Starting phenix.real_space_refine on Sat Aug 23 09:27:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0l_18796/08_2025/8r0l_18796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0l_18796/08_2025/8r0l_18796.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0l_18796/08_2025/8r0l_18796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0l_18796/08_2025/8r0l_18796.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0l_18796/08_2025/8r0l_18796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0l_18796/08_2025/8r0l_18796.cif" } resolution = 2.43 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= 0.046 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 40 5.16 5 C 7356 2.51 5 N 1752 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11200 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2116 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 28 Chain: "B" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2120 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2123 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "D" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2120 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 2120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2120 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 273} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {'LFA': 4, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {'LFA': 4, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'LFA': 4, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'LFA': 4, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 73 Unusual residues: {'LFA': 4, 'RET': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Time building chain proxies: 2.88, per 1000 atoms: 0.26 Number of scatterers: 11200 At special positions: 0 Unit cell: (93.632, 92.796, 81.928, 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 40 16.00 O 2052 8.00 N 1752 7.00 C 7356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 516.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 79.9% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 15 through 42 Processing helix chain 'A' and resid 43 through 46 removed outlier: 3.666A pdb=" N VAL A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 50 through 78 removed outlier: 4.084A pdb=" N VAL A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 97 through 117 removed outlier: 3.755A pdb=" N VAL A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.841A pdb=" N VAL A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 148 removed outlier: 3.889A pdb=" N ARG A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 189 through 220 removed outlier: 3.602A pdb=" N LEU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 208 " --> pdb=" O MET A 204 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Proline residue: A 211 - end of helix removed outlier: 3.675A pdb=" N TYR A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 262 removed outlier: 4.815A pdb=" N CYS A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 249 " --> pdb=" O CYS A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.907A pdb=" N ALA B 11 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 42 Processing helix chain 'B' and resid 43 through 46 removed outlier: 3.667A pdb=" N VAL B 46 " --> pdb=" O ARG B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 77 removed outlier: 4.086A pdb=" N VAL B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 97 through 117 removed outlier: 3.759A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Proline residue: B 108 - end of helix removed outlier: 3.843A pdb=" N VAL B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 148 Processing helix chain 'B' and resid 155 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 189 through 220 removed outlier: 3.604A pdb=" N LEU B 195 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA B 208 " --> pdb=" O MET B 204 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Proline residue: B 211 - end of helix removed outlier: 3.664A pdb=" N TYR B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 262 removed outlier: 4.816A pdb=" N CYS B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS B 249 " --> pdb=" O CYS B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.843A pdb=" N ALA C 11 " --> pdb=" O PRO C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 42 Processing helix chain 'C' and resid 43 through 46 removed outlier: 3.653A pdb=" N VAL C 46 " --> pdb=" O ARG C 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 50 through 78 removed outlier: 4.083A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 97 through 117 removed outlier: 3.768A pdb=" N VAL C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Proline residue: C 108 - end of helix removed outlier: 3.833A pdb=" N VAL C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 removed outlier: 3.551A pdb=" N LEU C 130 " --> pdb=" O ARG C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 189 through 220 removed outlier: 3.603A pdb=" N LEU C 195 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 208 " --> pdb=" O MET C 204 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 209 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TYR C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Proline residue: C 211 - end of helix removed outlier: 3.666A pdb=" N TYR C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 262 removed outlier: 4.808A pdb=" N CYS C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS C 249 " --> pdb=" O CYS C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 42 Processing helix chain 'D' and resid 43 through 46 removed outlier: 3.668A pdb=" N VAL D 46 " --> pdb=" O ARG D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 50 through 78 removed outlier: 4.092A pdb=" N VAL D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 97 through 117 removed outlier: 3.773A pdb=" N VAL D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Proline residue: D 108 - end of helix removed outlier: 3.846A pdb=" N VAL D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 148 removed outlier: 3.897A pdb=" N ARG D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU D 130 " --> pdb=" O ARG D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 189 through 220 removed outlier: 3.605A pdb=" N LEU D 195 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 208 " --> pdb=" O MET D 204 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL D 209 " --> pdb=" O SER D 205 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) Proline residue: D 211 - end of helix removed outlier: 3.662A pdb=" N TYR D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 262 removed outlier: 4.820A pdb=" N CYS D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 246 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS D 249 " --> pdb=" O CYS D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 42 Processing helix chain 'E' and resid 43 through 46 removed outlier: 3.675A pdb=" N VAL E 46 " --> pdb=" O ARG E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 50 through 78 removed outlier: 4.100A pdb=" N VAL E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 97 through 117 removed outlier: 3.767A pdb=" N VAL E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Proline residue: E 108 - end of helix removed outlier: 3.841A pdb=" N VAL E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 148 removed outlier: 3.902A pdb=" N ARG E 129 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 130 " --> pdb=" O ARG E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 185 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 189 through 220 removed outlier: 3.599A pdb=" N LEU E 195 " --> pdb=" O GLU E 191 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA E 208 " --> pdb=" O MET E 204 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL E 209 " --> pdb=" O SER E 205 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N TYR E 210 " --> pdb=" O GLY E 206 " (cutoff:3.500A) Proline residue: E 211 - end of helix removed outlier: 3.670A pdb=" N TYR E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 262 removed outlier: 4.834A pdb=" N CYS E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS E 249 " --> pdb=" O CYS E 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 272 removed outlier: 6.396A pdb=" N ILE A 271 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 272 removed outlier: 6.396A pdb=" N ILE B 271 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 272 removed outlier: 6.395A pdb=" N ILE C 271 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 272 removed outlier: 6.397A pdb=" N ILE D 271 " --> pdb=" O GLN D 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AB1, first strand: chain 'E' and resid 271 through 272 removed outlier: 6.396A pdb=" N ILE E 271 " --> pdb=" O GLN E 278 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2466 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: 1.63 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2807 1.33 - 1.46: 3236 1.46 - 1.59: 5077 1.59 - 1.71: 0 1.71 - 1.84: 70 Bond restraints: 11190 Sorted by residual: bond pdb=" CA SER A 228 " pdb=" CB SER A 228 " ideal model delta sigma weight residual 1.530 1.455 0.074 1.56e-02 4.11e+03 2.26e+01 bond pdb=" CA SER C 228 " pdb=" CB SER C 228 " ideal model delta sigma weight residual 1.530 1.456 0.074 1.56e-02 4.11e+03 2.23e+01 bond pdb=" CA SER D 228 " pdb=" CB SER D 228 " ideal model delta sigma weight residual 1.530 1.456 0.074 1.56e-02 4.11e+03 2.23e+01 bond pdb=" CA SER E 228 " pdb=" CB SER E 228 " ideal model delta sigma weight residual 1.530 1.456 0.074 1.56e-02 4.11e+03 2.22e+01 bond pdb=" CA SER B 228 " pdb=" CB SER B 228 " ideal model delta sigma weight residual 1.530 1.457 0.072 1.56e-02 4.11e+03 2.15e+01 ... (remaining 11185 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 13158 2.17 - 4.34: 1867 4.34 - 6.51: 148 6.51 - 8.67: 17 8.67 - 10.84: 5 Bond angle restraints: 15195 Sorted by residual: angle pdb=" C ASN D 89 " pdb=" CA ASN D 89 " pdb=" CB ASN D 89 " ideal model delta sigma weight residual 113.45 102.61 10.84 1.98e+00 2.55e-01 3.00e+01 angle pdb=" N ILE C 150 " pdb=" CA ILE C 150 " pdb=" C ILE C 150 " ideal model delta sigma weight residual 110.42 115.61 -5.19 9.60e-01 1.09e+00 2.93e+01 angle pdb=" C TRP E 86 " pdb=" N VAL E 87 " pdb=" CA VAL E 87 " ideal model delta sigma weight residual 123.43 117.85 5.58 1.10e+00 8.26e-01 2.57e+01 angle pdb=" C TRP C 86 " pdb=" N VAL C 87 " pdb=" CA VAL C 87 " ideal model delta sigma weight residual 123.43 117.85 5.58 1.10e+00 8.26e-01 2.57e+01 angle pdb=" CA THR D 28 " pdb=" CB THR D 28 " pdb=" OG1 THR D 28 " ideal model delta sigma weight residual 109.60 102.15 7.45 1.50e+00 4.44e-01 2.47e+01 ... (remaining 15190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 6042 21.87 - 43.74: 358 43.74 - 65.61: 58 65.61 - 87.48: 2 87.48 - 109.36: 10 Dihedral angle restraints: 6470 sinusoidal: 2430 harmonic: 4040 Sorted by residual: dihedral pdb=" CD ARG C 38 " pdb=" NE ARG C 38 " pdb=" CZ ARG C 38 " pdb=" NH1 ARG C 38 " ideal model delta sinusoidal sigma weight residual 0.00 -45.91 45.91 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" C ILE C 150 " pdb=" N ILE C 150 " pdb=" CA ILE C 150 " pdb=" CB ILE C 150 " ideal model delta harmonic sigma weight residual -122.00 -133.24 11.24 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA VAL E 148 " pdb=" C VAL E 148 " pdb=" N VAL E 149 " pdb=" CA VAL E 149 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 6467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1066 0.060 - 0.120: 602 0.120 - 0.181: 159 0.181 - 0.241: 21 0.241 - 0.301: 2 Chirality restraints: 1850 Sorted by residual: chirality pdb=" CA ILE C 150 " pdb=" N ILE C 150 " pdb=" C ILE C 150 " pdb=" CB ILE C 150 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ILE D 5 " pdb=" N ILE D 5 " pdb=" C ILE D 5 " pdb=" CB ILE D 5 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE A 5 " pdb=" N ILE A 5 " pdb=" C ILE A 5 " pdb=" CB ILE A 5 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1847 not shown) Planarity restraints: 1785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET C 405 " 0.063 2.00e-02 2.50e+03 7.86e-02 7.73e+01 pdb=" C13 RET C 405 " 0.004 2.00e-02 2.50e+03 pdb=" C14 RET C 405 " -0.134 2.00e-02 2.50e+03 pdb=" C15 RET C 405 " 0.092 2.00e-02 2.50e+03 pdb=" C20 RET C 405 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET D 405 " -0.063 2.00e-02 2.50e+03 7.84e-02 7.68e+01 pdb=" C13 RET D 405 " -0.004 2.00e-02 2.50e+03 pdb=" C14 RET D 405 " 0.133 2.00e-02 2.50e+03 pdb=" C15 RET D 405 " -0.091 2.00e-02 2.50e+03 pdb=" C20 RET D 405 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET E 405 " -0.061 2.00e-02 2.50e+03 7.62e-02 7.27e+01 pdb=" C13 RET E 405 " -0.004 2.00e-02 2.50e+03 pdb=" C14 RET E 405 " 0.130 2.00e-02 2.50e+03 pdb=" C15 RET E 405 " -0.089 2.00e-02 2.50e+03 pdb=" C20 RET E 405 " 0.024 2.00e-02 2.50e+03 ... (remaining 1782 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 823 2.71 - 3.26: 11267 3.26 - 3.80: 20412 3.80 - 4.35: 27642 4.35 - 4.90: 43720 Nonbonded interactions: 103864 Sorted by model distance: nonbonded pdb=" OD2 ASP D 80 " pdb=" OD1 ASN D 89 " model vdw 2.159 3.040 nonbonded pdb=" O PHE D 169 " pdb=" OG1 THR D 173 " model vdw 2.295 3.040 nonbonded pdb=" O PHE C 169 " pdb=" OG1 THR C 173 " model vdw 2.296 3.040 nonbonded pdb=" O PHE A 169 " pdb=" OG1 THR A 173 " model vdw 2.296 3.040 nonbonded pdb=" O PHE B 169 " pdb=" OG1 THR B 173 " model vdw 2.298 3.040 ... (remaining 103859 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 284 or (resid 401 and (name C11 or name C12 or n \ ame C13 or name C14)) or (resid 403 and (name C12)) or resid 405)) selection = (chain 'B' and (resid 3 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 183 through 284 or (re \ sid 401 and (name C11 or name C12 or name C13 or name C14)) or (resid 403 and (n \ ame C12)) or resid 405)) selection = (chain 'C' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 181 or (resid 182 and (name N or name CA or name C or name \ O or name CB or name CG or name CD )) or resid 183 through 284 or (resid 401 and \ (name C11 or name C12 or name C13 or name C14)) or (resid 403 and (name C12)) o \ r resid 405)) selection = (chain 'D' and (resid 3 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 183 through 284 or (re \ sid 401 and (name C11 or name C12 or name C13 or name C14)) or (resid 403 and (n \ ame C12)) or resid 405)) selection = (chain 'E' and (resid 3 through 181 or (resid 182 and (name N or name CA or name \ C or name O or name CB or name CG or name CD )) or resid 183 through 284 or (re \ sid 401 and (name C11 or name C12 or name C13 or name C14)) or (resid 403 and (n \ ame C12)) or resid 405)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.010 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 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 : 0.011 0.087 11195 Z= 0.722 Angle : 1.503 10.844 15195 Z= 1.015 Chirality : 0.074 0.301 1850 Planarity : 0.024 0.338 1785 Dihedral : 14.983 109.355 3870 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.52 % Allowed : 10.23 % Favored : 85.25 % Cbeta Deviations : 0.08 % 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 aren not related in a simple way. whole: -3.17 (0.18), residues: 1400 helix: -2.19 (0.12), residues: 1005 sheet: None (None), residues: 0 loop : -1.21 (0.29), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.005 ARG E 255 TYR 0.036 0.009 TYR E 50 PHE 0.048 0.009 PHE A 141 TRP 0.039 0.010 TRP D 103 HIS 0.013 0.003 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.01114 (11190) covalent geometry : angle 1.50326 (15195) hydrogen bonds : bond 0.20556 ( 844) hydrogen bonds : angle 7.82654 ( 2466) Misc. bond : bond 0.02526 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 0.374 Fit side-chains REVERT: A 94 MET cc_start: 0.7724 (mmp) cc_final: 0.7419 (mmp) REVERT: A 183 HIS cc_start: 0.7965 (t70) cc_final: 0.7753 (t70) REVERT: A 283 ILE cc_start: 0.6598 (OUTLIER) cc_final: 0.6308 (pt) REVERT: D 5 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.6830 (tp) REVERT: D 61 MET cc_start: 0.9096 (mmm) cc_final: 0.8524 (mmt) REVERT: D 102 GLU cc_start: 0.8717 (tt0) cc_final: 0.8469 (tm-30) REVERT: E 96 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8443 (mt) outliers start: 49 outliers final: 24 residues processed: 185 average time/residue: 0.5333 time to fit residues: 107.0356 Evaluate side-chains 168 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 89 ASN Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 81 HIS A 230 HIS B 187 GLN B 230 HIS C 81 HIS C 230 HIS D 81 HIS D 230 HIS E 230 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109240 restraints weight = 11355.366| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.15 r_work: 0.3235 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 11195 Z= 0.130 Angle : 0.553 5.346 15195 Z= 0.294 Chirality : 0.039 0.114 1850 Planarity : 0.005 0.029 1785 Dihedral : 8.515 59.564 1799 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 2.40 % Allowed : 13.00 % Favored : 84.61 % 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 aren not related in a simple way. whole: 0.76 (0.21), residues: 1400 helix: 1.09 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.96 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 154 TYR 0.014 0.002 TYR E 68 PHE 0.015 0.002 PHE D 137 TRP 0.012 0.001 TRP C 225 HIS 0.004 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00271 (11190) covalent geometry : angle 0.55318 (15195) hydrogen bonds : bond 0.04508 ( 844) hydrogen bonds : angle 3.83048 ( 2466) Misc. bond : bond 0.00029 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.428 Fit side-chains REVERT: A 69 VAL cc_start: 0.8095 (t) cc_final: 0.7849 (m) REVERT: B 66 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8038 (tp) REVERT: C 66 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8097 (tp) REVERT: C 113 GLU cc_start: 0.8610 (tt0) cc_final: 0.8380 (tt0) REVERT: C 269 GLU cc_start: 0.8111 (tt0) cc_final: 0.7710 (tt0) REVERT: D 66 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8110 (tp) REVERT: E 66 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8105 (tp) REVERT: E 96 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8209 (mp) outliers start: 26 outliers final: 6 residues processed: 179 average time/residue: 0.5782 time to fit residues: 112.1515 Evaluate side-chains 162 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 151 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 96 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 18 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN C 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.106276 restraints weight = 11483.498| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.17 r_work: 0.3194 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11195 Z= 0.165 Angle : 0.534 5.155 15195 Z= 0.289 Chirality : 0.041 0.159 1850 Planarity : 0.005 0.035 1785 Dihedral : 7.977 59.134 1773 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 4.33 % Allowed : 12.53 % Favored : 83.13 % 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 aren not related in a simple way. whole: 2.07 (0.22), residues: 1400 helix: 2.14 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.78 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 255 TYR 0.016 0.002 TYR D 100 PHE 0.013 0.002 PHE D 137 TRP 0.013 0.001 TRP C 225 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00377 (11190) covalent geometry : angle 0.53387 (15195) hydrogen bonds : bond 0.04783 ( 844) hydrogen bonds : angle 3.66686 ( 2466) Misc. bond : bond 0.00018 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.358 Fit side-chains REVERT: A 38 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8195 (ttp-170) REVERT: A 129 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7314 (ttm170) REVERT: B 66 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7988 (tp) REVERT: B 280 ASP cc_start: 0.8461 (m-30) cc_final: 0.8228 (m-30) REVERT: C 66 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8030 (tp) REVERT: C 113 GLU cc_start: 0.8664 (tt0) cc_final: 0.8449 (tt0) REVERT: C 269 GLU cc_start: 0.8120 (tt0) cc_final: 0.7723 (tt0) REVERT: D 61 MET cc_start: 0.8962 (mmm) cc_final: 0.8644 (mmt) REVERT: D 66 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8079 (tp) REVERT: D 129 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7557 (ttp-170) REVERT: D 130 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8094 (mm) REVERT: E 66 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8131 (tp) REVERT: E 96 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8194 (mp) REVERT: E 129 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7485 (ttm170) REVERT: E 280 ASP cc_start: 0.8411 (m-30) cc_final: 0.8205 (m-30) outliers start: 47 outliers final: 16 residues processed: 177 average time/residue: 0.6087 time to fit residues: 116.3442 Evaluate side-chains 173 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 83 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104955 restraints weight = 11557.685| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.17 r_work: 0.3180 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11195 Z= 0.209 Angle : 0.561 5.329 15195 Z= 0.304 Chirality : 0.043 0.134 1850 Planarity : 0.005 0.037 1785 Dihedral : 8.464 59.225 1773 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.69 % Allowed : 13.82 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.15 (0.22), residues: 1400 helix: 2.22 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.83 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 255 TYR 0.016 0.002 TYR E 68 PHE 0.015 0.003 PHE C 137 TRP 0.014 0.002 TRP C 225 HIS 0.003 0.001 HIS A 81 Details of bonding type rmsd covalent geometry : bond 0.00492 (11190) covalent geometry : angle 0.56105 (15195) hydrogen bonds : bond 0.05051 ( 844) hydrogen bonds : angle 3.74039 ( 2466) Misc. bond : bond 0.00034 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 0.446 Fit side-chains REVERT: A 38 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8173 (ttp-170) REVERT: A 129 ARG cc_start: 0.7739 (ttm170) cc_final: 0.7349 (ttm170) REVERT: A 130 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8294 (mm) REVERT: A 187 GLN cc_start: 0.8390 (mt0) cc_final: 0.8142 (mt0) REVERT: B 66 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8016 (tp) REVERT: B 280 ASP cc_start: 0.8485 (m-30) cc_final: 0.8256 (m-30) REVERT: C 66 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8004 (tp) REVERT: C 150 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7829 (mp) REVERT: D 61 MET cc_start: 0.8949 (mmm) cc_final: 0.8676 (mmt) REVERT: D 66 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8117 (tp) REVERT: D 129 ARG cc_start: 0.7792 (ttm170) cc_final: 0.7501 (ttp-170) REVERT: D 130 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8099 (mm) REVERT: E 15 GLN cc_start: 0.7903 (mt0) cc_final: 0.7680 (mt0) REVERT: E 66 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8143 (tp) REVERT: E 96 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8169 (mp) REVERT: E 129 ARG cc_start: 0.7874 (ttm170) cc_final: 0.7491 (ttm170) REVERT: E 130 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8216 (mm) outliers start: 40 outliers final: 21 residues processed: 169 average time/residue: 0.5918 time to fit residues: 108.4396 Evaluate side-chains 176 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ARG Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.121952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107366 restraints weight = 11397.897| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.16 r_work: 0.3214 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11195 Z= 0.139 Angle : 0.493 5.076 15195 Z= 0.266 Chirality : 0.040 0.124 1850 Planarity : 0.005 0.037 1785 Dihedral : 7.810 58.877 1773 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.23 % Allowed : 13.82 % Favored : 82.95 % 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 aren not related in a simple way. whole: 2.54 (0.22), residues: 1400 helix: 2.53 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.74 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.013 0.002 TYR A 68 PHE 0.012 0.002 PHE D 137 TRP 0.013 0.001 TRP D 225 HIS 0.002 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00311 (11190) covalent geometry : angle 0.49279 (15195) hydrogen bonds : bond 0.04293 ( 844) hydrogen bonds : angle 3.53500 ( 2466) Misc. bond : bond 0.00010 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.424 Fit side-chains REVERT: A 130 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8211 (mm) REVERT: B 66 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8015 (tp) REVERT: B 280 ASP cc_start: 0.8432 (m-30) cc_final: 0.8229 (m-30) REVERT: C 66 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8121 (tp) REVERT: D 61 MET cc_start: 0.8942 (mmm) cc_final: 0.8662 (mmt) REVERT: D 66 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8139 (tp) REVERT: D 129 ARG cc_start: 0.7727 (ttm170) cc_final: 0.7452 (ttp-170) REVERT: D 130 LEU cc_start: 0.8352 (mt) cc_final: 0.8073 (mm) REVERT: E 15 GLN cc_start: 0.7855 (mt0) cc_final: 0.7632 (mt0) REVERT: E 66 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8120 (tp) REVERT: E 96 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8093 (mp) REVERT: E 130 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8167 (mm) outliers start: 35 outliers final: 16 residues processed: 169 average time/residue: 0.5980 time to fit residues: 109.3172 Evaluate side-chains 174 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 116 optimal weight: 0.0670 chunk 1 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN E 187 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.123012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108347 restraints weight = 11543.315| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.18 r_work: 0.3228 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11195 Z= 0.124 Angle : 0.474 5.058 15195 Z= 0.255 Chirality : 0.039 0.121 1850 Planarity : 0.004 0.037 1785 Dihedral : 7.401 59.838 1773 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.95 % Allowed : 13.82 % Favored : 83.23 % 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 aren not related in a simple way. whole: 2.81 (0.22), residues: 1400 helix: 2.75 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : -0.69 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 57 TYR 0.012 0.002 TYR A 68 PHE 0.011 0.002 PHE D 137 TRP 0.012 0.001 TRP C 225 HIS 0.002 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00269 (11190) covalent geometry : angle 0.47442 (15195) hydrogen bonds : bond 0.04068 ( 844) hydrogen bonds : angle 3.45284 ( 2466) Misc. bond : bond 0.00006 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 0.437 Fit side-chains REVERT: B 66 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7918 (tp) REVERT: C 57 ARG cc_start: 0.8330 (ttm-80) cc_final: 0.8123 (ttm-80) REVERT: C 66 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8082 (tp) REVERT: C 269 GLU cc_start: 0.8092 (tt0) cc_final: 0.7694 (tt0) REVERT: C 283 ILE cc_start: 0.6924 (OUTLIER) cc_final: 0.6479 (mm) REVERT: D 61 MET cc_start: 0.8935 (mmm) cc_final: 0.8632 (mmt) REVERT: D 130 LEU cc_start: 0.8333 (mt) cc_final: 0.8056 (mm) REVERT: E 15 GLN cc_start: 0.7824 (mt0) cc_final: 0.7603 (mt0) REVERT: E 66 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8097 (tp) REVERT: E 130 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8137 (mm) outliers start: 32 outliers final: 15 residues processed: 163 average time/residue: 0.5808 time to fit residues: 102.4899 Evaluate side-chains 172 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain C residue 15 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 97 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 15 GLN D 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105899 restraints weight = 11419.061| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.17 r_work: 0.3194 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11195 Z= 0.194 Angle : 0.536 5.172 15195 Z= 0.290 Chirality : 0.042 0.134 1850 Planarity : 0.005 0.037 1785 Dihedral : 7.974 59.961 1769 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.69 % Allowed : 13.00 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.22), residues: 1400 helix: 2.44 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.70 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 57 TYR 0.017 0.002 TYR D 100 PHE 0.015 0.003 PHE C 137 TRP 0.014 0.002 TRP C 225 HIS 0.002 0.001 HIS D 249 Details of bonding type rmsd covalent geometry : bond 0.00455 (11190) covalent geometry : angle 0.53597 (15195) hydrogen bonds : bond 0.04828 ( 844) hydrogen bonds : angle 3.65432 ( 2466) Misc. bond : bond 0.00033 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.429 Fit side-chains REVERT: A 129 ARG cc_start: 0.7696 (ttm170) cc_final: 0.7306 (ttm170) REVERT: A 130 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8257 (mm) REVERT: B 66 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7978 (tp) REVERT: C 66 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8120 (tp) REVERT: C 150 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7842 (mp) REVERT: D 5 ILE cc_start: 0.7743 (OUTLIER) cc_final: 0.6743 (tt) REVERT: D 61 MET cc_start: 0.8957 (mmm) cc_final: 0.8722 (mmt) REVERT: D 129 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7461 (ttp-170) REVERT: D 130 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8080 (mm) REVERT: E 15 GLN cc_start: 0.7901 (mt0) cc_final: 0.7676 (mt0) REVERT: E 66 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8102 (tp) REVERT: E 129 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7460 (ttm170) REVERT: E 130 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8193 (mm) outliers start: 40 outliers final: 18 residues processed: 164 average time/residue: 0.6340 time to fit residues: 112.2665 Evaluate side-chains 171 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 145 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 56 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 74 optimal weight: 0.0570 chunk 9 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.124683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110090 restraints weight = 11383.500| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.17 r_work: 0.3250 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11195 Z= 0.105 Angle : 0.457 5.037 15195 Z= 0.245 Chirality : 0.038 0.119 1850 Planarity : 0.004 0.037 1785 Dihedral : 6.891 58.184 1769 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.03 % Allowed : 14.84 % Favored : 83.13 % 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 aren not related in a simple way. whole: 2.95 (0.22), residues: 1400 helix: 2.87 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : -0.68 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 57 TYR 0.010 0.001 TYR E 68 PHE 0.011 0.002 PHE D 137 TRP 0.013 0.001 TRP C 225 HIS 0.003 0.001 HIS E 18 Details of bonding type rmsd covalent geometry : bond 0.00216 (11190) covalent geometry : angle 0.45681 (15195) hydrogen bonds : bond 0.03759 ( 844) hydrogen bonds : angle 3.38631 ( 2466) Misc. bond : bond 0.00009 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.438 Fit side-chains REVERT: A 269 GLU cc_start: 0.8260 (tt0) cc_final: 0.7938 (pt0) REVERT: B 66 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7908 (tp) REVERT: B 280 ASP cc_start: 0.8317 (m-30) cc_final: 0.8085 (m-30) REVERT: C 66 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8088 (tp) REVERT: C 269 GLU cc_start: 0.8054 (tt0) cc_final: 0.7672 (tt0) REVERT: C 283 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6502 (mm) REVERT: D 61 MET cc_start: 0.8918 (mmm) cc_final: 0.8626 (mmt) REVERT: D 130 LEU cc_start: 0.8339 (mt) cc_final: 0.8063 (mm) REVERT: E 15 GLN cc_start: 0.7806 (mt0) cc_final: 0.7587 (mt0) REVERT: E 66 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8111 (tp) REVERT: E 269 GLU cc_start: 0.8127 (tt0) cc_final: 0.7665 (tt0) outliers start: 22 outliers final: 10 residues processed: 160 average time/residue: 0.6132 time to fit residues: 106.2210 Evaluate side-chains 165 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.120300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105694 restraints weight = 11331.459| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.16 r_work: 0.3192 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11195 Z= 0.215 Angle : 0.556 5.218 15195 Z= 0.301 Chirality : 0.043 0.136 1850 Planarity : 0.005 0.036 1785 Dihedral : 8.021 58.448 1769 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.58 % Allowed : 14.29 % Favored : 83.13 % 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 aren not related in a simple way. whole: 2.43 (0.22), residues: 1400 helix: 2.43 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.72 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 57 TYR 0.020 0.002 TYR D 100 PHE 0.015 0.003 PHE B 22 TRP 0.014 0.002 TRP C 225 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00508 (11190) covalent geometry : angle 0.55598 (15195) hydrogen bonds : bond 0.04953 ( 844) hydrogen bonds : angle 3.67828 ( 2466) Misc. bond : bond 0.00040 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.449 Fit side-chains REVERT: A 129 ARG cc_start: 0.7704 (ttm170) cc_final: 0.7315 (ttm170) REVERT: A 130 LEU cc_start: 0.8354 (mt) cc_final: 0.8088 (mm) REVERT: B 66 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7950 (tp) REVERT: B 280 ASP cc_start: 0.8481 (m-30) cc_final: 0.8278 (m-30) REVERT: C 66 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8122 (tp) REVERT: C 150 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7790 (mp) REVERT: D 5 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.6732 (tt) REVERT: D 61 MET cc_start: 0.8960 (mmm) cc_final: 0.8734 (mmt) REVERT: D 129 ARG cc_start: 0.7749 (ttm170) cc_final: 0.7453 (ttp-170) REVERT: D 130 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8080 (mm) REVERT: E 15 GLN cc_start: 0.7901 (mt0) cc_final: 0.7683 (mt0) REVERT: E 66 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8171 (tp) REVERT: E 129 ARG cc_start: 0.7850 (ttm170) cc_final: 0.7453 (ttm170) REVERT: E 130 LEU cc_start: 0.8448 (mp) cc_final: 0.8200 (mm) REVERT: E 269 GLU cc_start: 0.8271 (tt0) cc_final: 0.7658 (tt0) outliers start: 28 outliers final: 13 residues processed: 161 average time/residue: 0.6383 time to fit residues: 110.3560 Evaluate side-chains 163 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN B 15 GLN D 89 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.123592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108939 restraints weight = 11356.625| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.17 r_work: 0.3238 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11195 Z= 0.122 Angle : 0.477 4.965 15195 Z= 0.257 Chirality : 0.039 0.122 1850 Planarity : 0.004 0.037 1785 Dihedral : 7.121 56.168 1769 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.94 % Allowed : 14.93 % Favored : 83.13 % 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 aren not related in a simple way. whole: 2.80 (0.22), residues: 1400 helix: 2.73 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.68 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 57 TYR 0.014 0.002 TYR D 100 PHE 0.011 0.002 PHE D 137 TRP 0.012 0.001 TRP D 225 HIS 0.003 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00265 (11190) covalent geometry : angle 0.47659 (15195) hydrogen bonds : bond 0.03989 ( 844) hydrogen bonds : angle 3.45202 ( 2466) Misc. bond : bond 0.00008 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.417 Fit side-chains REVERT: B 66 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7896 (tp) REVERT: C 66 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8078 (tp) REVERT: C 269 GLU cc_start: 0.8080 (tt0) cc_final: 0.7660 (tt0) REVERT: D 5 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.6804 (tt) REVERT: D 61 MET cc_start: 0.8928 (mmm) cc_final: 0.8689 (mmt) REVERT: D 130 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8073 (mm) REVERT: E 15 GLN cc_start: 0.7820 (mt0) cc_final: 0.7597 (mt0) REVERT: E 66 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8118 (tp) REVERT: E 130 LEU cc_start: 0.8338 (mp) cc_final: 0.8101 (mm) REVERT: E 269 GLU cc_start: 0.8166 (tt0) cc_final: 0.7663 (tt0) outliers start: 21 outliers final: 11 residues processed: 158 average time/residue: 0.5160 time to fit residues: 88.5949 Evaluate side-chains 164 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 274 SER Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 283 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 99 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.122018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107321 restraints weight = 11420.255| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.17 r_work: 0.3213 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11195 Z= 0.154 Angle : 0.504 5.023 15195 Z= 0.272 Chirality : 0.040 0.128 1850 Planarity : 0.004 0.037 1785 Dihedral : 7.403 54.486 1769 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.94 % Allowed : 14.56 % Favored : 83.50 % 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 aren not related in a simple way. whole: 2.68 (0.22), residues: 1400 helix: 2.63 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.70 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 57 TYR 0.017 0.002 TYR D 100 PHE 0.012 0.002 PHE D 137 TRP 0.013 0.001 TRP D 225 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00352 (11190) covalent geometry : angle 0.50392 (15195) hydrogen bonds : bond 0.04379 ( 844) hydrogen bonds : angle 3.53649 ( 2466) Misc. bond : bond 0.00022 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3875.17 seconds wall clock time: 66 minutes 51.07 seconds (4011.07 seconds total)