30) cc_final: 0.8550 (m-30) REVERT: N 111 GLU cc_start: 0.8799 (mp0) cc_final: 0.8485 (mp0) REVERT: N 171 GLU cc_start: 0.8178 (pp20) cc_final: 0.7919 (pp20) REVERT: N 172 ASP cc_start: 0.9193 (t70) cc_final: 0.8760 (t0) outliers start: 19 outliers final: 12 residues processed: 483 average time/residue: 0.6576 time to fit residues: 353.1757 Evaluate side-chains 480 residues out of total 2058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 468 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain D residue 58 SER Chi-restraints excluded: chain E residue 145 SER Chi-restraints excluded: chain F residue 46 SER Chi-restraints excluded: chain F residue 166 GLN Chi-restraints excluded: chain F residue 167 SER Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain I residue 26 LYS Chi-restraints excluded: chain I residue 58 SER Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 55 LYS Chi-restraints excluded: chain L residue 167 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 153 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 87 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 GLN C 166 GLN D 166 GLN F 84 GLN F 128 GLN F 166 GLN N 98 GLN N 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.076753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.059844 restraints weight = 39925.784| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.03 r_work: 0.2558 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19894 Z= 0.173 Angle : 0.631 12.423 26894 Z= 0.326 Chirality : 0.036 0.142 3052 Planarity : 0.004 0.039 3444 Dihedral : 3.610 24.610 2688 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.83 % Allowed : 23.42 % Favored : 75.75 % 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: 2.52 (0.18), residues: 2422 helix: 2.40 (0.13), residues: 1848 sheet: None (None), residues: 0 loop : -0.85 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 3 TYR 0.009 0.001 TYR F 168 PHE 0.017 0.002 PHE I 59 TRP 0.005 0.000 TRP J 112 HIS 0.004 0.001 HIS H 90 Details of bonding type rmsd covalent geometry : bond 0.00425 (19894) covalent geometry : angle 0.63130 (26894) hydrogen bonds : bond 0.03766 ( 1230) hydrogen bonds : angle 3.31449 ( 3639) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7255.24 seconds wall clock time: 124 minutes 1.23 seconds (7441.23 seconds total)