Starting phenix.real_space_refine on Fri Jan 16 15:02:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rvb_24706/01_2026/7rvb_24706.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rvb_24706/01_2026/7rvb_24706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7rvb_24706/01_2026/7rvb_24706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rvb_24706/01_2026/7rvb_24706.map" model { file = "/net/cci-nas-00/data/ceres_data/7rvb_24706/01_2026/7rvb_24706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rvb_24706/01_2026/7rvb_24706.cif" } resolution = 2.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 432 5.16 5 C 25416 2.51 5 N 7152 2.21 5 O 7224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40224 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "B" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "C" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "D" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "E" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "F" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "G" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "H" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "I" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "J" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "K" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "L" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "M" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "N" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "O" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "P" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "Q" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "R" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "S" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "T" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "V" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "W" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "X" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Chain: "Y" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1676 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 8, 'TRANS': 200} Residues with excluded nonbonded symmetry interactions: 360 residue: pdb=" N GLU A 31 " occ=0.98 ... (7 atoms not shown) pdb=" OE2 GLU A 31 " occ=0.93 residue: pdb=" N LEU A 42 " occ=0.96 ... (6 atoms not shown) pdb=" CD2 LEU A 42 " occ=0.96 residue: pdb=" N ALA A 45 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA A 45 " occ=0.91 residue: pdb=" N SER A 46 " occ=0.97 ... (4 atoms not shown) pdb=" OG SER A 46 " occ=0.83 residue: pdb=" N SER A 47 " occ=0.97 ... (4 atoms not shown) pdb=" OG SER A 47 " occ=0.95 residue: pdb=" N ARG A 59 " occ=0.97 ... (9 atoms not shown) pdb=" NH2 ARG A 59 " occ=0.96 residue: pdb=" N HIS A 76 " occ=0.98 ... (8 atoms not shown) pdb=" NE2 HIS A 76 " occ=0.95 residue: pdb=" N SER A 129 " occ=0.97 ... (4 atoms not shown) pdb=" OG SER A 129 " occ=0.86 residue: pdb=" N SER A 139 " occ=0.97 ... (4 atoms not shown) pdb=" OG SER A 139 " occ=0.50 residue: pdb=" N ILE A 148 " occ=0.98 ... (6 atoms not shown) pdb=" CD1 ILE A 148 " occ=0.96 residue: pdb=" N GLU A 155 " occ=0.95 ... (7 atoms not shown) pdb=" OE2 GLU A 155 " occ=0.92 residue: pdb=" N ALA A 158 " occ=0.97 ... (3 atoms not shown) pdb=" CB ALA A 158 " occ=0.90 ... (remaining 348 not shown) Time building chain proxies: 8.95, per 1000 atoms: 0.22 Number of scatterers: 40224 At special positions: 0 Unit cell: (132.862, 132.862, 132.862, 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 432 16.00 O 7224 8.00 N 7152 7.00 C 25416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS V 61 " distance=2.02 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS V 22 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS T 61 " distance=2.02 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS T 22 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS S 61 " distance=2.02 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS S 22 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS K 61 " distance=2.02 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS K 22 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS I 61 " distance=2.02 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS I 22 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS L 61 " distance=2.02 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS L 22 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS Q 61 " distance=2.02 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS Q 22 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS R 61 " distance=2.02 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS R 22 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS Y 61 " distance=2.02 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS Y 22 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS O 61 " distance=2.02 Simple disulfide: pdb=" SG CYS M 61 " - pdb=" SG CYS O 22 " distance=2.02 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS X 61 " distance=2.02 Simple disulfide: pdb=" SG CYS N 61 " - pdb=" SG CYS X 22 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS W 61 " distance=2.02 Simple disulfide: pdb=" SG CYS P 61 " - pdb=" SG CYS W 22 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.59 Conformation dependent library (CDL) restraints added in 1.8 seconds 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 73.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 52 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 53 " --> pdb=" O HIS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 92 Processing helix chain 'A' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA A 115 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 230 Processing helix chain 'B' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 53 " --> pdb=" O HIS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 92 Processing helix chain 'B' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA B 115 " --> pdb=" O ASN B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET B 152 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.518A pdb=" N SER B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 230 Processing helix chain 'C' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP C 51 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 52 " --> pdb=" O TYR C 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 53 " --> pdb=" O HIS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 92 Processing helix chain 'C' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA C 115 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET C 152 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL C 156 " --> pdb=" O MET C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 218 through 230 Processing helix chain 'D' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET D 53 " --> pdb=" O HIS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 92 Processing helix chain 'D' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA D 115 " --> pdb=" O ASN D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.594A pdb=" N MET D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL D 156 " --> pdb=" O MET D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER D 193 " --> pdb=" O ARG D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 218 through 230 Processing helix chain 'E' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER E 52 " --> pdb=" O TYR E 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET E 53 " --> pdb=" O HIS E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 92 Processing helix chain 'E' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA E 115 " --> pdb=" O ASN E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 152 removed outlier: 3.594A pdb=" N MET E 152 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL E 156 " --> pdb=" O MET E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER E 193 " --> pdb=" O ARG E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 217 No H-bonds generated for 'chain 'E' and resid 215 through 217' Processing helix chain 'E' and resid 218 through 230 Processing helix chain 'F' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER F 52 " --> pdb=" O TYR F 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET F 53 " --> pdb=" O HIS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 92 Processing helix chain 'F' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL F 156 " --> pdb=" O MET F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER F 193 " --> pdb=" O ARG F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 217 No H-bonds generated for 'chain 'F' and resid 215 through 217' Processing helix chain 'F' and resid 218 through 230 Processing helix chain 'G' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP G 51 " --> pdb=" O SER G 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER G 52 " --> pdb=" O TYR G 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET G 53 " --> pdb=" O HIS G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 92 Processing helix chain 'G' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA G 115 " --> pdb=" O ASN G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL G 156 " --> pdb=" O MET G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.505A pdb=" N SER G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 218 through 230 Processing helix chain 'H' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP H 51 " --> pdb=" O SER H 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER H 52 " --> pdb=" O TYR H 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET H 53 " --> pdb=" O HIS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 92 Processing helix chain 'H' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA H 115 " --> pdb=" O ASN H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET H 152 " --> pdb=" O ILE H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL H 156 " --> pdb=" O MET H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.518A pdb=" N SER H 193 " --> pdb=" O ARG H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 215 through 217 No H-bonds generated for 'chain 'H' and resid 215 through 217' Processing helix chain 'H' and resid 218 through 230 Processing helix chain 'I' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP I 51 " --> pdb=" O SER I 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER I 52 " --> pdb=" O TYR I 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET I 53 " --> pdb=" O HIS I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 92 Processing helix chain 'I' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA I 115 " --> pdb=" O ASN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 removed outlier: 3.594A pdb=" N MET I 152 " --> pdb=" O ILE I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL I 156 " --> pdb=" O MET I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER I 193 " --> pdb=" O ARG I 189 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 217 No H-bonds generated for 'chain 'I' and resid 215 through 217' Processing helix chain 'I' and resid 218 through 230 Processing helix chain 'J' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP J 51 " --> pdb=" O SER J 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER J 52 " --> pdb=" O TYR J 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET J 53 " --> pdb=" O HIS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 92 Processing helix chain 'J' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA J 115 " --> pdb=" O ASN J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET J 152 " --> pdb=" O ILE J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL J 156 " --> pdb=" O MET J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 178 through 193 removed outlier: 3.545A pdb=" N SER J 193 " --> pdb=" O ARG J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 215 through 217 No H-bonds generated for 'chain 'J' and resid 215 through 217' Processing helix chain 'J' and resid 218 through 230 Processing helix chain 'K' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP K 51 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER K 52 " --> pdb=" O TYR K 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET K 53 " --> pdb=" O HIS K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 92 Processing helix chain 'K' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) Processing helix chain 'K' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL K 156 " --> pdb=" O MET K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER K 193 " --> pdb=" O ARG K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 217 No H-bonds generated for 'chain 'K' and resid 215 through 217' Processing helix chain 'K' and resid 218 through 230 Processing helix chain 'L' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP L 51 " --> pdb=" O SER L 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER L 52 " --> pdb=" O TYR L 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET L 53 " --> pdb=" O HIS L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 92 Processing helix chain 'L' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA L 115 " --> pdb=" O ASN L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL L 156 " --> pdb=" O MET L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 193 removed outlier: 3.518A pdb=" N SER L 193 " --> pdb=" O ARG L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 217 No H-bonds generated for 'chain 'L' and resid 215 through 217' Processing helix chain 'L' and resid 218 through 230 Processing helix chain 'M' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP M 51 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER M 52 " --> pdb=" O TYR M 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET M 53 " --> pdb=" O HIS M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 92 Processing helix chain 'M' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA M 115 " --> pdb=" O ASN M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET M 152 " --> pdb=" O ILE M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL M 156 " --> pdb=" O MET M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.545A pdb=" N SER M 193 " --> pdb=" O ARG M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 215 through 217 No H-bonds generated for 'chain 'M' and resid 215 through 217' Processing helix chain 'M' and resid 218 through 230 Processing helix chain 'N' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP N 51 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER N 52 " --> pdb=" O TYR N 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET N 53 " --> pdb=" O HIS N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 92 Processing helix chain 'N' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA N 115 " --> pdb=" O ASN N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 152 removed outlier: 3.594A pdb=" N MET N 152 " --> pdb=" O ILE N 148 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL N 156 " --> pdb=" O MET N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER N 193 " --> pdb=" O ARG N 189 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 217 No H-bonds generated for 'chain 'N' and resid 215 through 217' Processing helix chain 'N' and resid 218 through 230 Processing helix chain 'O' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP O 51 " --> pdb=" O SER O 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER O 52 " --> pdb=" O TYR O 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET O 53 " --> pdb=" O HIS O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 92 Processing helix chain 'O' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA O 115 " --> pdb=" O ASN O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 141 through 152 removed outlier: 3.594A pdb=" N MET O 152 " --> pdb=" O ILE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL O 156 " --> pdb=" O MET O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 178 through 193 removed outlier: 3.545A pdb=" N SER O 193 " --> pdb=" O ARG O 189 " (cutoff:3.500A) Processing helix chain 'O' and resid 215 through 217 No H-bonds generated for 'chain 'O' and resid 215 through 217' Processing helix chain 'O' and resid 218 through 230 Processing helix chain 'P' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP P 51 " --> pdb=" O SER P 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER P 52 " --> pdb=" O TYR P 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET P 53 " --> pdb=" O HIS P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 64 through 92 Processing helix chain 'P' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA P 115 " --> pdb=" O ASN P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET P 152 " --> pdb=" O ILE P 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL P 156 " --> pdb=" O MET P 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 193 removed outlier: 3.505A pdb=" N SER P 193 " --> pdb=" O ARG P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 215 through 217 No H-bonds generated for 'chain 'P' and resid 215 through 217' Processing helix chain 'P' and resid 218 through 230 Processing helix chain 'Q' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP Q 51 " --> pdb=" O SER Q 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER Q 52 " --> pdb=" O TYR Q 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET Q 53 " --> pdb=" O HIS Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 92 Processing helix chain 'Q' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA Q 115 " --> pdb=" O ASN Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET Q 152 " --> pdb=" O ILE Q 148 " (cutoff:3.500A) Processing helix chain 'Q' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL Q 156 " --> pdb=" O MET Q 152 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 193 removed outlier: 3.558A pdb=" N SER Q 193 " --> pdb=" O ARG Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 217 No H-bonds generated for 'chain 'Q' and resid 215 through 217' Processing helix chain 'Q' and resid 218 through 230 Processing helix chain 'R' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER R 52 " --> pdb=" O TYR R 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET R 53 " --> pdb=" O HIS R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 92 Processing helix chain 'R' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA R 115 " --> pdb=" O ASN R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET R 152 " --> pdb=" O ILE R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL R 156 " --> pdb=" O MET R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 178 through 193 removed outlier: 3.545A pdb=" N SER R 193 " --> pdb=" O ARG R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 217 No H-bonds generated for 'chain 'R' and resid 215 through 217' Processing helix chain 'R' and resid 218 through 230 Processing helix chain 'S' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP S 51 " --> pdb=" O SER S 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER S 52 " --> pdb=" O TYR S 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET S 53 " --> pdb=" O HIS S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 64 through 92 Processing helix chain 'S' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA S 115 " --> pdb=" O ASN S 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET S 152 " --> pdb=" O ILE S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL S 156 " --> pdb=" O MET S 152 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 193 removed outlier: 3.505A pdb=" N SER S 193 " --> pdb=" O ARG S 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 215 through 217 No H-bonds generated for 'chain 'S' and resid 215 through 217' Processing helix chain 'S' and resid 218 through 230 Processing helix chain 'T' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP T 51 " --> pdb=" O SER T 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER T 52 " --> pdb=" O TYR T 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET T 53 " --> pdb=" O HIS T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 64 through 92 Processing helix chain 'T' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA T 115 " --> pdb=" O ASN T 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET T 152 " --> pdb=" O ILE T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL T 156 " --> pdb=" O MET T 152 " (cutoff:3.500A) Processing helix chain 'T' and resid 178 through 193 removed outlier: 3.545A pdb=" N SER T 193 " --> pdb=" O ARG T 189 " (cutoff:3.500A) Processing helix chain 'T' and resid 215 through 217 No H-bonds generated for 'chain 'T' and resid 215 through 217' Processing helix chain 'T' and resid 218 through 230 Processing helix chain 'V' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP V 51 " --> pdb=" O SER V 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER V 52 " --> pdb=" O TYR V 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET V 53 " --> pdb=" O HIS V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 64 through 92 Processing helix chain 'V' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA V 115 " --> pdb=" O ASN V 111 " (cutoff:3.500A) Processing helix chain 'V' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET V 152 " --> pdb=" O ILE V 148 " (cutoff:3.500A) Processing helix chain 'V' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL V 156 " --> pdb=" O MET V 152 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 193 removed outlier: 3.505A pdb=" N SER V 193 " --> pdb=" O ARG V 189 " (cutoff:3.500A) Processing helix chain 'V' and resid 215 through 217 No H-bonds generated for 'chain 'V' and resid 215 through 217' Processing helix chain 'V' and resid 218 through 230 Processing helix chain 'W' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP W 51 " --> pdb=" O SER W 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER W 52 " --> pdb=" O TYR W 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET W 53 " --> pdb=" O HIS W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 92 Processing helix chain 'W' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA W 115 " --> pdb=" O ASN W 111 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET W 152 " --> pdb=" O ILE W 148 " (cutoff:3.500A) Processing helix chain 'W' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL W 156 " --> pdb=" O MET W 152 " (cutoff:3.500A) Processing helix chain 'W' and resid 178 through 193 removed outlier: 3.545A pdb=" N SER W 193 " --> pdb=" O ARG W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 215 through 217 No H-bonds generated for 'chain 'W' and resid 215 through 217' Processing helix chain 'W' and resid 218 through 230 Processing helix chain 'X' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP X 51 " --> pdb=" O SER X 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER X 52 " --> pdb=" O TYR X 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET X 53 " --> pdb=" O HIS X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 92 Processing helix chain 'X' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA X 115 " --> pdb=" O ASN X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 141 through 152 removed outlier: 3.594A pdb=" N MET X 152 " --> pdb=" O ILE X 148 " (cutoff:3.500A) Processing helix chain 'X' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL X 156 " --> pdb=" O MET X 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 178 through 193 removed outlier: 3.545A pdb=" N SER X 193 " --> pdb=" O ARG X 189 " (cutoff:3.500A) Processing helix chain 'X' and resid 215 through 217 No H-bonds generated for 'chain 'X' and resid 215 through 217' Processing helix chain 'X' and resid 218 through 230 Processing helix chain 'Y' and resid 29 through 58 removed outlier: 3.663A pdb=" N TRP Y 51 " --> pdb=" O SER Y 47 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER Y 52 " --> pdb=" O TYR Y 48 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET Y 53 " --> pdb=" O HIS Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 92 Processing helix chain 'Y' and resid 111 through 138 removed outlier: 3.717A pdb=" N ALA Y 115 " --> pdb=" O ASN Y 111 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 152 removed outlier: 3.593A pdb=" N MET Y 152 " --> pdb=" O ILE Y 148 " (cutoff:3.500A) Processing helix chain 'Y' and resid 152 through 174 removed outlier: 4.184A pdb=" N VAL Y 156 " --> pdb=" O MET Y 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 178 through 193 removed outlier: 3.505A pdb=" N SER Y 193 " --> pdb=" O ARG Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 215 through 217 No H-bonds generated for 'chain 'Y' and resid 215 through 217' Processing helix chain 'Y' and resid 218 through 230 2784 hydrogen bonds defined for protein. 8352 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: 7.01 Time building geometry restraints manager: 4.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 13128 1.34 - 1.46: 8591 1.46 - 1.58: 18985 1.58 - 1.69: 0 1.69 - 1.81: 624 Bond restraints: 41328 Sorted by residual: bond pdb=" CB GLU L 100 " pdb=" CG GLU L 100 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB GLU D 100 " pdb=" CG GLU D 100 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB GLU J 100 " pdb=" CG GLU J 100 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB GLU E 100 " pdb=" CG GLU E 100 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CB GLU Y 100 " pdb=" CG GLU Y 100 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 ... (remaining 41323 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 54984 1.76 - 3.52: 672 3.52 - 5.29: 128 5.29 - 7.05: 24 7.05 - 8.81: 16 Bond angle restraints: 55824 Sorted by residual: angle pdb=" CG ARG V 185 " pdb=" CD ARG V 185 " pdb=" NE ARG V 185 " ideal model delta sigma weight residual 112.00 120.81 -8.81 2.20e+00 2.07e-01 1.60e+01 angle pdb=" CG ARG G 185 " pdb=" CD ARG G 185 " pdb=" NE ARG G 185 " ideal model delta sigma weight residual 112.00 120.81 -8.81 2.20e+00 2.07e-01 1.60e+01 angle pdb=" CG ARG P 185 " pdb=" CD ARG P 185 " pdb=" NE ARG P 185 " ideal model delta sigma weight residual 112.00 120.81 -8.81 2.20e+00 2.07e-01 1.60e+01 angle pdb=" CG ARG Y 185 " pdb=" CD ARG Y 185 " pdb=" NE ARG Y 185 " ideal model delta sigma weight residual 112.00 120.75 -8.75 2.20e+00 2.07e-01 1.58e+01 angle pdb=" CG ARG S 185 " pdb=" CD ARG S 185 " pdb=" NE ARG S 185 " ideal model delta sigma weight residual 112.00 120.75 -8.75 2.20e+00 2.07e-01 1.58e+01 ... (remaining 55819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 20808 16.57 - 33.14: 2717 33.14 - 49.71: 935 49.71 - 66.29: 228 66.29 - 82.86: 56 Dihedral angle restraints: 24744 sinusoidal: 9984 harmonic: 14760 Sorted by residual: dihedral pdb=" CB CYS C 61 " pdb=" SG CYS C 61 " pdb=" SG CYS S 22 " pdb=" CB CYS S 22 " ideal model delta sinusoidal sigma weight residual -86.00 -149.55 63.55 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS M 61 " pdb=" SG CYS M 61 " pdb=" SG CYS O 22 " pdb=" CB CYS O 22 " ideal model delta sinusoidal sigma weight residual -86.00 -149.55 63.55 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS I 61 " pdb=" CB CYS I 61 " ideal model delta sinusoidal sigma weight residual -86.00 -149.55 63.55 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 24741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3425 0.027 - 0.054: 1463 0.054 - 0.081: 656 0.081 - 0.108: 161 0.108 - 0.134: 79 Chirality restraints: 5784 Sorted by residual: chirality pdb=" CA ILE P 200 " pdb=" N ILE P 200 " pdb=" C ILE P 200 " pdb=" CB ILE P 200 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE G 200 " pdb=" N ILE G 200 " pdb=" C ILE G 200 " pdb=" CB ILE G 200 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE Y 200 " pdb=" N ILE Y 200 " pdb=" C ILE Y 200 " pdb=" CB ILE Y 200 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 5781 not shown) Planarity restraints: 7152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 179 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO J 180 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO J 180 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO J 180 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY X 179 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO X 180 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO X 180 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO X 180 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY M 179 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO M 180 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO M 180 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO M 180 " -0.019 5.00e-02 4.00e+02 ... (remaining 7149 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 8171 2.79 - 3.32: 39943 3.32 - 3.84: 68177 3.84 - 4.37: 73868 4.37 - 4.90: 130370 Nonbonded interactions: 320529 Sorted by model distance: nonbonded pdb=" OD1 ASP D 154 " pdb=" OG1 THR K 205 " model vdw 2.260 3.040 nonbonded pdb=" OD1 ASP E 154 " pdb=" OG1 THR I 205 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR B 205 " pdb=" OD1 ASP T 154 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR H 205 " pdb=" OD1 ASP R 154 " model vdw 2.260 3.040 nonbonded pdb=" OG1 THR D 205 " pdb=" OD1 ASP K 154 " model vdw 2.260 3.040 ... (remaining 320524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=0.99 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: 9.150 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: 0.030 Extract box with map and model: 2.070 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 34.480 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 41352 Z= 0.175 Angle : 0.544 8.809 55872 Z= 0.301 Chirality : 0.038 0.134 5784 Planarity : 0.004 0.038 7152 Dihedral : 17.176 82.858 15024 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.55 % Allowed : 19.24 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.46 (0.12), residues: 4968 helix: 3.62 (0.08), residues: 3504 sheet: None (None), residues: 0 loop : -1.30 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 225 TYR 0.011 0.002 TYR N 88 PHE 0.005 0.001 PHE B 183 TRP 0.006 0.001 TRP S 186 HIS 0.004 0.001 HIS F 41 Details of bonding type rmsd covalent geometry : bond 0.00389 (41328) covalent geometry : angle 0.54254 (55824) SS BOND : bond 0.00680 ( 24) SS BOND : angle 1.37750 ( 48) hydrogen bonds : bond 0.14477 ( 2784) hydrogen bonds : angle 4.53739 ( 8352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 956 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 40 residues processed: 956 average time/residue: 1.1868 time to fit residues: 1284.3903 Evaluate side-chains 955 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 915 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain P residue 172 CYS Chi-restraints excluded: chain Q residue 172 CYS Chi-restraints excluded: chain Q residue 173 ILE Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain S residue 172 CYS Chi-restraints excluded: chain T residue 172 CYS Chi-restraints excluded: chain T residue 173 ILE Chi-restraints excluded: chain V residue 172 CYS Chi-restraints excluded: chain W residue 172 CYS Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain X residue 172 CYS Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain Y residue 172 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 470 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 138 GLN C 138 GLN D 138 GLN E 138 GLN F 138 GLN G 138 GLN H 138 GLN I 138 GLN J 138 GLN K 138 GLN L 138 GLN M 138 GLN N 138 GLN O 138 GLN P 138 GLN Q 138 GLN R 138 GLN S 138 GLN T 138 GLN V 138 GLN W 138 GLN X 138 GLN Y 138 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.071209 restraints weight = 53860.655| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.27 r_work: 0.2619 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2486 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2487 r_free = 0.2487 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2449 r_free = 0.2449 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 41352 Z= 0.199 Angle : 0.520 5.893 55872 Z= 0.292 Chirality : 0.039 0.137 5784 Planarity : 0.004 0.036 7152 Dihedral : 4.181 27.518 5432 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.31 % Allowed : 18.32 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.02 (0.12), residues: 4968 helix: 4.04 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.31 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 225 TYR 0.008 0.002 TYR N 57 PHE 0.004 0.001 PHE E 116 TRP 0.004 0.001 TRP B 54 HIS 0.004 0.001 HIS C 41 Details of bonding type rmsd covalent geometry : bond 0.00459 (41328) covalent geometry : angle 0.51849 (55824) SS BOND : bond 0.00825 ( 24) SS BOND : angle 1.55456 ( 48) hydrogen bonds : bond 0.09444 ( 2784) hydrogen bonds : angle 3.40771 ( 8352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 904 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 36 residues processed: 1000 average time/residue: 1.1243 time to fit residues: 1285.3556 Evaluate side-chains 992 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 956 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 211 ASN Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 173 ILE Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 173 ILE Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 173 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 343 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 456 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 121 optimal weight: 7.9990 chunk 335 optimal weight: 4.9990 chunk 376 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 138 GLN B 169 ASN C 138 GLN D 138 GLN E 138 GLN F 138 GLN G 138 GLN G 169 ASN H 138 GLN H 169 ASN I 138 GLN J 138 GLN K 138 GLN L 138 GLN L 169 ASN M 138 GLN N 138 GLN O 138 GLN P 138 GLN P 169 ASN Q 138 GLN R 138 GLN S 138 GLN S 169 ASN T 138 GLN V 138 GLN V 169 ASN W 138 GLN X 138 GLN Y 138 GLN Y 169 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.088762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.067009 restraints weight = 54545.139| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.25 r_work: 0.2567 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2440 r_free = 0.2440 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9073 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 41352 Z= 0.198 Angle : 0.508 5.884 55872 Z= 0.286 Chirality : 0.039 0.132 5784 Planarity : 0.004 0.036 7152 Dihedral : 3.666 13.550 5376 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.87 % Allowed : 17.96 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.22 (0.12), residues: 4968 helix: 4.20 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.27 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 225 TYR 0.009 0.002 TYR W 57 PHE 0.005 0.001 PHE E 116 TRP 0.005 0.001 TRP X 109 HIS 0.004 0.001 HIS D 41 Details of bonding type rmsd covalent geometry : bond 0.00458 (41328) covalent geometry : angle 0.50602 (55824) SS BOND : bond 0.00821 ( 24) SS BOND : angle 1.55218 ( 48) hydrogen bonds : bond 0.09393 ( 2784) hydrogen bonds : angle 3.30504 ( 8352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 912 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 168 outliers final: 96 residues processed: 1008 average time/residue: 1.0937 time to fit residues: 1262.5498 Evaluate side-chains 992 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 896 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain I residue 28 PHE Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 211 ASN Chi-restraints excluded: chain N residue 28 PHE Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 211 ASN Chi-restraints excluded: chain O residue 28 PHE Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 211 ASN Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 172 CYS Chi-restraints excluded: chain P residue 211 ASN Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 172 CYS Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 28 PHE Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 172 CYS Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain T residue 28 PHE Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain T residue 172 CYS Chi-restraints excluded: chain T residue 211 ASN Chi-restraints excluded: chain V residue 28 PHE Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 172 CYS Chi-restraints excluded: chain V residue 211 ASN Chi-restraints excluded: chain W residue 28 PHE Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain W residue 172 CYS Chi-restraints excluded: chain W residue 211 ASN Chi-restraints excluded: chain X residue 28 PHE Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain X residue 172 CYS Chi-restraints excluded: chain X residue 211 ASN Chi-restraints excluded: chain Y residue 28 PHE Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 172 CYS Chi-restraints excluded: chain Y residue 211 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 318 optimal weight: 9.9990 chunk 290 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 229 optimal weight: 10.0000 chunk 449 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 353 optimal weight: 3.9990 chunk 456 optimal weight: 4.9990 chunk 225 optimal weight: 5.9990 chunk 475 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 138 GLN H 138 GLN K 138 GLN L 138 GLN O 138 GLN P 138 GLN S 138 GLN V 138 GLN Y 138 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.092326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.070491 restraints weight = 54184.305| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.25 r_work: 0.2640 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 41352 Z= 0.141 Angle : 0.445 5.700 55872 Z= 0.247 Chirality : 0.036 0.132 5784 Planarity : 0.003 0.037 7152 Dihedral : 3.530 12.097 5376 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.31 % Allowed : 18.85 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.51 (0.12), residues: 4968 helix: 4.46 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.28 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 225 TYR 0.007 0.001 TYR G 88 PHE 0.004 0.001 PHE M 116 TRP 0.004 0.001 TRP V 51 HIS 0.004 0.001 HIS W 41 Details of bonding type rmsd covalent geometry : bond 0.00297 (41328) covalent geometry : angle 0.44443 (55824) SS BOND : bond 0.00499 ( 24) SS BOND : angle 0.94213 ( 48) hydrogen bonds : bond 0.07456 ( 2784) hydrogen bonds : angle 3.00866 ( 8352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 936 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 38 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8953 (mp0) REVERT: M 38 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8966 (mp0) REVERT: V 38 GLU cc_start: 0.9175 (OUTLIER) cc_final: 0.8960 (mp0) outliers start: 144 outliers final: 96 residues processed: 1032 average time/residue: 1.0750 time to fit residues: 1273.7898 Evaluate side-chains 1035 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 936 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain I residue 28 PHE Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 211 ASN Chi-restraints excluded: chain N residue 28 PHE Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 211 ASN Chi-restraints excluded: chain O residue 28 PHE Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 211 ASN Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 172 CYS Chi-restraints excluded: chain P residue 211 ASN Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 172 CYS Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 28 PHE Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 172 CYS Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain T residue 28 PHE Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain T residue 172 CYS Chi-restraints excluded: chain T residue 211 ASN Chi-restraints excluded: chain V residue 28 PHE Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 172 CYS Chi-restraints excluded: chain V residue 211 ASN Chi-restraints excluded: chain W residue 28 PHE Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain W residue 172 CYS Chi-restraints excluded: chain W residue 211 ASN Chi-restraints excluded: chain X residue 28 PHE Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain X residue 172 CYS Chi-restraints excluded: chain X residue 211 ASN Chi-restraints excluded: chain Y residue 28 PHE Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 172 CYS Chi-restraints excluded: chain Y residue 211 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 383 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 408 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 154 optimal weight: 6.9990 chunk 415 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 138 GLN C 138 GLN D 138 GLN E 138 GLN F 138 GLN G 138 GLN H 138 GLN I 138 GLN J 138 GLN K 138 GLN L 138 GLN M 138 GLN N 138 GLN O 138 GLN P 138 GLN Q 138 GLN R 138 GLN S 138 GLN T 138 GLN V 138 GLN W 138 GLN X 138 GLN Y 138 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.088819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.066990 restraints weight = 54118.291| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 2.25 r_work: 0.2579 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2451 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2448 r_free = 0.2448 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| r_final: 0.2448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9063 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 41352 Z= 0.179 Angle : 0.485 5.826 55872 Z= 0.271 Chirality : 0.038 0.133 5784 Planarity : 0.003 0.036 7152 Dihedral : 3.615 12.966 5376 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.80 % Allowed : 17.13 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.45 (0.12), residues: 4968 helix: 4.42 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.34 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 225 TYR 0.009 0.002 TYR W 88 PHE 0.005 0.001 PHE M 116 TRP 0.004 0.001 TRP D 109 HIS 0.004 0.001 HIS V 41 Details of bonding type rmsd covalent geometry : bond 0.00407 (41328) covalent geometry : angle 0.48331 (55824) SS BOND : bond 0.00722 ( 24) SS BOND : angle 1.36842 ( 48) hydrogen bonds : bond 0.08827 ( 2784) hydrogen bonds : angle 3.19742 ( 8352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1104 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 939 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 96 residues processed: 1035 average time/residue: 1.0754 time to fit residues: 1277.3068 Evaluate side-chains 1008 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 912 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain I residue 28 PHE Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 211 ASN Chi-restraints excluded: chain N residue 28 PHE Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 211 ASN Chi-restraints excluded: chain O residue 28 PHE Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 211 ASN Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 172 CYS Chi-restraints excluded: chain P residue 211 ASN Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 172 CYS Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 28 PHE Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 172 CYS Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain T residue 28 PHE Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain T residue 172 CYS Chi-restraints excluded: chain T residue 211 ASN Chi-restraints excluded: chain V residue 28 PHE Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 172 CYS Chi-restraints excluded: chain V residue 211 ASN Chi-restraints excluded: chain W residue 28 PHE Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain W residue 172 CYS Chi-restraints excluded: chain W residue 211 ASN Chi-restraints excluded: chain X residue 28 PHE Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain X residue 172 CYS Chi-restraints excluded: chain X residue 211 ASN Chi-restraints excluded: chain Y residue 28 PHE Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 172 CYS Chi-restraints excluded: chain Y residue 211 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 161 optimal weight: 6.9990 chunk 339 optimal weight: 0.5980 chunk 136 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 436 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.091439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.069648 restraints weight = 53555.355| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.24 r_work: 0.2632 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 41352 Z= 0.140 Angle : 0.440 5.682 55872 Z= 0.243 Chirality : 0.036 0.131 5784 Planarity : 0.003 0.037 7152 Dihedral : 3.512 12.360 5376 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.21 % Allowed : 18.78 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.64 (0.12), residues: 4968 helix: 4.56 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.26 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 225 TYR 0.007 0.001 TYR F 88 PHE 0.004 0.001 PHE V 116 TRP 0.004 0.001 TRP M 51 HIS 0.004 0.001 HIS V 41 Details of bonding type rmsd covalent geometry : bond 0.00295 (41328) covalent geometry : angle 0.43972 (55824) SS BOND : bond 0.00487 ( 24) SS BOND : angle 0.92269 ( 48) hydrogen bonds : bond 0.07404 ( 2784) hydrogen bonds : angle 2.98588 ( 8352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1008 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 912 time to evaluate : 1.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.7889 (pmt) cc_final: 0.6065 (pmt) REVERT: B 178 MET cc_start: 0.7938 (pmt) cc_final: 0.6121 (pmt) REVERT: C 178 MET cc_start: 0.7823 (pmt) cc_final: 0.6040 (pmt) REVERT: D 178 MET cc_start: 0.7603 (pmt) cc_final: 0.5883 (pmt) REVERT: E 178 MET cc_start: 0.7866 (pmt) cc_final: 0.6067 (pmt) REVERT: F 178 MET cc_start: 0.7774 (pmt) cc_final: 0.6007 (pmt) REVERT: G 178 MET cc_start: 0.7948 (pmt) cc_final: 0.6122 (pmt) REVERT: G 185 ARG cc_start: 0.8637 (mmp-170) cc_final: 0.8321 (mtm110) REVERT: H 178 MET cc_start: 0.7644 (pmt) cc_final: 0.5930 (pmt) REVERT: I 178 MET cc_start: 0.7811 (pmt) cc_final: 0.6040 (pmt) REVERT: J 178 MET cc_start: 0.7666 (pmt) cc_final: 0.5931 (pmt) REVERT: K 178 MET cc_start: 0.7682 (pmt) cc_final: 0.5953 (pmt) REVERT: L 178 MET cc_start: 0.7946 (pmt) cc_final: 0.6113 (pmt) REVERT: M 178 MET cc_start: 0.7803 (pmt) cc_final: 0.6034 (pmt) REVERT: N 178 MET cc_start: 0.7924 (pmt) cc_final: 0.6107 (pmt) REVERT: O 178 MET cc_start: 0.7865 (pmt) cc_final: 0.6061 (pmt) REVERT: P 178 MET cc_start: 0.7802 (pmt) cc_final: 0.6032 (pmt) REVERT: P 185 ARG cc_start: 0.8633 (mmp-170) cc_final: 0.8386 (mtm110) REVERT: Q 178 MET cc_start: 0.7885 (pmt) cc_final: 0.6064 (pmt) REVERT: R 178 MET cc_start: 0.7638 (pmt) cc_final: 0.5903 (pmt) REVERT: S 178 MET cc_start: 0.7891 (pmt) cc_final: 0.6086 (pmt) REVERT: S 185 ARG cc_start: 0.8627 (mmp-170) cc_final: 0.8340 (mtm110) REVERT: T 178 MET cc_start: 0.7889 (pmt) cc_final: 0.6065 (pmt) REVERT: V 178 MET cc_start: 0.7812 (pmt) cc_final: 0.6043 (pmt) REVERT: V 185 ARG cc_start: 0.8631 (mmp-170) cc_final: 0.8332 (mtm110) REVERT: W 178 MET cc_start: 0.7850 (pmt) cc_final: 0.6049 (pmt) REVERT: X 178 MET cc_start: 0.7876 (pmt) cc_final: 0.6068 (pmt) REVERT: Y 178 MET cc_start: 0.7648 (pmt) cc_final: 0.5911 (pmt) REVERT: Y 185 ARG cc_start: 0.8634 (mmp-170) cc_final: 0.8345 (mtm110) outliers start: 96 outliers final: 96 residues processed: 1008 average time/residue: 1.0648 time to fit residues: 1236.9789 Evaluate side-chains 1008 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 912 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain I residue 28 PHE Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 211 ASN Chi-restraints excluded: chain N residue 28 PHE Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 211 ASN Chi-restraints excluded: chain O residue 28 PHE Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 211 ASN Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 172 CYS Chi-restraints excluded: chain P residue 211 ASN Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 172 CYS Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 28 PHE Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 172 CYS Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain T residue 28 PHE Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain T residue 172 CYS Chi-restraints excluded: chain T residue 211 ASN Chi-restraints excluded: chain V residue 28 PHE Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 172 CYS Chi-restraints excluded: chain V residue 211 ASN Chi-restraints excluded: chain W residue 28 PHE Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain W residue 172 CYS Chi-restraints excluded: chain W residue 211 ASN Chi-restraints excluded: chain X residue 28 PHE Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain X residue 172 CYS Chi-restraints excluded: chain X residue 211 ASN Chi-restraints excluded: chain Y residue 28 PHE Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 172 CYS Chi-restraints excluded: chain Y residue 211 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 36 optimal weight: 9.9990 chunk 338 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 340 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 398 optimal weight: 3.9990 chunk 240 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.067530 restraints weight = 55510.512| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.28 r_work: 0.2559 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2417 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2453 r_free = 0.2453 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 30 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2451 r_free = 0.2451 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| r_final: 0.2451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 41352 Z= 0.164 Angle : 0.465 5.769 55872 Z= 0.258 Chirality : 0.037 0.130 5784 Planarity : 0.003 0.037 7152 Dihedral : 3.555 12.403 5376 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.76 % Allowed : 18.07 % Favored : 79.17 % 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: 4.57 (0.12), residues: 4968 helix: 4.51 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.27 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 225 TYR 0.008 0.001 TYR W 88 PHE 0.004 0.001 PHE N 116 TRP 0.004 0.001 TRP K 109 HIS 0.004 0.001 HIS M 41 Details of bonding type rmsd covalent geometry : bond 0.00364 (41328) covalent geometry : angle 0.46344 (55824) SS BOND : bond 0.00644 ( 24) SS BOND : angle 1.20632 ( 48) hydrogen bonds : bond 0.08322 ( 2784) hydrogen bonds : angle 3.10830 ( 8352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 957 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.7785 (pmt) cc_final: 0.6177 (pmt) REVERT: B 178 MET cc_start: 0.7906 (pmt) cc_final: 0.6252 (pmt) REVERT: C 178 MET cc_start: 0.7780 (pmt) cc_final: 0.6171 (pmt) REVERT: D 178 MET cc_start: 0.7610 (pmt) cc_final: 0.6051 (pmt) REVERT: E 178 MET cc_start: 0.7815 (pmt) cc_final: 0.6094 (pmt) REVERT: F 178 MET cc_start: 0.7734 (pmt) cc_final: 0.6014 (pmt) REVERT: H 178 MET cc_start: 0.7636 (pmt) cc_final: 0.6182 (pmt) REVERT: I 178 MET cc_start: 0.7779 (pmt) cc_final: 0.6142 (pmt) REVERT: K 178 MET cc_start: 0.7675 (pmt) cc_final: 0.5983 (pmt) REVERT: L 178 MET cc_start: 0.7838 (pmt) cc_final: 0.6121 (pmt) REVERT: N 178 MET cc_start: 0.7902 (pmt) cc_final: 0.6349 (pmt) REVERT: O 178 MET cc_start: 0.7788 (pmt) cc_final: 0.6290 (pmt) REVERT: R 178 MET cc_start: 0.7623 (pmt) cc_final: 0.6028 (pmt) REVERT: S 178 MET cc_start: 0.7840 (pmt) cc_final: 0.6201 (pmt) REVERT: T 178 MET cc_start: 0.7872 (pmt) cc_final: 0.6184 (pmt) REVERT: V 178 MET cc_start: 0.7741 (pmt) cc_final: 0.6256 (pmt) outliers start: 120 outliers final: 96 residues processed: 1029 average time/residue: 1.0742 time to fit residues: 1268.7414 Evaluate side-chains 1032 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 936 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 211 ASN Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 211 ASN Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 211 ASN Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 211 ASN Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 211 ASN Chi-restraints excluded: chain I residue 28 PHE Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain I residue 211 ASN Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain J residue 211 ASN Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain K residue 211 ASN Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain L residue 211 ASN Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain M residue 211 ASN Chi-restraints excluded: chain N residue 28 PHE Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain N residue 211 ASN Chi-restraints excluded: chain O residue 28 PHE Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain O residue 211 ASN Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 172 CYS Chi-restraints excluded: chain P residue 211 ASN Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 172 CYS Chi-restraints excluded: chain Q residue 211 ASN Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain S residue 28 PHE Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 172 CYS Chi-restraints excluded: chain S residue 211 ASN Chi-restraints excluded: chain T residue 28 PHE Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain T residue 172 CYS Chi-restraints excluded: chain T residue 211 ASN Chi-restraints excluded: chain V residue 28 PHE Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 172 CYS Chi-restraints excluded: chain V residue 211 ASN Chi-restraints excluded: chain W residue 28 PHE Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain W residue 172 CYS Chi-restraints excluded: chain W residue 211 ASN Chi-restraints excluded: chain X residue 28 PHE Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain X residue 172 CYS Chi-restraints excluded: chain X residue 211 ASN Chi-restraints excluded: chain Y residue 28 PHE Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 172 CYS Chi-restraints excluded: chain Y residue 211 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 59 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 95 optimal weight: 0.0270 chunk 472 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 355 optimal weight: 5.9990 chunk 397 optimal weight: 0.4980 chunk 79 optimal weight: 10.0000 chunk 352 optimal weight: 8.9990 overall best weight: 2.7044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.093049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.071626 restraints weight = 55242.643| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.27 r_work: 0.2651 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2540 r_free = 0.2540 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 42 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2539 r_free = 0.2539 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| r_final: 0.2539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 41352 Z= 0.119 Angle : 0.417 5.607 55872 Z= 0.228 Chirality : 0.034 0.136 5784 Planarity : 0.003 0.038 7152 Dihedral : 3.419 13.259 5376 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.28 % Allowed : 18.72 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.81 (0.12), residues: 4968 helix: 4.67 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.16 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 225 TYR 0.007 0.001 TYR F 88 PHE 0.004 0.001 PHE D 116 TRP 0.004 0.001 TRP V 51 HIS 0.004 0.001 HIS V 41 Details of bonding type rmsd covalent geometry : bond 0.00233 (41328) covalent geometry : angle 0.41666 (55824) SS BOND : bond 0.00337 ( 24) SS BOND : angle 0.70496 ( 48) hydrogen bonds : bond 0.06335 ( 2784) hydrogen bonds : angle 2.84067 ( 8352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 984 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.7687 (pmt) cc_final: 0.6024 (pmt) REVERT: B 178 MET cc_start: 0.7790 (pmt) cc_final: 0.6127 (pmt) REVERT: B 185 ARG cc_start: 0.8446 (mmp-170) cc_final: 0.8154 (mtm110) REVERT: C 178 MET cc_start: 0.7706 (pmt) cc_final: 0.6031 (pmt) REVERT: D 178 MET cc_start: 0.7544 (pmt) cc_final: 0.5957 (pmt) REVERT: E 178 MET cc_start: 0.7836 (pmt) cc_final: 0.6166 (pmt) REVERT: F 38 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8821 (mp0) REVERT: F 178 MET cc_start: 0.7696 (pmt) cc_final: 0.6034 (pmt) REVERT: G 178 MET cc_start: 0.7873 (pmt) cc_final: 0.6172 (pmt) REVERT: G 185 ARG cc_start: 0.8466 (mmp-170) cc_final: 0.8123 (mtm110) REVERT: H 178 MET cc_start: 0.7612 (pmt) cc_final: 0.6015 (pmt) REVERT: H 185 ARG cc_start: 0.8460 (mmp-170) cc_final: 0.8150 (mtm110) REVERT: I 178 MET cc_start: 0.7750 (pmt) cc_final: 0.6086 (pmt) REVERT: J 178 MET cc_start: 0.7616 (pmt) cc_final: 0.5999 (pmt) REVERT: K 178 MET cc_start: 0.7641 (pmt) cc_final: 0.6022 (pmt) REVERT: L 178 MET cc_start: 0.7733 (pmt) cc_final: 0.6069 (pmt) REVERT: L 185 ARG cc_start: 0.8490 (mmp-170) cc_final: 0.8152 (mtm110) REVERT: M 38 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8814 (mp0) REVERT: M 178 MET cc_start: 0.7722 (pmt) cc_final: 0.6057 (pmt) REVERT: N 178 MET cc_start: 0.7825 (pmt) cc_final: 0.6140 (pmt) REVERT: O 178 MET cc_start: 0.7719 (pmt) cc_final: 0.6060 (pmt) REVERT: P 178 MET cc_start: 0.7705 (pmt) cc_final: 0.6061 (pmt) REVERT: P 185 ARG cc_start: 0.8413 (mmp-170) cc_final: 0.8141 (mtm110) REVERT: Q 178 MET cc_start: 0.7735 (pmt) cc_final: 0.6075 (pmt) REVERT: R 178 MET cc_start: 0.7547 (pmt) cc_final: 0.5943 (pmt) REVERT: S 178 MET cc_start: 0.7866 (pmt) cc_final: 0.6187 (pmt) REVERT: S 185 ARG cc_start: 0.8489 (mmp-170) cc_final: 0.8144 (mtm110) REVERT: T 178 MET cc_start: 0.7780 (pmt) cc_final: 0.6096 (pmt) REVERT: V 38 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8821 (mp0) REVERT: V 178 MET cc_start: 0.7702 (pmt) cc_final: 0.6054 (pmt) REVERT: V 185 ARG cc_start: 0.8485 (mmp-170) cc_final: 0.8154 (mtm110) REVERT: W 178 MET cc_start: 0.7788 (pmt) cc_final: 0.6120 (pmt) REVERT: X 178 MET cc_start: 0.7765 (pmt) cc_final: 0.6109 (pmt) REVERT: Y 178 MET cc_start: 0.7570 (pmt) cc_final: 0.5979 (pmt) REVERT: Y 185 ARG cc_start: 0.8472 (mmp-170) cc_final: 0.8157 (mtm110) outliers start: 99 outliers final: 72 residues processed: 1056 average time/residue: 1.0296 time to fit residues: 1256.2615 Evaluate side-chains 1249 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 1174 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 173 ILE Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 173 ILE Chi-restraints excluded: chain I residue 28 PHE Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 173 ILE Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain K residue 173 ILE Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 173 ILE Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 38 GLU Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 173 ILE Chi-restraints excluded: chain N residue 28 PHE Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain N residue 173 ILE Chi-restraints excluded: chain O residue 28 PHE Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain O residue 173 ILE Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 173 ILE Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 173 ILE Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 173 ILE Chi-restraints excluded: chain S residue 28 PHE Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 173 ILE Chi-restraints excluded: chain T residue 28 PHE Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain T residue 173 ILE Chi-restraints excluded: chain V residue 28 PHE Chi-restraints excluded: chain V residue 38 GLU Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain W residue 28 PHE Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain W residue 173 ILE Chi-restraints excluded: chain X residue 28 PHE Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain X residue 173 ILE Chi-restraints excluded: chain Y residue 28 PHE Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 173 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 326 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 442 optimal weight: 20.0000 chunk 363 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 355 optimal weight: 0.0470 chunk 451 optimal weight: 0.0170 chunk 128 optimal weight: 10.0000 chunk 445 optimal weight: 5.9990 chunk 144 optimal weight: 20.0000 overall best weight: 4.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN B 214 ASN C 214 ASN D 214 ASN E 214 ASN F 214 ASN G 214 ASN H 214 ASN I 214 ASN J 214 ASN K 214 ASN L 214 ASN M 214 ASN N 214 ASN O 214 ASN P 214 ASN Q 214 ASN R 214 ASN S 214 ASN T 214 ASN V 214 ASN W 214 ASN X 214 ASN Y 214 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.090351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.068689 restraints weight = 55318.049| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 2.29 r_work: 0.2593 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2457 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 51 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| r_final: 0.2486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41352 Z= 0.144 Angle : 0.466 5.680 55872 Z= 0.256 Chirality : 0.036 0.132 5784 Planarity : 0.004 0.038 7152 Dihedral : 3.465 12.235 5376 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.28 % Allowed : 20.19 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.75 (0.12), residues: 4968 helix: 4.63 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.16 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 225 TYR 0.008 0.001 TYR A 88 PHE 0.004 0.001 PHE N 116 TRP 0.004 0.001 TRP H 51 HIS 0.003 0.001 HIS V 41 Details of bonding type rmsd covalent geometry : bond 0.00311 (41328) covalent geometry : angle 0.46535 (55824) SS BOND : bond 0.00513 ( 24) SS BOND : angle 0.95718 ( 48) hydrogen bonds : bond 0.07341 ( 2784) hydrogen bonds : angle 2.96038 ( 8352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1251 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1152 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.7556 (pmt) cc_final: 0.5933 (pmt) REVERT: B 178 MET cc_start: 0.7799 (pmt) cc_final: 0.6111 (pmt) REVERT: B 185 ARG cc_start: 0.8443 (mmp-170) cc_final: 0.8153 (mtm110) REVERT: C 178 MET cc_start: 0.7688 (pmt) cc_final: 0.6008 (pmt) REVERT: D 178 MET cc_start: 0.7533 (pmt) cc_final: 0.5938 (pmt) REVERT: E 178 MET cc_start: 0.7763 (pmt) cc_final: 0.6105 (pmt) REVERT: F 178 MET cc_start: 0.7679 (pmt) cc_final: 0.5999 (pmt) REVERT: G 178 MET cc_start: 0.7805 (pmt) cc_final: 0.6117 (pmt) REVERT: G 185 ARG cc_start: 0.8469 (mmp-170) cc_final: 0.8117 (mtm110) REVERT: H 178 MET cc_start: 0.7640 (pmt) cc_final: 0.6016 (pmt) REVERT: H 185 ARG cc_start: 0.8432 (mmp-170) cc_final: 0.8134 (mtm110) REVERT: I 178 MET cc_start: 0.7673 (pmt) cc_final: 0.6013 (pmt) REVERT: J 178 MET cc_start: 0.7501 (pmt) cc_final: 0.5921 (pmt) REVERT: K 178 MET cc_start: 0.7612 (pmt) cc_final: 0.5980 (pmt) REVERT: L 178 MET cc_start: 0.7666 (pmt) cc_final: 0.6017 (pmt) REVERT: L 185 ARG cc_start: 0.8500 (mmp-170) cc_final: 0.8151 (mtm110) REVERT: M 178 MET cc_start: 0.7757 (pmt) cc_final: 0.6064 (pmt) REVERT: N 178 MET cc_start: 0.7806 (pmt) cc_final: 0.6110 (pmt) REVERT: O 178 MET cc_start: 0.7601 (pmt) cc_final: 0.5966 (pmt) REVERT: P 178 MET cc_start: 0.7587 (pmt) cc_final: 0.5954 (pmt) REVERT: P 185 ARG cc_start: 0.8404 (mmp-170) cc_final: 0.8133 (mtm110) REVERT: Q 178 MET cc_start: 0.7698 (pmt) cc_final: 0.6038 (pmt) REVERT: R 178 MET cc_start: 0.7513 (pmt) cc_final: 0.5894 (pmt) REVERT: S 178 MET cc_start: 0.7717 (pmt) cc_final: 0.6059 (pmt) REVERT: S 185 ARG cc_start: 0.8487 (mmp-170) cc_final: 0.8134 (mtm110) REVERT: T 178 MET cc_start: 0.7752 (pmt) cc_final: 0.6061 (pmt) REVERT: V 178 MET cc_start: 0.7590 (pmt) cc_final: 0.5945 (pmt) REVERT: V 185 ARG cc_start: 0.8489 (mmp-170) cc_final: 0.8146 (mtm110) REVERT: W 178 MET cc_start: 0.7700 (pmt) cc_final: 0.6049 (pmt) REVERT: X 178 MET cc_start: 0.7736 (pmt) cc_final: 0.6066 (pmt) REVERT: Y 178 MET cc_start: 0.7665 (pmt) cc_final: 0.6014 (pmt) REVERT: Y 185 ARG cc_start: 0.8461 (mmp-170) cc_final: 0.8160 (mtm110) outliers start: 99 outliers final: 72 residues processed: 1224 average time/residue: 1.1572 time to fit residues: 1616.8697 Evaluate side-chains 1160 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1088 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain B residue 135 GLN Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain C residue 135 GLN Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 135 GLN Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain F residue 135 GLN Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain G residue 135 GLN Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 135 GLN Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain I residue 135 GLN Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain J residue 135 GLN Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain K residue 135 GLN Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain M residue 135 GLN Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain N residue 135 GLN Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain O residue 135 GLN Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain P residue 135 GLN Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 172 CYS Chi-restraints excluded: chain Q residue 135 GLN Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 172 CYS Chi-restraints excluded: chain R residue 135 GLN Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain S residue 135 GLN Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 172 CYS Chi-restraints excluded: chain T residue 135 GLN Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain T residue 172 CYS Chi-restraints excluded: chain V residue 135 GLN Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 172 CYS Chi-restraints excluded: chain W residue 135 GLN Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain W residue 172 CYS Chi-restraints excluded: chain X residue 135 GLN Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain X residue 172 CYS Chi-restraints excluded: chain Y residue 135 GLN Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 172 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 121 optimal weight: 9.9990 chunk 437 optimal weight: 2.9990 chunk 277 optimal weight: 9.9990 chunk 145 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 448 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 125 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.087746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.066041 restraints weight = 55296.720| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.31 r_work: 0.2534 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2396 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2429 r_free = 0.2429 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 54 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2427 r_free = 0.2427 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| r_final: 0.2427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 41352 Z= 0.183 Angle : 0.505 5.844 55872 Z= 0.273 Chirality : 0.038 0.131 5784 Planarity : 0.004 0.038 7152 Dihedral : 3.590 12.836 5376 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.04 % Allowed : 20.17 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.58 (0.12), residues: 4968 helix: 4.50 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.22 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 225 TYR 0.009 0.002 TYR M 57 PHE 0.005 0.001 PHE M 36 TRP 0.004 0.001 TRP E 109 HIS 0.005 0.001 HIS V 39 Details of bonding type rmsd covalent geometry : bond 0.00418 (41328) covalent geometry : angle 0.50385 (55824) SS BOND : bond 0.00725 ( 24) SS BOND : angle 1.35155 ( 48) hydrogen bonds : bond 0.08876 ( 2784) hydrogen bonds : angle 3.16255 ( 8352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9936 Ramachandran restraints generated. 4968 Oldfield, 0 Emsley, 4968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1233 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 1101 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.9288 (tppp) cc_final: 0.9019 (mmmm) REVERT: A 178 MET cc_start: 0.7782 (pmt) cc_final: 0.6197 (pmt) REVERT: B 105 LYS cc_start: 0.9276 (tppp) cc_final: 0.8994 (mmmm) REVERT: B 178 MET cc_start: 0.7973 (pmt) cc_final: 0.6339 (pmt) REVERT: C 105 LYS cc_start: 0.9281 (tppp) cc_final: 0.9005 (mmmm) REVERT: C 178 MET cc_start: 0.7908 (pmt) cc_final: 0.6268 (pmt) REVERT: D 105 LYS cc_start: 0.9224 (tppp) cc_final: 0.8938 (mmmm) REVERT: D 178 MET cc_start: 0.7797 (pmt) cc_final: 0.6219 (pmt) REVERT: E 105 LYS cc_start: 0.9238 (tppp) cc_final: 0.8949 (mmmm) REVERT: E 178 MET cc_start: 0.7912 (pmt) cc_final: 0.6189 (pmt) REVERT: F 105 LYS cc_start: 0.9322 (tppp) cc_final: 0.9064 (mmmm) REVERT: F 178 MET cc_start: 0.7919 (pmt) cc_final: 0.6154 (pmt) REVERT: G 105 LYS cc_start: 0.9268 (tppp) cc_final: 0.8986 (mmmm) REVERT: H 105 LYS cc_start: 0.9240 (tppp) cc_final: 0.8946 (mmmm) REVERT: H 178 MET cc_start: 0.7836 (pmt) cc_final: 0.6348 (pmt) REVERT: I 178 MET cc_start: 0.7907 (pmt) cc_final: 0.6232 (pmt) REVERT: J 105 LYS cc_start: 0.9233 (tppp) cc_final: 0.8945 (mmmm) REVERT: K 178 MET cc_start: 0.7867 (pmt) cc_final: 0.6129 (pmt) REVERT: L 178 MET cc_start: 0.7881 (pmt) cc_final: 0.6141 (pmt) REVERT: M 105 LYS cc_start: 0.9297 (tppp) cc_final: 0.9033 (mmmm) REVERT: N 105 LYS cc_start: 0.9275 (tppp) cc_final: 0.8996 (mmmm) REVERT: N 178 MET cc_start: 0.7934 (pmt) cc_final: 0.6413 (pmt) REVERT: O 178 MET cc_start: 0.7739 (pmt) cc_final: 0.6266 (pmt) REVERT: P 105 LYS cc_start: 0.9300 (tppp) cc_final: 0.9026 (mmmm) REVERT: R 178 MET cc_start: 0.7795 (pmt) cc_final: 0.6170 (pmt) REVERT: S 178 MET cc_start: 0.7911 (pmt) cc_final: 0.6276 (pmt) REVERT: T 178 MET cc_start: 0.7901 (pmt) cc_final: 0.6238 (pmt) REVERT: V 178 MET cc_start: 0.7803 (pmt) cc_final: 0.6294 (pmt) outliers start: 132 outliers final: 72 residues processed: 1173 average time/residue: 1.1240 time to fit residues: 1503.7810 Evaluate side-chains 1197 residues out of total 4344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 1125 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain F residue 28 PHE Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain G residue 28 PHE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain H residue 28 PHE Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain I residue 28 PHE Chi-restraints excluded: chain I residue 136 CYS Chi-restraints excluded: chain I residue 172 CYS Chi-restraints excluded: chain J residue 28 PHE Chi-restraints excluded: chain J residue 136 CYS Chi-restraints excluded: chain J residue 172 CYS Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 136 CYS Chi-restraints excluded: chain K residue 172 CYS Chi-restraints excluded: chain L residue 28 PHE Chi-restraints excluded: chain L residue 136 CYS Chi-restraints excluded: chain L residue 172 CYS Chi-restraints excluded: chain M residue 28 PHE Chi-restraints excluded: chain M residue 136 CYS Chi-restraints excluded: chain M residue 172 CYS Chi-restraints excluded: chain N residue 28 PHE Chi-restraints excluded: chain N residue 136 CYS Chi-restraints excluded: chain N residue 172 CYS Chi-restraints excluded: chain O residue 28 PHE Chi-restraints excluded: chain O residue 136 CYS Chi-restraints excluded: chain O residue 172 CYS Chi-restraints excluded: chain P residue 28 PHE Chi-restraints excluded: chain P residue 136 CYS Chi-restraints excluded: chain P residue 172 CYS Chi-restraints excluded: chain Q residue 28 PHE Chi-restraints excluded: chain Q residue 136 CYS Chi-restraints excluded: chain Q residue 172 CYS Chi-restraints excluded: chain R residue 28 PHE Chi-restraints excluded: chain R residue 136 CYS Chi-restraints excluded: chain R residue 172 CYS Chi-restraints excluded: chain S residue 28 PHE Chi-restraints excluded: chain S residue 136 CYS Chi-restraints excluded: chain S residue 172 CYS Chi-restraints excluded: chain T residue 28 PHE Chi-restraints excluded: chain T residue 136 CYS Chi-restraints excluded: chain T residue 172 CYS Chi-restraints excluded: chain V residue 28 PHE Chi-restraints excluded: chain V residue 136 CYS Chi-restraints excluded: chain V residue 172 CYS Chi-restraints excluded: chain W residue 28 PHE Chi-restraints excluded: chain W residue 136 CYS Chi-restraints excluded: chain W residue 172 CYS Chi-restraints excluded: chain X residue 28 PHE Chi-restraints excluded: chain X residue 136 CYS Chi-restraints excluded: chain X residue 172 CYS Chi-restraints excluded: chain Y residue 28 PHE Chi-restraints excluded: chain Y residue 136 CYS Chi-restraints excluded: chain Y residue 172 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 188 optimal weight: 8.9990 chunk 115 optimal weight: 0.3980 chunk 243 optimal weight: 7.9990 chunk 407 optimal weight: 5.9990 chunk 198 optimal weight: 20.0000 chunk 363 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 369 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 422 optimal weight: 8.9990 chunk 388 optimal weight: 9.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.067416 restraints weight = 55398.788| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.30 r_work: 0.2593 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2460 r_free = 0.2460 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.2460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 41352 Z= 0.155 Angle : 0.479 5.748 55872 Z= 0.257 Chirality : 0.036 0.138 5784 Planarity : 0.003 0.038 7152 Dihedral : 3.547 12.384 5376 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.66 % Allowed : 20.93 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.64 (0.12), residues: 4968 helix: 4.53 (0.08), residues: 3552 sheet: None (None), residues: 0 loop : -1.16 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 225 TYR 0.008 0.001 TYR T 88 PHE 0.004 0.001 PHE N 116 TRP 0.004 0.001 TRP M 109 HIS 0.004 0.001 HIS O 39 Details of bonding type rmsd covalent geometry : bond 0.00339 (41328) covalent geometry : angle 0.47802 (55824) SS BOND : bond 0.00577 ( 24) SS BOND : angle 1.07324 ( 48) hydrogen bonds : bond 0.07961 ( 2784) hydrogen bonds : angle 3.05299 ( 8352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27525.34 seconds wall clock time: 465 minutes 39.07 seconds (27939.07 seconds total)