Starting phenix.real_space_refine on Thu Feb 5 07:36:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n94_49159/02_2026/9n94_49159_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n94_49159/02_2026/9n94_49159.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n94_49159/02_2026/9n94_49159_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n94_49159/02_2026/9n94_49159_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n94_49159/02_2026/9n94_49159.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n94_49159/02_2026/9n94_49159.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.036 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 72 5.16 5 C 10240 2.51 5 N 2907 2.21 5 O 3075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16294 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "B" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "C" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "D" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "E" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "G" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "H" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "I" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 678 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "J" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 678 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "K" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 678 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "L" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 678 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "M" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "N" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 683 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 83} Chain: "O" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 678 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "P" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 678 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "Q" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 678 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "R" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "S" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "T" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "U" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "V" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "W" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain: "X" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 674 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Time building chain proxies: 3.94, per 1000 atoms: 0.24 Number of scatterers: 16294 At special positions: 0 Unit cell: (100.688, 104.284, 146.537, 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 72 16.00 O 3075 8.00 N 2907 7.00 C 10240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.40 Conformation dependent library (CDL) restraints added in 703.9 milliseconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3860 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 16 through 27 Processing helix chain 'A' and resid 32 through 37 Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.902A pdb=" N LEU A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.770A pdb=" N ARG A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.741A pdb=" N ARG A 78 " --> pdb=" O ASP A 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 32 through 37 removed outlier: 3.591A pdb=" N GLU B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 3.910A pdb=" N LEU B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.874A pdb=" N LEU B 76 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 77 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG B 78 " --> pdb=" O ASP B 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 16 through 27 Processing helix chain 'C' and resid 32 through 37 Processing helix chain 'C' and resid 41 through 52 removed outlier: 3.947A pdb=" N LEU C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 72 through 86 removed outlier: 3.836A pdb=" N LEU C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG C 77 " --> pdb=" O HIS C 73 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG C 78 " --> pdb=" O ASP C 74 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 86 " --> pdb=" O PHE C 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 16 through 27 Processing helix chain 'D' and resid 32 through 37 removed outlier: 3.586A pdb=" N GLU D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 52 removed outlier: 4.019A pdb=" N LEU D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.695A pdb=" N ARG D 78 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 16 through 27 Processing helix chain 'E' and resid 32 through 37 Processing helix chain 'E' and resid 41 through 52 removed outlier: 3.771A pdb=" N LEU E 45 " --> pdb=" O SER E 41 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 52 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 72 through 86 removed outlier: 3.936A pdb=" N LEU E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG E 77 " --> pdb=" O HIS E 73 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E 78 " --> pdb=" O ASP E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 Processing helix chain 'F' and resid 16 through 27 Processing helix chain 'F' and resid 32 through 37 Processing helix chain 'F' and resid 41 through 52 removed outlier: 3.694A pdb=" N LEU F 45 " --> pdb=" O SER F 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N MET F 48 " --> pdb=" O ASP F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 74 through 84 removed outlier: 3.906A pdb=" N ARG F 78 " --> pdb=" O ASP F 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 13 Processing helix chain 'G' and resid 16 through 27 Processing helix chain 'G' and resid 32 through 37 Processing helix chain 'G' and resid 41 through 52 removed outlier: 3.859A pdb=" N LEU G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 72 through 86 removed outlier: 3.860A pdb=" N LEU G 76 " --> pdb=" O ARG G 72 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG G 77 " --> pdb=" O HIS G 73 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG G 78 " --> pdb=" O ASP G 74 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA G 86 " --> pdb=" O PHE G 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 13 Processing helix chain 'H' and resid 16 through 27 Processing helix chain 'H' and resid 32 through 37 removed outlier: 3.539A pdb=" N GLU H 37 " --> pdb=" O LYS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 52 removed outlier: 3.923A pdb=" N LEU H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 72 through 86 removed outlier: 3.817A pdb=" N LEU H 76 " --> pdb=" O ARG H 72 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG H 77 " --> pdb=" O HIS H 73 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 16 through 27 Processing helix chain 'I' and resid 32 through 37 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.915A pdb=" N LEU I 45 " --> pdb=" O SER I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 72 through 85 removed outlier: 3.947A pdb=" N LEU I 76 " --> pdb=" O ARG I 72 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG I 77 " --> pdb=" O HIS I 73 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG I 78 " --> pdb=" O ASP I 74 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY I 85 " --> pdb=" O ASP I 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'J' and resid 16 through 27 Processing helix chain 'J' and resid 32 through 37 removed outlier: 3.587A pdb=" N GLU J 37 " --> pdb=" O LYS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 52 removed outlier: 3.935A pdb=" N LEU J 45 " --> pdb=" O SER J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 72 through 85 removed outlier: 3.942A pdb=" N LEU J 76 " --> pdb=" O ARG J 72 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG J 77 " --> pdb=" O HIS J 73 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG J 78 " --> pdb=" O ASP J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 Processing helix chain 'K' and resid 16 through 27 Processing helix chain 'K' and resid 32 through 37 Processing helix chain 'K' and resid 41 through 52 removed outlier: 3.945A pdb=" N LEU K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 72 through 85 removed outlier: 3.983A pdb=" N LEU K 76 " --> pdb=" O ARG K 72 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG K 77 " --> pdb=" O HIS K 73 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG K 78 " --> pdb=" O ASP K 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 13 Processing helix chain 'L' and resid 16 through 27 Processing helix chain 'L' and resid 32 through 37 Processing helix chain 'L' and resid 41 through 52 removed outlier: 3.902A pdb=" N LEU L 45 " --> pdb=" O SER L 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 71 Processing helix chain 'L' and resid 72 through 85 removed outlier: 3.772A pdb=" N LEU L 76 " --> pdb=" O ARG L 72 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG L 78 " --> pdb=" O ASP L 74 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'M' and resid 16 through 27 Processing helix chain 'M' and resid 32 through 37 Processing helix chain 'M' and resid 41 through 52 removed outlier: 3.933A pdb=" N LEU M 45 " --> pdb=" O SER M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 71 Processing helix chain 'M' and resid 74 through 86 removed outlier: 3.945A pdb=" N ARG M 78 " --> pdb=" O ASP M 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 13 Processing helix chain 'N' and resid 16 through 27 Processing helix chain 'N' and resid 32 through 37 Processing helix chain 'N' and resid 41 through 52 removed outlier: 3.930A pdb=" N LEU N 45 " --> pdb=" O SER N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 60 through 70 Processing helix chain 'N' and resid 74 through 86 removed outlier: 3.842A pdb=" N ARG N 78 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 13 removed outlier: 3.550A pdb=" N VAL O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 27 Processing helix chain 'O' and resid 32 through 37 Processing helix chain 'O' and resid 41 through 52 removed outlier: 3.969A pdb=" N LEU O 45 " --> pdb=" O SER O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 60 through 70 Processing helix chain 'O' and resid 72 through 85 removed outlier: 4.085A pdb=" N LEU O 76 " --> pdb=" O ARG O 72 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG O 77 " --> pdb=" O HIS O 73 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG O 78 " --> pdb=" O ASP O 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 Processing helix chain 'P' and resid 16 through 27 Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 41 through 52 removed outlier: 3.770A pdb=" N LEU P 45 " --> pdb=" O SER P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 70 Processing helix chain 'P' and resid 72 through 85 removed outlier: 3.914A pdb=" N LEU P 76 " --> pdb=" O ARG P 72 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG P 77 " --> pdb=" O HIS P 73 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG P 78 " --> pdb=" O ASP P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 13 Processing helix chain 'Q' and resid 16 through 27 Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.594A pdb=" N GLU Q 37 " --> pdb=" O LYS Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.934A pdb=" N LEU Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 70 Processing helix chain 'Q' and resid 74 through 85 removed outlier: 3.583A pdb=" N ARG Q 78 " --> pdb=" O ASP Q 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'R' and resid 16 through 27 Processing helix chain 'R' and resid 32 through 37 removed outlier: 3.616A pdb=" N GLU R 37 " --> pdb=" O LYS R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 52 removed outlier: 3.888A pdb=" N LEU R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 70 Processing helix chain 'R' and resid 72 through 84 removed outlier: 3.884A pdb=" N LEU R 76 " --> pdb=" O ARG R 72 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 13 Processing helix chain 'S' and resid 16 through 27 Processing helix chain 'S' and resid 32 through 37 Processing helix chain 'S' and resid 41 through 52 removed outlier: 3.834A pdb=" N LEU S 45 " --> pdb=" O SER S 41 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN S 52 " --> pdb=" O MET S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 70 Processing helix chain 'S' and resid 72 through 84 removed outlier: 3.885A pdb=" N LEU S 76 " --> pdb=" O ARG S 72 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG S 77 " --> pdb=" O HIS S 73 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG S 78 " --> pdb=" O ASP S 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 13 Processing helix chain 'T' and resid 16 through 27 Processing helix chain 'T' and resid 32 through 37 Processing helix chain 'T' and resid 41 through 52 removed outlier: 3.863A pdb=" N LEU T 45 " --> pdb=" O SER T 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 60 through 70 Processing helix chain 'T' and resid 74 through 84 removed outlier: 3.892A pdb=" N ARG T 78 " --> pdb=" O ASP T 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 13 Processing helix chain 'U' and resid 16 through 27 Processing helix chain 'U' and resid 32 through 37 removed outlier: 3.560A pdb=" N GLU U 37 " --> pdb=" O LYS U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 52 removed outlier: 3.926A pdb=" N LEU U 45 " --> pdb=" O SER U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 60 through 70 Processing helix chain 'U' and resid 74 through 84 removed outlier: 3.733A pdb=" N ARG U 78 " --> pdb=" O ASP U 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 13 Processing helix chain 'V' and resid 16 through 27 Processing helix chain 'V' and resid 32 through 37 removed outlier: 3.563A pdb=" N GLU V 37 " --> pdb=" O LYS V 33 " (cutoff:3.500A) Processing helix chain 'V' and resid 41 through 52 removed outlier: 4.008A pdb=" N LEU V 45 " --> pdb=" O SER V 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 70 Processing helix chain 'V' and resid 72 through 84 removed outlier: 3.914A pdb=" N LEU V 76 " --> pdb=" O ARG V 72 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG V 77 " --> pdb=" O HIS V 73 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG V 78 " --> pdb=" O ASP V 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 13 Processing helix chain 'W' and resid 16 through 27 Processing helix chain 'W' and resid 32 through 37 Processing helix chain 'W' and resid 41 through 52 removed outlier: 3.782A pdb=" N LEU W 45 " --> pdb=" O SER W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 70 Processing helix chain 'W' and resid 72 through 84 removed outlier: 4.020A pdb=" N LEU W 76 " --> pdb=" O ARG W 72 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG W 77 " --> pdb=" O HIS W 73 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG W 78 " --> pdb=" O ASP W 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 13 Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 32 through 37 Processing helix chain 'X' and resid 41 through 52 removed outlier: 3.857A pdb=" N LEU X 45 " --> pdb=" O SER X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 60 through 70 Processing helix chain 'X' and resid 72 through 84 removed outlier: 3.865A pdb=" N LEU X 76 " --> pdb=" O ARG X 72 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG X 77 " --> pdb=" O HIS X 73 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG X 78 " --> pdb=" O ASP X 74 " (cutoff:3.500A) 923 hydrogen bonds defined for protein. 2769 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4088 1.33 - 1.45: 2696 1.45 - 1.57: 9582 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16486 Sorted by residual: bond pdb=" N GLU E 56 " pdb=" CA GLU E 56 " ideal model delta sigma weight residual 1.453 1.485 -0.033 1.18e-02 7.18e+03 7.69e+00 bond pdb=" N ASP L 2 " pdb=" CA ASP L 2 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.20e-02 6.94e+03 7.20e+00 bond pdb=" N PRO O 3 " pdb=" CD PRO O 3 " ideal model delta sigma weight residual 1.473 1.509 -0.036 1.40e-02 5.10e+03 6.76e+00 bond pdb=" CG PRO O 3 " pdb=" CD PRO O 3 " ideal model delta sigma weight residual 1.503 1.419 0.084 3.40e-02 8.65e+02 6.10e+00 bond pdb=" CA ASN E 53 " pdb=" C ASN E 53 " ideal model delta sigma weight residual 1.523 1.558 -0.036 1.45e-02 4.76e+03 6.01e+00 ... (remaining 16481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 20964 0.99 - 1.98: 897 1.98 - 2.97: 189 2.97 - 3.96: 53 3.96 - 4.95: 12 Bond angle restraints: 22115 Sorted by residual: angle pdb=" CA ASP R 2 " pdb=" CB ASP R 2 " pdb=" CG ASP R 2 " ideal model delta sigma weight residual 112.60 116.96 -4.36 1.00e+00 1.00e+00 1.90e+01 angle pdb=" CA ASP C 2 " pdb=" CB ASP C 2 " pdb=" CG ASP C 2 " ideal model delta sigma weight residual 112.60 116.88 -4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" CA ASP G 2 " pdb=" CB ASP G 2 " pdb=" CG ASP G 2 " ideal model delta sigma weight residual 112.60 116.78 -4.18 1.00e+00 1.00e+00 1.75e+01 angle pdb=" CA ASP T 2 " pdb=" CB ASP T 2 " pdb=" CG ASP T 2 " ideal model delta sigma weight residual 112.60 116.72 -4.12 1.00e+00 1.00e+00 1.70e+01 angle pdb=" CA ASP K 2 " pdb=" CB ASP K 2 " pdb=" CG ASP K 2 " ideal model delta sigma weight residual 112.60 116.51 -3.91 1.00e+00 1.00e+00 1.53e+01 ... (remaining 22110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9285 17.86 - 35.72: 783 35.72 - 53.58: 144 53.58 - 71.44: 26 71.44 - 89.30: 9 Dihedral angle restraints: 10247 sinusoidal: 4368 harmonic: 5879 Sorted by residual: dihedral pdb=" CA MET H 1 " pdb=" C MET H 1 " pdb=" N ASP H 2 " pdb=" CA ASP H 2 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA MET Q 1 " pdb=" C MET Q 1 " pdb=" N ASP Q 2 " pdb=" CA ASP Q 2 " ideal model delta harmonic sigma weight residual 180.00 -161.94 -18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA MET V 1 " pdb=" C MET V 1 " pdb=" N ASP V 2 " pdb=" CA ASP V 2 " ideal model delta harmonic sigma weight residual -180.00 -163.41 -16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 10244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1701 0.034 - 0.067: 743 0.067 - 0.101: 120 0.101 - 0.135: 33 0.135 - 0.168: 5 Chirality restraints: 2602 Sorted by residual: chirality pdb=" CA GLU E 56 " pdb=" N GLU E 56 " pdb=" C GLU E 56 " pdb=" CB GLU E 56 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA MET X 1 " pdb=" N MET X 1 " pdb=" C MET X 1 " pdb=" CB MET X 1 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA MET P 1 " pdb=" N MET P 1 " pdb=" C MET P 1 " pdb=" CB MET P 1 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 2599 not shown) Planarity restraints: 2835 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP O 2 " 0.047 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO O 3 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO O 3 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO O 3 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 56 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.95e+00 pdb=" N PRO A 57 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU G 56 " 0.026 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO G 57 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 57 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 57 " 0.022 5.00e-02 4.00e+02 ... (remaining 2832 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 936 2.74 - 3.28: 14981 3.28 - 3.82: 23324 3.82 - 4.36: 27454 4.36 - 4.90: 51315 Nonbonded interactions: 118010 Sorted by model distance: nonbonded pdb=" NH2 ARG H 64 " pdb=" OE1 GLU H 83 " model vdw 2.195 3.120 nonbonded pdb=" NH2 ARG L 64 " pdb=" OE1 GLU L 83 " model vdw 2.216 3.120 nonbonded pdb=" NH2 ARG A 64 " pdb=" OE1 GLU A 83 " model vdw 2.236 3.120 nonbonded pdb=" NH2 ARG E 64 " pdb=" OE1 GLU E 83 " model vdw 2.236 3.120 nonbonded pdb=" OD1 ASN L 53 " pdb=" OE2 GLU L 56 " model vdw 2.239 3.040 ... (remaining 118005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 84) selection = (chain 'B' and resid 1 through 84) selection = (chain 'C' and resid 1 through 84) selection = (chain 'D' and resid 1 through 84) selection = (chain 'E' and resid 1 through 84) selection = (chain 'F' and resid 1 through 84) selection = (chain 'G' and resid 1 through 84) selection = (chain 'H' and resid 1 through 84) selection = (chain 'I' and resid 1 through 84) selection = (chain 'J' and resid 1 through 84) selection = (chain 'K' and resid 1 through 84) selection = (chain 'L' and resid 1 through 84) selection = (chain 'M' and resid 1 through 84) selection = (chain 'N' and resid 1 through 84) selection = (chain 'O' and resid 1 through 84) selection = (chain 'P' and resid 1 through 84) selection = (chain 'Q' and resid 1 through 84) selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.300 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 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 : 0.003 0.084 16486 Z= 0.190 Angle : 0.500 4.954 22115 Z= 0.306 Chirality : 0.038 0.168 2602 Planarity : 0.004 0.072 2835 Dihedral : 13.548 89.297 6387 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.65 % Favored : 98.20 % Rotamer: Outliers : 0.05 % Allowed : 0.11 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.19), residues: 1995 helix: 1.95 (0.14), residues: 1553 sheet: None (None), residues: 0 loop : -2.08 (0.21), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG O 64 PHE 0.008 0.001 PHE H 82 HIS 0.009 0.001 HIS T 59 Details of bonding type rmsd covalent geometry : bond 0.00344 (16486) covalent geometry : angle 0.50021 (22115) hydrogen bonds : bond 0.14305 ( 923) hydrogen bonds : angle 3.73520 ( 2769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 396 time to evaluate : 0.677 Fit side-chains REVERT: B 35 LYS cc_start: 0.8878 (mttt) cc_final: 0.8662 (mtmt) REVERT: B 71 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7827 (mtm180) REVERT: E 59 HIS cc_start: 0.7035 (m90) cc_final: 0.6722 (m170) REVERT: E 81 ASP cc_start: 0.7803 (m-30) cc_final: 0.7523 (m-30) REVERT: R 71 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8327 (mtt180) REVERT: S 10 SER cc_start: 0.9126 (t) cc_final: 0.8874 (t) REVERT: S 59 HIS cc_start: 0.7862 (m-70) cc_final: 0.7572 (m-70) REVERT: X 71 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7972 (mtt180) outliers start: 1 outliers final: 1 residues processed: 396 average time/residue: 0.2037 time to fit residues: 105.2132 Evaluate side-chains 359 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 1 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN L 53 ASN P 53 ASN X 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.106009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.089281 restraints weight = 22225.307| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.91 r_work: 0.2787 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16486 Z= 0.108 Angle : 0.393 4.078 22115 Z= 0.207 Chirality : 0.035 0.119 2602 Planarity : 0.004 0.041 2835 Dihedral : 3.109 25.177 2214 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.18 % Allowed : 4.43 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.19), residues: 1995 helix: 2.32 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -2.16 (0.20), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG W 71 PHE 0.006 0.001 PHE R 82 HIS 0.003 0.001 HIS T 9 Details of bonding type rmsd covalent geometry : bond 0.00258 (16486) covalent geometry : angle 0.39333 (22115) hydrogen bonds : bond 0.04298 ( 923) hydrogen bonds : angle 2.79848 ( 2769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 359 time to evaluate : 0.687 Fit side-chains REVERT: B 71 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7881 (mtm180) REVERT: B 83 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8318 (mt-10) REVERT: E 81 ASP cc_start: 0.8016 (m-30) cc_final: 0.7731 (m-30) REVERT: P 38 ARG cc_start: 0.8408 (mtt90) cc_final: 0.8034 (mtm-85) REVERT: R 71 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8395 (mtt180) REVERT: S 10 SER cc_start: 0.9147 (t) cc_final: 0.8899 (t) REVERT: W 74 ASP cc_start: 0.8803 (p0) cc_final: 0.8576 (p0) REVERT: X 71 ARG cc_start: 0.8272 (mmm-85) cc_final: 0.7909 (mtt180) outliers start: 22 outliers final: 19 residues processed: 372 average time/residue: 0.1893 time to fit residues: 91.9416 Evaluate side-chains 372 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 353 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 13 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 53 ASN Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 148 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 164 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN H 40 GLN L 53 ASN P 53 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.102701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.085638 restraints weight = 22639.574| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.94 r_work: 0.2775 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16486 Z= 0.112 Angle : 0.388 3.984 22115 Z= 0.202 Chirality : 0.034 0.110 2602 Planarity : 0.004 0.040 2835 Dihedral : 3.053 26.569 2214 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 0.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.23 % Allowed : 5.34 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.19), residues: 1995 helix: 2.53 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -2.10 (0.20), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 30 PHE 0.007 0.001 PHE O 82 HIS 0.003 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00273 (16486) covalent geometry : angle 0.38758 (22115) hydrogen bonds : bond 0.04310 ( 923) hydrogen bonds : angle 2.74527 ( 2769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 359 time to evaluate : 0.689 Fit side-chains REVERT: A 28 LEU cc_start: 0.8836 (tp) cc_final: 0.8551 (tp) REVERT: C 83 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8568 (mt-10) REVERT: E 81 ASP cc_start: 0.8034 (m-30) cc_final: 0.7760 (m-30) REVERT: H 38 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.8220 (mtm-85) REVERT: R 71 ARG cc_start: 0.8629 (mmm-85) cc_final: 0.8411 (mtt180) REVERT: S 10 SER cc_start: 0.9189 (t) cc_final: 0.8934 (t) REVERT: X 71 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.7935 (mtt180) outliers start: 23 outliers final: 20 residues processed: 371 average time/residue: 0.2183 time to fit residues: 104.6733 Evaluate side-chains 375 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 355 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 13 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 12 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 107 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 150 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN L 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.100119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.083027 restraints weight = 22680.882| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.93 r_work: 0.2691 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 16486 Z= 0.189 Angle : 0.497 5.601 22115 Z= 0.249 Chirality : 0.038 0.120 2602 Planarity : 0.004 0.041 2835 Dihedral : 3.298 27.797 2214 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.23 % Allowed : 6.78 % Favored : 91.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.24 (0.19), residues: 1995 helix: 2.38 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -2.16 (0.20), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 64 PHE 0.008 0.001 PHE O 82 HIS 0.005 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00483 (16486) covalent geometry : angle 0.49656 (22115) hydrogen bonds : bond 0.06085 ( 923) hydrogen bonds : angle 3.10107 ( 2769) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 356 time to evaluate : 0.611 Fit side-chains REVERT: B 83 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8305 (mt-10) REVERT: E 81 ASP cc_start: 0.8069 (m-30) cc_final: 0.7750 (m-30) REVERT: H 38 ARG cc_start: 0.8521 (mtm-85) cc_final: 0.8274 (mtm-85) REVERT: R 71 ARG cc_start: 0.8691 (mmm-85) cc_final: 0.8421 (mtt180) REVERT: S 10 SER cc_start: 0.9193 (t) cc_final: 0.8926 (t) REVERT: X 71 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.7937 (mtt180) outliers start: 23 outliers final: 20 residues processed: 369 average time/residue: 0.1887 time to fit residues: 90.4455 Evaluate side-chains 371 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 351 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 13 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 92 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 163 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN L 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.100071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.082867 restraints weight = 22424.542| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 1.93 r_work: 0.2668 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16486 Z= 0.124 Angle : 0.398 3.954 22115 Z= 0.207 Chirality : 0.035 0.112 2602 Planarity : 0.004 0.040 2835 Dihedral : 3.141 26.935 2214 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.18 % Allowed : 7.10 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.19), residues: 1995 helix: 2.54 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -2.07 (0.20), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 30 PHE 0.006 0.001 PHE O 82 HIS 0.004 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00306 (16486) covalent geometry : angle 0.39818 (22115) hydrogen bonds : bond 0.04586 ( 923) hydrogen bonds : angle 2.83937 ( 2769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 352 time to evaluate : 0.539 Fit side-chains REVERT: A 59 HIS cc_start: 0.7932 (m-70) cc_final: 0.7724 (m170) REVERT: B 83 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8196 (mt-10) REVERT: E 81 ASP cc_start: 0.8027 (m-30) cc_final: 0.7754 (m-30) REVERT: H 38 ARG cc_start: 0.8516 (mtm-85) cc_final: 0.8311 (mtm-85) REVERT: R 71 ARG cc_start: 0.8614 (mmm-85) cc_final: 0.8363 (mtt180) REVERT: S 10 SER cc_start: 0.9181 (t) cc_final: 0.8921 (t) REVERT: X 71 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7911 (mtt180) outliers start: 22 outliers final: 20 residues processed: 365 average time/residue: 0.1840 time to fit residues: 87.1672 Evaluate side-chains 370 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 350 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 168 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN L 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.099196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.081885 restraints weight = 22538.422| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 1.94 r_work: 0.2636 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2498 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 16486 Z= 0.151 Angle : 0.431 4.392 22115 Z= 0.221 Chirality : 0.036 0.115 2602 Planarity : 0.004 0.040 2835 Dihedral : 3.171 27.274 2214 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.44 % Allowed : 7.48 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.19), residues: 1995 helix: 2.52 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -2.07 (0.21), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 71 PHE 0.007 0.001 PHE O 82 HIS 0.004 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00382 (16486) covalent geometry : angle 0.43148 (22115) hydrogen bonds : bond 0.05147 ( 923) hydrogen bonds : angle 2.91666 ( 2769) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 349 time to evaluate : 0.656 Fit side-chains REVERT: A 59 HIS cc_start: 0.7892 (m-70) cc_final: 0.7657 (m170) REVERT: B 83 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8154 (mt-10) REVERT: E 81 ASP cc_start: 0.7914 (m-30) cc_final: 0.7605 (m-30) REVERT: H 38 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8230 (mtm-85) REVERT: R 71 ARG cc_start: 0.8575 (mmm-85) cc_final: 0.8318 (mtt180) REVERT: S 10 SER cc_start: 0.9074 (t) cc_final: 0.8804 (t) REVERT: X 71 ARG cc_start: 0.8345 (mmm-85) cc_final: 0.7854 (mtt180) outliers start: 27 outliers final: 23 residues processed: 366 average time/residue: 0.1897 time to fit residues: 90.3654 Evaluate side-chains 370 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 347 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 13 SER Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 163 optimal weight: 0.4980 chunk 156 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 53 ASN L 53 ASN M 9 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.087696 restraints weight = 22322.646| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.83 r_work: 0.2713 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16486 Z= 0.107 Angle : 0.373 4.327 22115 Z= 0.197 Chirality : 0.034 0.109 2602 Planarity : 0.003 0.040 2835 Dihedral : 3.082 26.799 2214 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.12 % Allowed : 8.01 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.19), residues: 1995 helix: 2.66 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -1.96 (0.21), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 30 PHE 0.006 0.001 PHE O 82 HIS 0.003 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00259 (16486) covalent geometry : angle 0.37282 (22115) hydrogen bonds : bond 0.04129 ( 923) hydrogen bonds : angle 2.74788 ( 2769) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 352 time to evaluate : 0.678 Fit side-chains REVERT: E 81 ASP cc_start: 0.8018 (m-30) cc_final: 0.7721 (m-30) REVERT: H 38 ARG cc_start: 0.8473 (mtm-85) cc_final: 0.8189 (mtm-85) REVERT: R 71 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8359 (mtt180) REVERT: S 10 SER cc_start: 0.9200 (t) cc_final: 0.8941 (t) REVERT: X 71 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.7888 (mtt180) outliers start: 21 outliers final: 20 residues processed: 364 average time/residue: 0.1952 time to fit residues: 92.1068 Evaluate side-chains 370 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 350 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 19 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 156 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 53 ASN Q 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.102602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.085973 restraints weight = 22364.719| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.83 r_work: 0.2749 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16486 Z= 0.151 Angle : 0.431 4.294 22115 Z= 0.221 Chirality : 0.036 0.115 2602 Planarity : 0.004 0.040 2835 Dihedral : 3.153 27.352 2214 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 0.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 8.17 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.19), residues: 1995 helix: 2.57 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -1.99 (0.21), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 71 PHE 0.006 0.001 PHE O 82 HIS 0.004 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00381 (16486) covalent geometry : angle 0.43083 (22115) hydrogen bonds : bond 0.05122 ( 923) hydrogen bonds : angle 2.90061 ( 2769) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 346 time to evaluate : 0.629 Fit side-chains REVERT: B 83 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8280 (mt-10) REVERT: E 81 ASP cc_start: 0.8015 (m-30) cc_final: 0.7719 (m-30) REVERT: H 38 ARG cc_start: 0.8472 (mtm-85) cc_final: 0.8266 (mtm-85) REVERT: R 71 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8384 (mtt180) REVERT: S 10 SER cc_start: 0.9173 (t) cc_final: 0.8905 (t) REVERT: X 71 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7887 (mtt180) outliers start: 25 outliers final: 25 residues processed: 361 average time/residue: 0.2040 time to fit residues: 95.2530 Evaluate side-chains 370 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 345 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 53 ASN Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 132 optimal weight: 3.9990 chunk 123 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 135 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 53 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.086135 restraints weight = 22399.341| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.84 r_work: 0.2775 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16486 Z= 0.144 Angle : 0.422 4.558 22115 Z= 0.218 Chirality : 0.035 0.114 2602 Planarity : 0.004 0.039 2835 Dihedral : 3.158 27.118 2214 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 0.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.23 % Allowed : 8.49 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.19), residues: 1995 helix: 2.58 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -1.98 (0.21), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 71 PHE 0.006 0.001 PHE O 82 HIS 0.004 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00362 (16486) covalent geometry : angle 0.42187 (22115) hydrogen bonds : bond 0.04959 ( 923) hydrogen bonds : angle 2.88485 ( 2769) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 350 time to evaluate : 0.515 Fit side-chains REVERT: B 71 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7873 (mtm180) REVERT: B 83 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8260 (mt-10) REVERT: E 81 ASP cc_start: 0.8029 (m-30) cc_final: 0.7734 (m-30) REVERT: H 38 ARG cc_start: 0.8471 (mtm-85) cc_final: 0.8267 (mtm-85) REVERT: R 71 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8387 (mtt180) REVERT: S 10 SER cc_start: 0.9194 (t) cc_final: 0.8930 (t) REVERT: X 71 ARG cc_start: 0.8377 (mmm-85) cc_final: 0.7903 (mtt180) outliers start: 23 outliers final: 23 residues processed: 363 average time/residue: 0.1898 time to fit residues: 89.2090 Evaluate side-chains 372 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 349 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 53 ASN Q 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.084865 restraints weight = 22327.245| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 1.83 r_work: 0.2687 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16486 Z= 0.143 Angle : 0.421 4.714 22115 Z= 0.218 Chirality : 0.035 0.114 2602 Planarity : 0.004 0.039 2835 Dihedral : 3.152 27.095 2214 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.28 % Allowed : 8.44 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.19), residues: 1995 helix: 2.58 (0.14), residues: 1567 sheet: None (None), residues: 0 loop : -1.98 (0.21), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 71 PHE 0.006 0.001 PHE O 82 HIS 0.004 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00360 (16486) covalent geometry : angle 0.42070 (22115) hydrogen bonds : bond 0.04934 ( 923) hydrogen bonds : angle 2.87708 ( 2769) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 348 time to evaluate : 0.659 Fit side-chains REVERT: B 71 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7886 (mtm180) REVERT: B 83 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8282 (mt-10) REVERT: E 81 ASP cc_start: 0.8017 (m-30) cc_final: 0.7721 (m-30) REVERT: H 38 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8283 (mtm-85) REVERT: K 38 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7868 (mtm180) REVERT: R 71 ARG cc_start: 0.8611 (mmm-85) cc_final: 0.8376 (mtt180) REVERT: S 10 SER cc_start: 0.9198 (t) cc_final: 0.8932 (t) REVERT: X 71 ARG cc_start: 0.8365 (mmm-85) cc_final: 0.7891 (mtt180) outliers start: 24 outliers final: 23 residues processed: 362 average time/residue: 0.1904 time to fit residues: 89.5611 Evaluate side-chains 372 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 348 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN Chi-restraints excluded: chain B residue 53 ASN Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain H residue 12 SER Chi-restraints excluded: chain H residue 13 SER Chi-restraints excluded: chain H residue 69 SER Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain K residue 38 ARG Chi-restraints excluded: chain L residue 53 ASN Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain M residue 69 SER Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain Q residue 12 SER Chi-restraints excluded: chain Q residue 53 ASN Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain T residue 56 GLU Chi-restraints excluded: chain U residue 12 SER Chi-restraints excluded: chain U residue 69 SER Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 12 SER Chi-restraints excluded: chain X residue 53 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 GLN B 53 ASN Q 53 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.103261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.086671 restraints weight = 22307.296| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.83 r_work: 0.2693 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16486 Z= 0.131 Angle : 0.406 4.748 22115 Z= 0.212 Chirality : 0.035 0.113 2602 Planarity : 0.004 0.039 2835 Dihedral : 3.133 26.978 2214 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.28 % Allowed : 8.55 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.19), residues: 1995 helix: 2.56 (0.14), residues: 1577 sheet: None (None), residues: 0 loop : -1.83 (0.21), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 71 PHE 0.006 0.001 PHE O 82 HIS 0.004 0.001 HIS D 9 Details of bonding type rmsd covalent geometry : bond 0.00325 (16486) covalent geometry : angle 0.40648 (22115) hydrogen bonds : bond 0.04676 ( 923) hydrogen bonds : angle 2.84154 ( 2769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3775.60 seconds wall clock time: 65 minutes 3.40 seconds (3903.40 seconds total)