Starting phenix.real_space_refine on Wed Mar 4 01:38:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ob4_12794/03_2026/7ob4_12794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ob4_12794/03_2026/7ob4_12794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ob4_12794/03_2026/7ob4_12794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ob4_12794/03_2026/7ob4_12794.map" model { file = "/net/cci-nas-00/data/ceres_data/7ob4_12794/03_2026/7ob4_12794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ob4_12794/03_2026/7ob4_12794.cif" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 28 5.16 5 C 6510 2.51 5 N 1652 2.21 5 O 1876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10066 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "I" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "J" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "K" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "M" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "L" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "N" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "A" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "C" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "E" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Chain: "F" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Time building chain proxies: 2.39, per 1000 atoms: 0.24 Number of scatterers: 10066 At special positions: 0 Unit cell: (161.355, 92.649, 52.05, 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 28 16.00 O 1876 8.00 N 1652 7.00 C 6510 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 510.0 milliseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2436 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 22 sheets defined 0.0% alpha, 45.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 16 current: chain 'C' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 16 current: chain 'E' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 13 through 16 current: chain 'G' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 13 through 16 current: chain 'I' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 13 through 16 current: chain 'K' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 13 through 16 current: chain 'M' and resid 13 through 16 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 19 through 21 current: chain 'C' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 21 current: chain 'E' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 19 through 21 current: chain 'G' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 19 through 21 current: chain 'I' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 19 through 21 current: chain 'K' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 19 through 21 current: chain 'M' and resid 19 through 21 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 34 current: chain 'C' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 25 through 34 current: chain 'E' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 25 through 34 current: chain 'G' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 25 through 34 current: chain 'I' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 25 through 34 current: chain 'K' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 25 through 34 current: chain 'M' and resid 25 through 34 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 59 through 65 current: chain 'C' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 59 through 65 current: chain 'E' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 59 through 65 current: chain 'G' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 59 through 65 current: chain 'I' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 59 through 65 current: chain 'K' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 59 through 65 current: chain 'M' and resid 59 through 65 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 71 through 73 current: chain 'C' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 73 current: chain 'E' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 71 through 73 current: chain 'G' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 71 through 73 current: chain 'I' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 71 through 73 current: chain 'K' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 71 through 73 current: chain 'M' and resid 71 through 73 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 76 through 77 current: chain 'C' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 76 through 77 current: chain 'E' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 76 through 77 current: chain 'G' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 76 through 77 current: chain 'I' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 76 through 77 current: chain 'K' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 76 through 77 current: chain 'M' and resid 76 through 77 No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 79 through 82 current: chain 'C' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 79 through 82 current: chain 'E' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 79 through 82 current: chain 'G' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 79 through 82 current: chain 'I' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 79 through 82 current: chain 'K' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 79 through 82 current: chain 'M' and resid 79 through 82 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 92 through 99 current: chain 'C' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 92 through 99 current: chain 'E' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 99 current: chain 'G' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 92 through 99 current: chain 'I' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 92 through 99 current: chain 'K' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 92 through 99 current: chain 'M' and resid 92 through 99 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 103 through 108 current: chain 'C' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 103 through 108 current: chain 'E' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 103 through 108 current: chain 'G' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 103 through 108 current: chain 'I' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 103 through 108 current: chain 'K' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 103 through 108 current: chain 'M' and resid 103 through 108 No H-bonds generated for sheet with id=AA9 Processing sheet with id=A10, first strand: chain 'A' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 115 through 115 current: chain 'C' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 115 through 115 current: chain 'E' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 115 through 115 current: chain 'G' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 115 through 115 current: chain 'I' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 115 through 115 current: chain 'K' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 115 through 115 current: chain 'M' and resid 115 through 115 No H-bonds generated for sheet with id=A10 Processing sheet with id=A11, first strand: chain 'A' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 118 through 122 current: chain 'C' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 118 through 122 current: chain 'E' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 118 through 122 current: chain 'G' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 118 through 122 current: chain 'I' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 118 through 122 current: chain 'K' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 118 through 122 current: chain 'M' and resid 118 through 122 No H-bonds generated for sheet with id=A11 Processing sheet with id=BA1, first strand: chain 'B' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 16 current: chain 'D' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 13 through 16 current: chain 'F' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 13 through 16 current: chain 'H' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 13 through 16 current: chain 'J' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 13 through 16 current: chain 'L' and resid 13 through 16 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 13 through 16 current: chain 'N' and resid 13 through 16 No H-bonds generated for sheet with id=BA1 Processing sheet with id=BA2, first strand: chain 'B' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 19 through 21 current: chain 'D' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 21 current: chain 'F' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 21 current: chain 'H' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 19 through 21 current: chain 'J' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 19 through 21 current: chain 'L' and resid 19 through 21 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 19 through 21 current: chain 'N' and resid 19 through 21 No H-bonds generated for sheet with id=BA2 Processing sheet with id=BA3, first strand: chain 'B' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 25 through 34 current: chain 'D' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 34 current: chain 'F' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 25 through 34 current: chain 'H' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 25 through 34 current: chain 'J' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 25 through 34 current: chain 'L' and resid 25 through 34 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 25 through 34 current: chain 'N' and resid 25 through 34 No H-bonds generated for sheet with id=BA3 Processing sheet with id=BA4, first strand: chain 'B' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 59 through 65 current: chain 'D' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 59 through 65 current: chain 'F' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 59 through 65 current: chain 'H' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 59 through 65 current: chain 'J' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 59 through 65 current: chain 'L' and resid 59 through 65 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 59 through 65 current: chain 'N' and resid 59 through 65 No H-bonds generated for sheet with id=BA4 Processing sheet with id=BA5, first strand: chain 'B' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 73 current: chain 'D' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 71 through 73 current: chain 'F' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 71 through 73 current: chain 'H' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 71 through 73 current: chain 'J' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 71 through 73 current: chain 'L' and resid 71 through 73 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 71 through 73 current: chain 'N' and resid 71 through 73 No H-bonds generated for sheet with id=BA5 Processing sheet with id=BA6, first strand: chain 'B' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 76 through 77 current: chain 'D' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 76 through 77 current: chain 'F' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 76 through 77 current: chain 'H' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 76 through 77 current: chain 'J' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 76 through 77 current: chain 'L' and resid 76 through 77 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 76 through 77 current: chain 'N' and resid 76 through 77 No H-bonds generated for sheet with id=BA6 Processing sheet with id=BA7, first strand: chain 'B' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 79 through 82 current: chain 'D' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 79 through 82 current: chain 'F' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 79 through 82 current: chain 'H' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 79 through 82 current: chain 'J' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 79 through 82 current: chain 'L' and resid 79 through 82 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 79 through 82 current: chain 'N' and resid 79 through 82 No H-bonds generated for sheet with id=BA7 Processing sheet with id=BA8, first strand: chain 'B' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 92 through 99 current: chain 'D' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 92 through 99 current: chain 'F' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 92 through 99 current: chain 'H' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 92 through 99 current: chain 'J' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 92 through 99 current: chain 'L' and resid 92 through 99 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 92 through 99 current: chain 'N' and resid 92 through 99 No H-bonds generated for sheet with id=BA8 Processing sheet with id=BA9, first strand: chain 'B' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 103 through 108 current: chain 'D' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 103 through 108 current: chain 'F' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 103 through 108 current: chain 'H' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 103 through 108 current: chain 'J' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 103 through 108 current: chain 'L' and resid 103 through 108 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 103 through 108 current: chain 'N' and resid 103 through 108 No H-bonds generated for sheet with id=BA9 Processing sheet with id=B10, first strand: chain 'B' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 115 through 115 current: chain 'D' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 115 through 115 current: chain 'F' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 115 through 115 current: chain 'H' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 115 through 115 current: chain 'J' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 115 through 115 current: chain 'L' and resid 115 through 115 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 115 through 115 current: chain 'N' and resid 115 through 115 No H-bonds generated for sheet with id=B10 Processing sheet with id=B11, first strand: chain 'B' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 118 through 122 current: chain 'D' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 118 through 122 current: chain 'F' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 118 through 122 current: chain 'H' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 118 through 122 current: chain 'J' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 118 through 122 current: chain 'L' and resid 118 through 122 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 118 through 122 current: chain 'N' and resid 118 through 122 No H-bonds generated for sheet with id=B11 No hydrogen bonds 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: 0.35 Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1648 1.32 - 1.44: 2835 1.44 - 1.56: 5764 1.56 - 1.69: 1 1.69 - 1.81: 56 Bond restraints: 10304 Sorted by residual: bond pdb=" N GLY N 101 " pdb=" CA GLY N 101 " ideal model delta sigma weight residual 1.443 1.393 0.050 1.37e-02 5.33e+03 1.33e+01 bond pdb=" C LEU I 82 " pdb=" O LEU I 82 " ideal model delta sigma weight residual 1.236 1.277 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" C MET M 30 " pdb=" O MET M 30 " ideal model delta sigma weight residual 1.233 1.274 -0.040 1.17e-02 7.31e+03 1.19e+01 bond pdb=" C ALA N 25 " pdb=" O ALA N 25 " ideal model delta sigma weight residual 1.234 1.193 0.040 1.19e-02 7.06e+03 1.16e+01 bond pdb=" CA SER N 100 " pdb=" C SER N 100 " ideal model delta sigma weight residual 1.525 1.564 -0.039 1.25e-02 6.40e+03 9.84e+00 ... (remaining 10299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 12799 1.67 - 3.35: 941 3.35 - 5.02: 209 5.02 - 6.70: 45 6.70 - 8.37: 6 Bond angle restraints: 14000 Sorted by residual: angle pdb=" N ALA B 81 " pdb=" CA ALA B 81 " pdb=" C ALA B 81 " ideal model delta sigma weight residual 108.02 100.98 7.04 1.78e+00 3.16e-01 1.57e+01 angle pdb=" N ALA I 81 " pdb=" CA ALA I 81 " pdb=" C ALA I 81 " ideal model delta sigma weight residual 107.49 99.12 8.37 2.16e+00 2.14e-01 1.50e+01 angle pdb=" CA TYR B 69 " pdb=" C TYR B 69 " pdb=" O TYR B 69 " ideal model delta sigma weight residual 120.70 116.53 4.17 1.08e+00 8.57e-01 1.49e+01 angle pdb=" N HIS A 31 " pdb=" CA HIS A 31 " pdb=" CB HIS A 31 " ideal model delta sigma weight residual 110.99 117.72 -6.73 1.77e+00 3.19e-01 1.45e+01 angle pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" C VAL B 32 " ideal model delta sigma weight residual 108.12 102.66 5.46 1.44e+00 4.82e-01 1.44e+01 ... (remaining 13995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 5544 17.01 - 34.02: 432 34.02 - 51.02: 75 51.02 - 68.03: 25 68.03 - 85.04: 14 Dihedral angle restraints: 6090 sinusoidal: 2324 harmonic: 3766 Sorted by residual: dihedral pdb=" C SER N 100 " pdb=" N SER N 100 " pdb=" CA SER N 100 " pdb=" CB SER N 100 " ideal model delta harmonic sigma weight residual -122.60 -114.58 -8.02 0 2.50e+00 1.60e-01 1.03e+01 dihedral pdb=" C VAL B 32 " pdb=" N VAL B 32 " pdb=" CA VAL B 32 " pdb=" CB VAL B 32 " ideal model delta harmonic sigma weight residual -122.00 -114.04 -7.96 0 2.50e+00 1.60e-01 1.01e+01 dihedral pdb=" CB GLU C 89 " pdb=" CG GLU C 89 " pdb=" CD GLU C 89 " pdb=" OE1 GLU C 89 " ideal model delta sinusoidal sigma weight residual 0.00 -85.04 85.04 1 3.00e+01 1.11e-03 9.74e+00 ... (remaining 6087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1232 0.080 - 0.159: 324 0.159 - 0.239: 73 0.239 - 0.318: 8 0.318 - 0.397: 1 Chirality restraints: 1638 Sorted by residual: chirality pdb=" CA SER N 100 " pdb=" N SER N 100 " pdb=" C SER N 100 " pdb=" CB SER N 100 " both_signs ideal model delta sigma weight residual False 2.51 2.91 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA HIS B 31 " pdb=" N HIS B 31 " pdb=" C HIS B 31 " pdb=" CB HIS B 31 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CA VAL B 32 " pdb=" N VAL B 32 " pdb=" C VAL B 32 " pdb=" CB VAL B 32 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1635 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 30 " 0.019 2.00e-02 2.50e+03 3.96e-02 1.57e+01 pdb=" C MET F 30 " -0.069 2.00e-02 2.50e+03 pdb=" O MET F 30 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS F 31 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 30 " 0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C MET H 30 " -0.065 2.00e-02 2.50e+03 pdb=" O MET H 30 " 0.025 2.00e-02 2.50e+03 pdb=" N HIS H 31 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET L 30 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C MET L 30 " -0.057 2.00e-02 2.50e+03 pdb=" O MET L 30 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS L 31 " 0.019 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1223 2.74 - 3.28: 10196 3.28 - 3.82: 17486 3.82 - 4.36: 21582 4.36 - 4.90: 40257 Nonbonded interactions: 90744 Sorted by model distance: nonbonded pdb=" OG1 THR A 119 " pdb=" OH TYR C 114 " model vdw 2.206 3.040 nonbonded pdb=" NH2 ARG J 103 " pdb=" OD1 ASP L 74 " model vdw 2.254 3.120 nonbonded pdb=" O VAL D 28 " pdb=" OH TYR D 69 " model vdw 2.282 3.040 nonbonded pdb=" N SER B 85 " pdb=" O ILE D 84 " model vdw 2.306 3.120 nonbonded pdb=" NH2 ARG K 103 " pdb=" OD1 ASP M 74 " model vdw 2.309 3.120 ... (remaining 90739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.730 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.400 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 10304 Z= 0.534 Angle : 1.030 8.374 14000 Z= 0.651 Chirality : 0.073 0.397 1638 Planarity : 0.004 0.081 1722 Dihedral : 13.887 85.041 3654 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 23.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.09 % Allowed : 12.91 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 104 TYR 0.010 0.002 TYR H 114 PHE 0.012 0.002 PHE F 64 TRP 0.012 0.002 TRP N 79 HIS 0.005 0.001 HIS M 31 Details of bonding type rmsd covalent geometry : bond 0.00932 (10304) covalent geometry : angle 1.02959 (14000) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 354 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 MET cc_start: 0.5845 (ttm) cc_final: 0.5498 (ttm) REVERT: I 15 LYS cc_start: 0.7999 (mttt) cc_final: 0.7646 (mttt) REVERT: K 117 SER cc_start: 0.8679 (m) cc_final: 0.8457 (m) REVERT: M 13 MET cc_start: 0.6480 (ttm) cc_final: 0.5936 (ttm) REVERT: M 30 MET cc_start: 0.7165 (ptm) cc_final: 0.5558 (mmt) REVERT: N 13 MET cc_start: 0.6380 (ttm) cc_final: 0.6157 (ttm) REVERT: N 30 MET cc_start: 0.7094 (ptm) cc_final: 0.6149 (mmt) REVERT: N 34 ARG cc_start: 0.7353 (tmt170) cc_final: 0.6935 (tmt170) REVERT: N 117 SER cc_start: 0.8320 (m) cc_final: 0.8073 (m) REVERT: A 31 HIS cc_start: 0.6626 (p90) cc_final: 0.6285 (m-70) REVERT: B 31 HIS cc_start: 0.7129 (p90) cc_final: 0.6002 (m-70) REVERT: F 13 MET cc_start: 0.5381 (ttm) cc_final: 0.5088 (ttm) REVERT: F 74 ASP cc_start: 0.8274 (t0) cc_final: 0.8021 (t0) outliers start: 1 outliers final: 1 residues processed: 354 average time/residue: 0.0837 time to fit residues: 43.4091 Evaluate side-chains 306 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 305 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 119 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.166953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.134918 restraints weight = 11728.080| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 3.06 r_work: 0.4312 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10304 Z= 0.205 Angle : 0.666 12.034 14000 Z= 0.338 Chirality : 0.050 0.158 1638 Planarity : 0.003 0.038 1722 Dihedral : 5.728 24.776 1387 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.48 % Allowed : 15.20 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 34 TYR 0.017 0.002 TYR N 69 PHE 0.016 0.002 PHE H 64 TRP 0.007 0.001 TRP N 79 HIS 0.022 0.002 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00460 (10304) covalent geometry : angle 0.66566 (14000) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 66 GLU cc_start: 0.7203 (mt-10) cc_final: 0.5640 (mt-10) REVERT: G 114 TYR cc_start: 0.8978 (p90) cc_final: 0.8328 (p90) REVERT: I 13 MET cc_start: 0.4663 (ttm) cc_final: 0.4216 (ttm) REVERT: I 17 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7905 (mt) REVERT: I 114 TYR cc_start: 0.8973 (p90) cc_final: 0.8600 (p90) REVERT: H 31 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.6919 (p-80) REVERT: H 114 TYR cc_start: 0.9025 (p90) cc_final: 0.8737 (p90) REVERT: J 15 LYS cc_start: 0.6874 (mttt) cc_final: 0.6472 (mttm) REVERT: J 84 ILE cc_start: 0.8002 (tp) cc_final: 0.7746 (tp) REVERT: K 114 TYR cc_start: 0.9039 (p90) cc_final: 0.8634 (p90) REVERT: K 117 SER cc_start: 0.9091 (m) cc_final: 0.8840 (m) REVERT: M 30 MET cc_start: 0.8595 (ptm) cc_final: 0.5719 (mmt) REVERT: M 35 LYS cc_start: 0.7634 (tmtt) cc_final: 0.6947 (mtpt) REVERT: M 114 TYR cc_start: 0.8424 (p90) cc_final: 0.8106 (p90) REVERT: L 62 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7237 (tm-30) REVERT: L 114 TYR cc_start: 0.8953 (p90) cc_final: 0.8470 (p90) REVERT: N 13 MET cc_start: 0.6524 (ttm) cc_final: 0.6188 (ttm) REVERT: N 17 LEU cc_start: 0.7948 (mm) cc_final: 0.7676 (mt) REVERT: N 30 MET cc_start: 0.8354 (ptm) cc_final: 0.6192 (mmp) REVERT: N 62 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7105 (tm-30) REVERT: N 117 SER cc_start: 0.8418 (m) cc_final: 0.8189 (m) REVERT: A 15 LYS cc_start: 0.6941 (mttt) cc_final: 0.6656 (mttm) REVERT: C 114 TYR cc_start: 0.9001 (p90) cc_final: 0.8621 (p90) REVERT: E 79 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.7967 (t60) REVERT: D 114 TYR cc_start: 0.9048 (p90) cc_final: 0.8508 (p90) REVERT: F 13 MET cc_start: 0.4237 (ttm) cc_final: 0.3899 (ttm) REVERT: F 15 LYS cc_start: 0.6894 (mttt) cc_final: 0.6651 (mttm) REVERT: F 74 ASP cc_start: 0.8767 (t0) cc_final: 0.8243 (t0) outliers start: 38 outliers final: 19 residues processed: 337 average time/residue: 0.0776 time to fit residues: 39.5345 Evaluate side-chains 331 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 309 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 79 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 101 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 122 optimal weight: 0.0050 chunk 114 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 70 optimal weight: 0.1980 chunk 42 optimal weight: 20.0000 chunk 112 optimal weight: 9.9990 overall best weight: 3.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 HIS B 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.173548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.142725 restraints weight = 11814.072| |-----------------------------------------------------------------------------| r_work (start): 0.4558 rms_B_bonded: 2.84 r_work: 0.4417 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10304 Z= 0.199 Angle : 0.602 8.866 14000 Z= 0.314 Chirality : 0.050 0.167 1638 Planarity : 0.003 0.028 1722 Dihedral : 5.673 20.430 1386 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.66 % Allowed : 15.93 % Favored : 80.40 % 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: -3.73 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 34 TYR 0.013 0.001 TYR A 114 PHE 0.012 0.002 PHE D 64 TRP 0.006 0.001 TRP N 79 HIS 0.021 0.003 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00447 (10304) covalent geometry : angle 0.60175 (14000) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 114 TYR cc_start: 0.8985 (p90) cc_final: 0.8384 (p90) REVERT: I 13 MET cc_start: 0.4299 (ttm) cc_final: 0.3911 (ttm) REVERT: H 31 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.6889 (p-80) REVERT: H 74 ASP cc_start: 0.8476 (t70) cc_final: 0.8261 (t0) REVERT: H 114 TYR cc_start: 0.9020 (p90) cc_final: 0.8657 (p90) REVERT: J 15 LYS cc_start: 0.6832 (mttt) cc_final: 0.6256 (mttm) REVERT: J 74 ASP cc_start: 0.8741 (t0) cc_final: 0.8446 (t0) REVERT: K 15 LYS cc_start: 0.7072 (mttt) cc_final: 0.6811 (mttp) REVERT: K 17 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7964 (mt) REVERT: K 114 TYR cc_start: 0.9037 (p90) cc_final: 0.8651 (p90) REVERT: K 117 SER cc_start: 0.9019 (m) cc_final: 0.8774 (m) REVERT: M 30 MET cc_start: 0.8534 (ptm) cc_final: 0.5758 (mmt) REVERT: M 35 LYS cc_start: 0.7688 (tmtt) cc_final: 0.6812 (mtmt) REVERT: M 114 TYR cc_start: 0.8431 (p90) cc_final: 0.8025 (p90) REVERT: L 17 LEU cc_start: 0.8309 (mm) cc_final: 0.8087 (mt) REVERT: N 13 MET cc_start: 0.6427 (ttm) cc_final: 0.6189 (ttm) REVERT: N 17 LEU cc_start: 0.7868 (mm) cc_final: 0.7626 (mt) REVERT: N 30 MET cc_start: 0.8402 (ptm) cc_final: 0.6090 (mmt) REVERT: N 35 LYS cc_start: 0.7445 (mttt) cc_final: 0.6988 (mmtp) REVERT: N 62 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7278 (tm-30) REVERT: N 70 LYS cc_start: 0.8360 (ttmt) cc_final: 0.8107 (ttpt) REVERT: A 15 LYS cc_start: 0.7013 (mttt) cc_final: 0.6764 (mttm) REVERT: A 74 ASP cc_start: 0.8000 (t70) cc_final: 0.7570 (t0) REVERT: B 31 HIS cc_start: 0.7038 (OUTLIER) cc_final: 0.4720 (m-70) REVERT: C 114 TYR cc_start: 0.8974 (p90) cc_final: 0.8742 (p90) REVERT: E 66 GLU cc_start: 0.7302 (tp30) cc_final: 0.6848 (tp30) REVERT: E 79 TRP cc_start: 0.9012 (OUTLIER) cc_final: 0.8396 (t60) REVERT: D 15 LYS cc_start: 0.6432 (mttt) cc_final: 0.6224 (mttm) REVERT: D 114 TYR cc_start: 0.8984 (p90) cc_final: 0.8499 (p90) REVERT: F 74 ASP cc_start: 0.8971 (t0) cc_final: 0.8215 (t0) outliers start: 40 outliers final: 20 residues processed: 328 average time/residue: 0.0713 time to fit residues: 35.4314 Evaluate side-chains 327 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 303 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain B residue 31 HIS Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 79 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 75 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 9 optimal weight: 20.0000 overall best weight: 4.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS B 31 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.171072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.140245 restraints weight = 11902.042| |-----------------------------------------------------------------------------| r_work (start): 0.4555 rms_B_bonded: 2.83 r_work: 0.4427 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10304 Z= 0.206 Angle : 0.596 6.781 14000 Z= 0.310 Chirality : 0.050 0.162 1638 Planarity : 0.003 0.032 1722 Dihedral : 5.668 19.364 1386 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.75 % Allowed : 17.86 % 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: -3.75 (0.19), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 34 TYR 0.014 0.001 TYR E 105 PHE 0.011 0.002 PHE J 64 TRP 0.005 0.001 TRP N 79 HIS 0.018 0.003 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00461 (10304) covalent geometry : angle 0.59605 (14000) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 322 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: G 82 LEU cc_start: 0.8741 (tp) cc_final: 0.8218 (mm) REVERT: G 114 TYR cc_start: 0.8969 (p90) cc_final: 0.8294 (p90) REVERT: I 13 MET cc_start: 0.4286 (ttm) cc_final: 0.3896 (ttm) REVERT: I 82 LEU cc_start: 0.8812 (tp) cc_final: 0.8515 (tp) REVERT: H 31 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6862 (p-80) REVERT: H 82 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8165 (mm) REVERT: H 114 TYR cc_start: 0.9020 (p90) cc_final: 0.8688 (p90) REVERT: J 15 LYS cc_start: 0.6701 (mttt) cc_final: 0.6318 (mttm) REVERT: J 66 GLU cc_start: 0.7580 (tp30) cc_final: 0.7065 (tp30) REVERT: K 15 LYS cc_start: 0.6985 (mttt) cc_final: 0.6730 (mttp) REVERT: K 114 TYR cc_start: 0.9040 (p90) cc_final: 0.8665 (p90) REVERT: K 117 SER cc_start: 0.8993 (m) cc_final: 0.8781 (m) REVERT: M 35 LYS cc_start: 0.7666 (tmtt) cc_final: 0.6776 (mtmt) REVERT: M 114 TYR cc_start: 0.8405 (p90) cc_final: 0.7988 (p90) REVERT: N 13 MET cc_start: 0.6421 (ttm) cc_final: 0.6206 (ttm) REVERT: N 17 LEU cc_start: 0.7980 (mm) cc_final: 0.7733 (mt) REVERT: N 30 MET cc_start: 0.8471 (ptm) cc_final: 0.6053 (mmt) REVERT: N 35 LYS cc_start: 0.7335 (mttt) cc_final: 0.6863 (mmtp) REVERT: N 62 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7383 (tm-30) REVERT: N 70 LYS cc_start: 0.8475 (ttmt) cc_final: 0.8220 (ttmt) REVERT: A 15 LYS cc_start: 0.7148 (mttt) cc_final: 0.6867 (mttp) REVERT: A 74 ASP cc_start: 0.7886 (t70) cc_final: 0.7516 (t0) REVERT: C 66 GLU cc_start: 0.7411 (mm-30) cc_final: 0.7158 (tp30) REVERT: C 114 TYR cc_start: 0.8980 (p90) cc_final: 0.8611 (p90) REVERT: E 79 TRP cc_start: 0.9024 (OUTLIER) cc_final: 0.8537 (t60) REVERT: E 114 TYR cc_start: 0.9032 (p90) cc_final: 0.8508 (p90) REVERT: D 99 ASP cc_start: 0.8363 (t0) cc_final: 0.8049 (t0) REVERT: D 114 TYR cc_start: 0.9013 (p90) cc_final: 0.8511 (p90) REVERT: F 74 ASP cc_start: 0.8967 (t70) cc_final: 0.8259 (t0) outliers start: 30 outliers final: 20 residues processed: 327 average time/residue: 0.0756 time to fit residues: 37.4851 Evaluate side-chains 326 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 79 TRP Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 84 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 72 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 overall best weight: 5.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.167057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.136675 restraints weight = 12028.937| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 2.79 r_work: 0.4396 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10304 Z= 0.253 Angle : 0.639 11.934 14000 Z= 0.329 Chirality : 0.052 0.272 1638 Planarity : 0.003 0.038 1722 Dihedral : 5.797 20.739 1386 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.11 % Allowed : 18.77 % Favored : 78.11 % 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: -3.82 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 34 TYR 0.014 0.001 TYR A 114 PHE 0.012 0.002 PHE D 64 TRP 0.004 0.001 TRP C 79 HIS 0.019 0.003 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00565 (10304) covalent geometry : angle 0.63940 (14000) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 319 time to evaluate : 0.413 Fit side-chains REVERT: G 82 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8169 (mm) REVERT: G 114 TYR cc_start: 0.8923 (p90) cc_final: 0.8311 (p90) REVERT: I 13 MET cc_start: 0.4263 (ttm) cc_final: 0.3863 (ttm) REVERT: I 82 LEU cc_start: 0.8897 (tp) cc_final: 0.8666 (tp) REVERT: H 17 LEU cc_start: 0.7670 (mm) cc_final: 0.7277 (mp) REVERT: H 31 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6830 (p-80) REVERT: H 66 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7462 (tp30) REVERT: H 82 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8059 (mm) REVERT: J 15 LYS cc_start: 0.6820 (mttt) cc_final: 0.6412 (mttm) REVERT: K 82 LEU cc_start: 0.8867 (tp) cc_final: 0.8560 (tp) REVERT: K 114 TYR cc_start: 0.9013 (p90) cc_final: 0.8600 (p90) REVERT: K 117 SER cc_start: 0.9052 (m) cc_final: 0.8829 (m) REVERT: M 35 LYS cc_start: 0.7713 (tmtt) cc_final: 0.6894 (mtmt) REVERT: M 114 TYR cc_start: 0.8417 (p90) cc_final: 0.7983 (p90) REVERT: N 13 MET cc_start: 0.6404 (ttm) cc_final: 0.6177 (ttm) REVERT: N 30 MET cc_start: 0.8669 (ptm) cc_final: 0.6152 (mmt) REVERT: N 35 LYS cc_start: 0.7200 (mttt) cc_final: 0.6785 (mmtp) REVERT: N 70 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8212 (tttt) REVERT: N 114 TYR cc_start: 0.8445 (p90) cc_final: 0.8069 (p90) REVERT: A 15 LYS cc_start: 0.7105 (mttt) cc_final: 0.6670 (mttp) REVERT: A 74 ASP cc_start: 0.8047 (t70) cc_final: 0.7791 (t0) REVERT: C 17 LEU cc_start: 0.8003 (mm) cc_final: 0.7747 (mm) REVERT: C 66 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7183 (tp30) REVERT: C 82 LEU cc_start: 0.8788 (tp) cc_final: 0.8200 (mm) REVERT: C 114 TYR cc_start: 0.9070 (p90) cc_final: 0.8739 (p90) REVERT: D 114 TYR cc_start: 0.9011 (p90) cc_final: 0.8537 (p90) REVERT: F 66 GLU cc_start: 0.7823 (tp30) cc_final: 0.7602 (tp30) REVERT: F 74 ASP cc_start: 0.8978 (t70) cc_final: 0.8551 (t0) outliers start: 34 outliers final: 20 residues processed: 323 average time/residue: 0.0772 time to fit residues: 38.0075 Evaluate side-chains 326 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 303 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 7 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.165055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.135165 restraints weight = 12278.826| |-----------------------------------------------------------------------------| r_work (start): 0.4511 rms_B_bonded: 2.80 r_work: 0.4360 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10304 Z= 0.265 Angle : 0.657 14.411 14000 Z= 0.333 Chirality : 0.052 0.191 1638 Planarity : 0.003 0.038 1722 Dihedral : 5.884 22.167 1386 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.75 % Allowed : 19.87 % Favored : 77.38 % 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: -3.93 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 34 TYR 0.019 0.002 TYR H 114 PHE 0.020 0.002 PHE F 33 TRP 0.004 0.001 TRP D 79 HIS 0.017 0.002 HIS F 31 Details of bonding type rmsd covalent geometry : bond 0.00589 (10304) covalent geometry : angle 0.65707 (14000) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 317 time to evaluate : 0.349 Fit side-chains REVERT: G 74 ASP cc_start: 0.8881 (t70) cc_final: 0.8628 (t0) REVERT: G 114 TYR cc_start: 0.8956 (p90) cc_final: 0.8467 (p90) REVERT: I 13 MET cc_start: 0.4244 (ttm) cc_final: 0.3850 (ttm) REVERT: I 74 ASP cc_start: 0.8691 (t0) cc_final: 0.8411 (t0) REVERT: H 31 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6787 (p-80) REVERT: H 66 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7494 (tp30) REVERT: H 82 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8140 (mm) REVERT: H 114 TYR cc_start: 0.9014 (p90) cc_final: 0.8792 (p90) REVERT: J 15 LYS cc_start: 0.6782 (mttt) cc_final: 0.6333 (mttm) REVERT: J 82 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7978 (mm) REVERT: K 15 LYS cc_start: 0.7106 (mttt) cc_final: 0.6817 (mttp) REVERT: K 82 LEU cc_start: 0.8874 (tp) cc_final: 0.8633 (tp) REVERT: K 114 TYR cc_start: 0.9018 (p90) cc_final: 0.8474 (p90) REVERT: K 117 SER cc_start: 0.9079 (m) cc_final: 0.8662 (m) REVERT: M 35 LYS cc_start: 0.7558 (tmtt) cc_final: 0.6790 (mtmt) REVERT: M 66 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7024 (tp30) REVERT: M 74 ASP cc_start: 0.9048 (t0) cc_final: 0.8735 (t0) REVERT: M 105 TYR cc_start: 0.8517 (m-80) cc_final: 0.8257 (m-80) REVERT: M 114 TYR cc_start: 0.8409 (p90) cc_final: 0.7922 (p90) REVERT: N 13 MET cc_start: 0.6417 (ttm) cc_final: 0.6193 (ttm) REVERT: N 30 MET cc_start: 0.8805 (ptm) cc_final: 0.6234 (mmt) REVERT: N 114 TYR cc_start: 0.8407 (p90) cc_final: 0.8027 (p90) REVERT: A 15 LYS cc_start: 0.7016 (mttt) cc_final: 0.6772 (mttp) REVERT: A 74 ASP cc_start: 0.8075 (t70) cc_final: 0.7749 (t0) REVERT: B 33 PHE cc_start: 0.6289 (t80) cc_final: 0.5982 (t80) REVERT: B 74 ASP cc_start: 0.8013 (t70) cc_final: 0.7810 (t0) REVERT: C 82 LEU cc_start: 0.9042 (tp) cc_final: 0.8391 (mm) REVERT: C 114 TYR cc_start: 0.9088 (p90) cc_final: 0.8751 (p90) REVERT: E 85 SER cc_start: 0.8866 (t) cc_final: 0.8659 (p) REVERT: D 66 GLU cc_start: 0.8003 (tp30) cc_final: 0.7591 (tp30) REVERT: D 114 TYR cc_start: 0.9027 (p90) cc_final: 0.8510 (p90) REVERT: F 74 ASP cc_start: 0.8927 (t70) cc_final: 0.8546 (t0) outliers start: 30 outliers final: 22 residues processed: 322 average time/residue: 0.0743 time to fit residues: 36.6615 Evaluate side-chains 330 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 305 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 30 MET Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain M residue 31 HIS Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 76 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 0.0270 chunk 78 optimal weight: 6.9990 overall best weight: 3.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.168699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.138693 restraints weight = 12122.351| |-----------------------------------------------------------------------------| r_work (start): 0.4560 rms_B_bonded: 2.83 r_work: 0.4413 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10304 Z= 0.183 Angle : 0.631 13.901 14000 Z= 0.317 Chirality : 0.051 0.162 1638 Planarity : 0.003 0.037 1722 Dihedral : 5.764 20.896 1386 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.47 % Allowed : 20.97 % Favored : 76.56 % 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: -3.93 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 34 TYR 0.016 0.001 TYR H 114 PHE 0.013 0.002 PHE B 33 TRP 0.006 0.001 TRP C 79 HIS 0.018 0.002 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00417 (10304) covalent geometry : angle 0.63080 (14000) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: G 74 ASP cc_start: 0.8855 (t70) cc_final: 0.8510 (t0) REVERT: G 82 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8398 (mm) REVERT: G 114 TYR cc_start: 0.8944 (p90) cc_final: 0.8486 (p90) REVERT: I 13 MET cc_start: 0.4302 (ttm) cc_final: 0.3898 (ttm) REVERT: H 31 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6825 (p-80) REVERT: H 82 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8268 (mm) REVERT: H 114 TYR cc_start: 0.9053 (p90) cc_final: 0.8787 (p90) REVERT: J 15 LYS cc_start: 0.6859 (mttt) cc_final: 0.6448 (mttm) REVERT: J 66 GLU cc_start: 0.7649 (tp30) cc_final: 0.7150 (tp30) REVERT: J 82 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8213 (mm) REVERT: K 15 LYS cc_start: 0.7069 (mttt) cc_final: 0.6830 (mttp) REVERT: K 66 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: K 70 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7980 (ttmt) REVERT: K 114 TYR cc_start: 0.8990 (p90) cc_final: 0.8527 (p90) REVERT: K 117 SER cc_start: 0.9016 (m) cc_final: 0.8611 (m) REVERT: M 66 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7351 (tp30) REVERT: M 74 ASP cc_start: 0.8930 (t0) cc_final: 0.8613 (t0) REVERT: M 105 TYR cc_start: 0.8503 (m-80) cc_final: 0.8165 (m-80) REVERT: M 114 TYR cc_start: 0.8435 (p90) cc_final: 0.8001 (p90) REVERT: L 114 TYR cc_start: 0.8825 (p90) cc_final: 0.8620 (p90) REVERT: N 13 MET cc_start: 0.6406 (ttm) cc_final: 0.6168 (ttm) REVERT: N 35 LYS cc_start: 0.7020 (mmtt) cc_final: 0.6487 (mmtp) REVERT: N 66 GLU cc_start: 0.6547 (mt-10) cc_final: 0.6250 (mt-10) REVERT: N 114 TYR cc_start: 0.8418 (p90) cc_final: 0.8084 (p90) REVERT: A 15 LYS cc_start: 0.7109 (mttt) cc_final: 0.6849 (mttp) REVERT: A 74 ASP cc_start: 0.8142 (t70) cc_final: 0.7798 (t0) REVERT: B 74 ASP cc_start: 0.8040 (t70) cc_final: 0.7813 (t0) REVERT: C 66 GLU cc_start: 0.7749 (mm-30) cc_final: 0.6996 (tp30) REVERT: C 70 LYS cc_start: 0.8369 (ttmt) cc_final: 0.8131 (ttpt) REVERT: C 82 LEU cc_start: 0.8998 (tp) cc_final: 0.8381 (mm) REVERT: C 114 TYR cc_start: 0.9070 (p90) cc_final: 0.8703 (p90) REVERT: E 85 SER cc_start: 0.8877 (t) cc_final: 0.8655 (p) REVERT: D 66 GLU cc_start: 0.7954 (tp30) cc_final: 0.7257 (tp30) REVERT: D 114 TYR cc_start: 0.9019 (p90) cc_final: 0.8548 (p90) REVERT: F 74 ASP cc_start: 0.8927 (t70) cc_final: 0.8583 (t0) outliers start: 27 outliers final: 19 residues processed: 320 average time/residue: 0.0771 time to fit residues: 37.4988 Evaluate side-chains 324 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 300 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 56 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.166335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.136009 restraints weight = 12218.147| |-----------------------------------------------------------------------------| r_work (start): 0.4545 rms_B_bonded: 2.88 r_work: 0.4409 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10304 Z= 0.235 Angle : 0.647 13.374 14000 Z= 0.328 Chirality : 0.052 0.176 1638 Planarity : 0.003 0.036 1722 Dihedral : 5.831 20.533 1386 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.02 % Allowed : 20.79 % Favored : 76.19 % 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: -3.99 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 34 TYR 0.017 0.001 TYR H 114 PHE 0.017 0.002 PHE H 64 TRP 0.004 0.001 TRP C 79 HIS 0.017 0.002 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00529 (10304) covalent geometry : angle 0.64674 (14000) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 308 time to evaluate : 0.410 Fit side-chains revert: symmetry clash REVERT: G 74 ASP cc_start: 0.8883 (t70) cc_final: 0.8550 (t0) REVERT: G 82 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8263 (mm) REVERT: G 114 TYR cc_start: 0.8908 (p90) cc_final: 0.8472 (p90) REVERT: I 13 MET cc_start: 0.4161 (ttm) cc_final: 0.3768 (ttm) REVERT: H 31 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6855 (p-80) REVERT: H 82 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8301 (mm) REVERT: H 114 TYR cc_start: 0.8998 (p90) cc_final: 0.8709 (p90) REVERT: J 15 LYS cc_start: 0.6759 (mttt) cc_final: 0.6327 (mttm) REVERT: J 66 GLU cc_start: 0.7710 (tp30) cc_final: 0.7210 (tp30) REVERT: J 82 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8055 (mm) REVERT: K 15 LYS cc_start: 0.6969 (mttt) cc_final: 0.6743 (mttp) REVERT: K 114 TYR cc_start: 0.8921 (p90) cc_final: 0.8245 (p90) REVERT: K 117 SER cc_start: 0.9011 (m) cc_final: 0.8617 (m) REVERT: M 114 TYR cc_start: 0.8378 (p90) cc_final: 0.7923 (p90) REVERT: L 70 LYS cc_start: 0.8560 (ttmt) cc_final: 0.7887 (ttmt) REVERT: L 114 TYR cc_start: 0.8798 (p90) cc_final: 0.8572 (p90) REVERT: N 13 MET cc_start: 0.6446 (ttm) cc_final: 0.6193 (ttm) REVERT: N 30 MET cc_start: 0.8765 (ptp) cc_final: 0.5912 (mmt) REVERT: N 35 LYS cc_start: 0.7063 (mmtt) cc_final: 0.6470 (mmtp) REVERT: N 66 GLU cc_start: 0.6605 (mt-10) cc_final: 0.5510 (mt-10) REVERT: N 114 TYR cc_start: 0.8392 (p90) cc_final: 0.8042 (p90) REVERT: A 15 LYS cc_start: 0.7011 (mttt) cc_final: 0.6764 (mttp) REVERT: A 74 ASP cc_start: 0.8209 (t70) cc_final: 0.7835 (t0) REVERT: B 74 ASP cc_start: 0.8009 (t70) cc_final: 0.7769 (t0) REVERT: C 66 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7465 (mm-30) REVERT: C 82 LEU cc_start: 0.9000 (tp) cc_final: 0.8358 (mm) REVERT: C 114 TYR cc_start: 0.9006 (p90) cc_final: 0.8639 (p90) REVERT: E 85 SER cc_start: 0.8839 (t) cc_final: 0.8621 (p) REVERT: D 66 GLU cc_start: 0.7823 (tp30) cc_final: 0.7319 (tp30) REVERT: F 66 GLU cc_start: 0.7549 (tp30) cc_final: 0.7329 (tp30) REVERT: F 74 ASP cc_start: 0.8915 (t70) cc_final: 0.8585 (t0) outliers start: 33 outliers final: 26 residues processed: 317 average time/residue: 0.0761 time to fit residues: 36.6646 Evaluate side-chains 325 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 295 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 90 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 20.0000 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.168022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.137965 restraints weight = 12122.130| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 2.78 r_work: 0.4419 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10304 Z= 0.204 Angle : 0.656 13.756 14000 Z= 0.330 Chirality : 0.051 0.173 1638 Planarity : 0.003 0.037 1722 Dihedral : 5.805 20.482 1386 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.02 % Allowed : 20.79 % Favored : 76.19 % 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: -4.03 (0.18), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 34 TYR 0.015 0.001 TYR H 114 PHE 0.018 0.002 PHE F 33 TRP 0.005 0.001 TRP C 79 HIS 0.019 0.002 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00462 (10304) covalent geometry : angle 0.65592 (14000) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 290 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: G 74 ASP cc_start: 0.8857 (t70) cc_final: 0.8555 (t0) REVERT: G 82 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8299 (mm) REVERT: G 114 TYR cc_start: 0.8930 (p90) cc_final: 0.8532 (p90) REVERT: I 13 MET cc_start: 0.4206 (ttm) cc_final: 0.3800 (ttm) REVERT: H 31 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.6902 (p-80) REVERT: H 82 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8291 (mm) REVERT: H 114 TYR cc_start: 0.9017 (p90) cc_final: 0.8749 (p90) REVERT: J 15 LYS cc_start: 0.6823 (mttt) cc_final: 0.6462 (mttm) REVERT: J 66 GLU cc_start: 0.7695 (tp30) cc_final: 0.7154 (tp30) REVERT: J 82 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8052 (mm) REVERT: K 66 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7309 (mm-30) REVERT: K 70 LYS cc_start: 0.8435 (ttmt) cc_final: 0.8109 (ttmt) REVERT: K 114 TYR cc_start: 0.8921 (p90) cc_final: 0.8266 (p90) REVERT: K 117 SER cc_start: 0.9010 (m) cc_final: 0.8621 (m) REVERT: M 114 TYR cc_start: 0.8395 (p90) cc_final: 0.7990 (p90) REVERT: L 70 LYS cc_start: 0.8560 (ttmt) cc_final: 0.7898 (ttmt) REVERT: L 114 TYR cc_start: 0.8812 (p90) cc_final: 0.8591 (p90) REVERT: N 13 MET cc_start: 0.6448 (ttm) cc_final: 0.6195 (ttm) REVERT: N 30 MET cc_start: 0.8773 (ptp) cc_final: 0.5943 (mmt) REVERT: N 35 LYS cc_start: 0.7096 (mmtt) cc_final: 0.6516 (mmtp) REVERT: N 66 GLU cc_start: 0.6605 (mt-10) cc_final: 0.5647 (mt-10) REVERT: N 114 TYR cc_start: 0.8414 (p90) cc_final: 0.8090 (p90) REVERT: A 15 LYS cc_start: 0.7090 (mttt) cc_final: 0.6843 (mttp) REVERT: A 74 ASP cc_start: 0.8210 (t70) cc_final: 0.7869 (t0) REVERT: B 74 ASP cc_start: 0.8031 (t70) cc_final: 0.7801 (t0) REVERT: C 82 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8342 (mm) REVERT: C 114 TYR cc_start: 0.9006 (p90) cc_final: 0.8606 (p90) REVERT: E 85 SER cc_start: 0.8894 (t) cc_final: 0.8647 (p) REVERT: D 66 GLU cc_start: 0.7668 (tp30) cc_final: 0.7259 (tp30) REVERT: D 114 TYR cc_start: 0.9004 (p90) cc_final: 0.8506 (p90) REVERT: F 74 ASP cc_start: 0.8883 (t70) cc_final: 0.8608 (t0) outliers start: 33 outliers final: 26 residues processed: 301 average time/residue: 0.0757 time to fit residues: 34.7990 Evaluate side-chains 316 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 31 HIS Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 16 VAL Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 106 THR Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 chunk 105 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 90 optimal weight: 30.0000 chunk 35 optimal weight: 20.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.160857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.131274 restraints weight = 12450.753| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 2.79 r_work: 0.4352 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 10304 Z= 0.367 Angle : 0.748 13.583 14000 Z= 0.384 Chirality : 0.054 0.184 1638 Planarity : 0.004 0.035 1722 Dihedral : 6.240 23.827 1386 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 3.11 % Allowed : 20.70 % Favored : 76.19 % 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: -4.16 (0.17), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 34 TYR 0.020 0.002 TYR H 114 PHE 0.021 0.003 PHE F 64 TRP 0.003 0.001 TRP G 79 HIS 0.019 0.003 HIS I 31 Details of bonding type rmsd covalent geometry : bond 0.00820 (10304) covalent geometry : angle 0.74800 (14000) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 321 time to evaluate : 0.304 Fit side-chains REVERT: G 74 ASP cc_start: 0.8921 (t70) cc_final: 0.8631 (t0) REVERT: G 82 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8271 (mm) REVERT: I 13 MET cc_start: 0.4282 (ttm) cc_final: 0.3837 (ttm) REVERT: H 82 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8219 (mm) REVERT: J 15 LYS cc_start: 0.6909 (mttt) cc_final: 0.6515 (mttm) REVERT: J 66 GLU cc_start: 0.7714 (tp30) cc_final: 0.7219 (tp30) REVERT: K 15 LYS cc_start: 0.7093 (mttt) cc_final: 0.6803 (mttp) REVERT: L 70 LYS cc_start: 0.8613 (ttmt) cc_final: 0.7986 (ttmt) REVERT: N 13 MET cc_start: 0.6374 (ttm) cc_final: 0.6062 (ttm) REVERT: N 30 MET cc_start: 0.8766 (ptp) cc_final: 0.5905 (mmp) REVERT: N 35 LYS cc_start: 0.7039 (mmtt) cc_final: 0.6391 (mmtp) REVERT: N 66 GLU cc_start: 0.6622 (mt-10) cc_final: 0.5878 (mt-10) REVERT: A 15 LYS cc_start: 0.7112 (mttt) cc_final: 0.6903 (mttp) REVERT: A 33 PHE cc_start: 0.6375 (t80) cc_final: 0.6117 (t80) REVERT: A 74 ASP cc_start: 0.8228 (t70) cc_final: 0.7849 (t0) REVERT: B 33 PHE cc_start: 0.6417 (t80) cc_final: 0.6162 (t80) REVERT: B 74 ASP cc_start: 0.7916 (t70) cc_final: 0.7651 (t0) REVERT: E 17 LEU cc_start: 0.8462 (mm) cc_final: 0.8252 (mp) REVERT: E 85 SER cc_start: 0.8902 (t) cc_final: 0.8595 (p) REVERT: D 66 GLU cc_start: 0.7709 (tp30) cc_final: 0.7234 (tp30) REVERT: F 74 ASP cc_start: 0.8878 (t70) cc_final: 0.8570 (t0) outliers start: 34 outliers final: 29 residues processed: 331 average time/residue: 0.0734 time to fit residues: 37.2446 Evaluate side-chains 343 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 312 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 106 THR Chi-restraints excluded: chain I residue 117 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain J residue 31 HIS Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 106 THR Chi-restraints excluded: chain J residue 117 SER Chi-restraints excluded: chain J residue 121 VAL Chi-restraints excluded: chain K residue 66 GLU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 117 SER Chi-restraints excluded: chain L residue 60 THR Chi-restraints excluded: chain L residue 117 SER Chi-restraints excluded: chain N residue 31 HIS Chi-restraints excluded: chain N residue 117 SER Chi-restraints excluded: chain A residue 117 SER Chi-restraints excluded: chain B residue 117 SER Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 SER Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 65 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.164016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.133930 restraints weight = 12391.891| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 2.86 r_work: 0.4382 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.4382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 10304 Z= 0.268 Angle : 0.717 13.677 14000 Z= 0.362 Chirality : 0.054 0.195 1638 Planarity : 0.003 0.037 1722 Dihedral : 6.134 22.444 1386 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.93 % Allowed : 21.52 % Favored : 75.55 % 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: -4.16 (0.17), residues: 1232 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.13), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 34 TYR 0.020 0.002 TYR G 114 PHE 0.019 0.002 PHE D 33 TRP 0.005 0.001 TRP F 79 HIS 0.019 0.003 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00602 (10304) covalent geometry : angle 0.71730 (14000) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1952.11 seconds wall clock time: 34 minutes 36.13 seconds (2076.13 seconds total)