Starting phenix.real_space_refine on Tue Jul 29 07:49:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0l_18796/07_2025/8r0l_18796.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0l_18796/07_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_18796/07_2025/8r0l_18796.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0l_18796/07_2025/8r0l_18796.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0l_18796/07_2025/8r0l_18796.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0l_18796/07_2025/8r0l_18796.cif" } resolution = 2.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} 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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP: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: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP: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: 8.20, per 1000 atoms: 0.73 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: 2.72 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.08 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: 3.54 Time building geometry restraints manager: 3.25 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 29.570 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.039 0.010 TRP D 103 HIS 0.013 0.003 HIS B 81 PHE 0.048 0.009 PHE A 141 TYR 0.036 0.009 TYR E 50 ARG 0.031 0.005 ARG E 255 Details of bonding type rmsd hydrogen bonds : bond 0.20556 ( 844) hydrogen bonds : angle 7.82654 ( 2466) covalent geometry : bond 0.01114 (11190) covalent geometry : angle 1.50326 (15195) 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 : 1.087 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: 1.1640 time to fit residues: 234.2746 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 : 1.133 ------------------------------------------------------------------------------- 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 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 0.0870 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.0470 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 66 optimal weight: 0.4980 chunk 81 optimal weight: 0.5980 chunk 127 optimal weight: 0.4980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.125353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111194 restraints weight = 11197.809| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.14 r_work: 0.3263 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11195 Z= 0.119 Angle : 0.541 5.466 15195 Z= 0.286 Chirality : 0.039 0.120 1850 Planarity : 0.005 0.028 1785 Dihedral : 8.249 58.387 1799 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.21 % Allowed : 13.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.21), residues: 1400 helix: 1.23 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.91 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 225 HIS 0.005 0.001 HIS B 18 PHE 0.012 0.002 PHE D 137 TYR 0.012 0.002 TYR B 68 ARG 0.004 0.000 ARG D 154 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 844) hydrogen bonds : angle 3.77450 ( 2466) covalent geometry : bond 0.00217 (11190) covalent geometry : angle 0.54062 (15195) Misc. bond : bond 0.00034 ( 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 186 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 1.233 Fit side-chains REVERT: A 247 LEU cc_start: 0.8432 (mt) cc_final: 0.8190 (mp) REVERT: B 66 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7989 (tp) REVERT: C 66 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8069 (tp) REVERT: C 69 VAL cc_start: 0.7939 (t) cc_final: 0.7736 (m) REVERT: C 113 GLU cc_start: 0.8579 (tt0) cc_final: 0.8365 (tt0) REVERT: C 269 GLU cc_start: 0.8039 (tt0) cc_final: 0.7632 (tt0) REVERT: D 66 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8100 (tp) REVERT: E 66 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8104 (tp) REVERT: E 96 ILE cc_start: 0.8540 (OUTLIER) cc_final: 0.8217 (mp) outliers start: 24 outliers final: 6 residues processed: 177 average time/residue: 1.2110 time to fit residues: 232.7843 Evaluate side-chains 158 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 1.296 ------------------------------------------------------------------------------- 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 16 optimal weight: 0.6980 chunk 109 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 126 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 HIS B 187 GLN C 15 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.121151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106489 restraints weight = 11421.191| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.16 r_work: 0.3199 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11195 Z= 0.162 Angle : 0.532 5.201 15195 Z= 0.288 Chirality : 0.041 0.155 1850 Planarity : 0.005 0.035 1785 Dihedral : 7.846 54.220 1773 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 3.87 % Allowed : 12.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.22), residues: 1400 helix: 2.19 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.77 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 225 HIS 0.003 0.001 HIS E 249 PHE 0.013 0.002 PHE E 22 TYR 0.016 0.002 TYR E 68 ARG 0.003 0.000 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 844) hydrogen bonds : angle 3.64394 ( 2466) covalent geometry : bond 0.00370 (11190) covalent geometry : angle 0.53219 (15195) Misc. bond : bond 0.00020 ( 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 196 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 1.696 Fit side-chains REVERT: A 129 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7293 (ttm170) REVERT: B 66 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7981 (tp) REVERT: C 66 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8028 (tp) REVERT: C 269 GLU cc_start: 0.8107 (tt0) cc_final: 0.7714 (tt0) REVERT: D 61 MET cc_start: 0.8954 (mmm) cc_final: 0.8579 (mmt) REVERT: D 66 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8084 (tp) REVERT: D 129 ARG cc_start: 0.7736 (ttm170) cc_final: 0.7405 (ttm170) REVERT: D 130 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8074 (mm) REVERT: E 66 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8120 (tp) REVERT: E 96 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8236 (mp) REVERT: E 280 ASP cc_start: 0.8360 (m-30) cc_final: 0.8145 (m-30) outliers start: 42 outliers final: 13 residues processed: 176 average time/residue: 1.6247 time to fit residues: 309.0745 Evaluate side-chains 165 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 159 LEU Chi-restraints excluded: chain C residue 247 LEU 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 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 107 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN D 15 GLN E 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.121249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106575 restraints weight = 11359.446| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.16 r_work: 0.3205 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2041 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= 0.162 Angle : 0.521 5.149 15195 Z= 0.282 Chirality : 0.041 0.129 1850 Planarity : 0.005 0.036 1785 Dihedral : 7.826 54.669 1773 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.41 % Allowed : 13.92 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.22), residues: 1400 helix: 2.41 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.78 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 225 HIS 0.002 0.001 HIS D 249 PHE 0.013 0.002 PHE E 22 TYR 0.015 0.002 TYR B 68 ARG 0.003 0.000 ARG C 255 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 844) hydrogen bonds : angle 3.60720 ( 2466) covalent geometry : bond 0.00369 (11190) covalent geometry : angle 0.52113 (15195) Misc. bond : bond 0.00013 ( 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: 37 poor density : 149 time to evaluate : 1.228 Fit side-chains REVERT: A 15 GLN cc_start: 0.7771 (mt0) cc_final: 0.6900 (mm-40) REVERT: A 129 ARG cc_start: 0.7643 (ttm170) cc_final: 0.7240 (ttm170) REVERT: A 197 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7923 (tttt) REVERT: B 66 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8049 (tp) REVERT: C 66 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8057 (tp) REVERT: C 150 ILE cc_start: 0.8141 (OUTLIER) cc_final: 0.7804 (mp) REVERT: D 61 MET cc_start: 0.8954 (mmm) cc_final: 0.8633 (mmt) REVERT: D 66 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8074 (tp) REVERT: D 129 ARG cc_start: 0.7729 (ttm170) cc_final: 0.7446 (ttp-170) REVERT: D 130 LEU cc_start: 0.8352 (mt) cc_final: 0.8074 (mm) REVERT: E 66 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8146 (tp) REVERT: E 113 GLU cc_start: 0.8583 (tt0) cc_final: 0.8358 (tt0) REVERT: E 280 ASP cc_start: 0.8359 (m-30) cc_final: 0.8157 (m-30) outliers start: 37 outliers final: 18 residues processed: 165 average time/residue: 1.4337 time to fit residues: 256.5673 Evaluate side-chains 173 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 197 LYS Chi-restraints excluded: chain B residue 66 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 56 optimal weight: 0.0050 chunk 2 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- 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 = 0.3481 r_free = 0.3481 target = 0.121133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106557 restraints weight = 11326.789| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.16 r_work: 0.3206 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11195 Z= 0.164 Angle : 0.517 5.096 15195 Z= 0.280 Chirality : 0.041 0.128 1850 Planarity : 0.005 0.035 1785 Dihedral : 7.767 57.419 1771 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.69 % Allowed : 13.64 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.22), residues: 1400 helix: 2.46 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.74 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 225 HIS 0.002 0.001 HIS D 249 PHE 0.013 0.002 PHE C 137 TYR 0.015 0.002 TYR E 68 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.04562 ( 844) hydrogen bonds : angle 3.59425 ( 2466) covalent geometry : bond 0.00376 (11190) covalent geometry : angle 0.51719 (15195) Misc. bond : bond 0.00015 ( 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 191 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 151 time to evaluate : 1.094 Fit side-chains REVERT: A 129 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7249 (ttm170) REVERT: A 130 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 197 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7942 (tttt) REVERT: B 66 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8011 (tp) REVERT: C 66 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8101 (tp) REVERT: C 150 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7801 (mp) REVERT: D 61 MET cc_start: 0.8955 (mmm) cc_final: 0.8701 (mmt) REVERT: D 66 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8151 (tp) REVERT: D 129 ARG cc_start: 0.7752 (ttm170) cc_final: 0.7467 (ttp-170) REVERT: D 130 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8093 (mm) REVERT: E 15 GLN cc_start: 0.7856 (mt0) cc_final: 0.7639 (mt0) REVERT: E 66 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8124 (tp) REVERT: E 129 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7462 (ttm170) REVERT: E 130 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8157 (mm) outliers start: 40 outliers final: 17 residues processed: 167 average time/residue: 1.2788 time to fit residues: 230.7360 Evaluate side-chains 178 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 215 LEU 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 150 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 GLN D 187 GLN E 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.122307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107699 restraints weight = 11417.493| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.17 r_work: 0.3221 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11195 Z= 0.136 Angle : 0.489 5.094 15195 Z= 0.264 Chirality : 0.040 0.124 1850 Planarity : 0.004 0.036 1785 Dihedral : 7.462 59.753 1771 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.76 % Allowed : 14.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.66 (0.22), residues: 1400 helix: 2.60 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.66 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 225 HIS 0.002 0.001 HIS E 249 PHE 0.012 0.002 PHE C 137 TYR 0.013 0.002 TYR E 68 ARG 0.002 0.000 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 844) hydrogen bonds : angle 3.50303 ( 2466) covalent geometry : bond 0.00303 (11190) covalent geometry : angle 0.48947 (15195) Misc. bond : bond 0.00008 ( 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 182 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 1.106 Fit side-chains REVERT: A 130 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8176 (mm) REVERT: A 197 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (tttt) REVERT: B 66 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7985 (tp) REVERT: C 66 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8100 (tp) REVERT: C 150 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7748 (mp) REVERT: C 269 GLU cc_start: 0.8131 (tt0) cc_final: 0.7713 (tt0) REVERT: D 61 MET cc_start: 0.8937 (mmm) cc_final: 0.8668 (mmt) REVERT: D 66 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8110 (tp) REVERT: D 129 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7435 (ttp-170) REVERT: D 130 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8066 (mm) REVERT: E 15 GLN cc_start: 0.7814 (mt0) cc_final: 0.7594 (mt0) REVERT: E 66 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8083 (tp) REVERT: E 113 GLU cc_start: 0.8610 (tt0) cc_final: 0.8402 (tt0) REVERT: E 130 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8133 (mm) outliers start: 30 outliers final: 11 residues processed: 163 average time/residue: 1.2497 time to fit residues: 220.5404 Evaluate side-chains 169 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 197 LYS 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 69 VAL Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 150 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 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 132 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 130 optimal weight: 0.4980 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3474 r_free = 0.3474 target = 0.120634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105988 restraints weight = 11535.341| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.17 r_work: 0.3197 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11195 Z= 0.187 Angle : 0.534 5.153 15195 Z= 0.289 Chirality : 0.042 0.133 1850 Planarity : 0.005 0.036 1785 Dihedral : 8.011 59.956 1771 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.23 % Allowed : 13.73 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.22), residues: 1400 helix: 2.43 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 225 HIS 0.002 0.001 HIS E 249 PHE 0.014 0.002 PHE C 137 TYR 0.016 0.002 TYR D 100 ARG 0.006 0.000 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.04751 ( 844) hydrogen bonds : angle 3.63553 ( 2466) covalent geometry : bond 0.00437 (11190) covalent geometry : angle 0.53356 (15195) Misc. bond : bond 0.00029 ( 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 184 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 1.095 Fit side-chains REVERT: A 129 ARG cc_start: 0.7658 (ttm170) cc_final: 0.7378 (mtp180) REVERT: A 130 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8281 (mm) REVERT: A 197 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7923 (tttt) REVERT: B 66 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8018 (tp) REVERT: C 66 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8105 (tp) REVERT: C 150 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7804 (mp) REVERT: D 61 MET cc_start: 0.8959 (mmm) cc_final: 0.8715 (mmt) REVERT: D 66 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8152 (tp) REVERT: D 129 ARG cc_start: 0.7765 (ttm170) cc_final: 0.7466 (ttp-170) REVERT: D 130 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8098 (mm) REVERT: E 15 GLN cc_start: 0.7894 (mt0) cc_final: 0.7664 (mt0) REVERT: E 66 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8080 (tp) REVERT: E 113 GLU cc_start: 0.8621 (tt0) cc_final: 0.8396 (tt0) REVERT: E 129 ARG cc_start: 0.7859 (ttm170) cc_final: 0.7466 (ttm170) REVERT: E 130 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8187 (mm) outliers start: 35 outliers final: 15 residues processed: 164 average time/residue: 1.4644 time to fit residues: 258.5723 Evaluate side-chains 173 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 A residue 197 LYS 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 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 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 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 131 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 74 optimal weight: 0.0030 chunk 130 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN D 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.109051 restraints weight = 11347.812| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.17 r_work: 0.3240 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11195 Z= 0.115 Angle : 0.469 5.055 15195 Z= 0.252 Chirality : 0.039 0.119 1850 Planarity : 0.004 0.037 1785 Dihedral : 7.188 59.447 1771 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.95 % Allowed : 14.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.22), residues: 1400 helix: 2.75 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.58 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 225 HIS 0.003 0.001 HIS E 18 PHE 0.012 0.002 PHE D 137 TYR 0.012 0.002 TYR A 68 ARG 0.006 0.000 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 844) hydrogen bonds : angle 3.42162 ( 2466) covalent geometry : bond 0.00245 (11190) covalent geometry : angle 0.46888 (15195) 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 181 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 1.156 Fit side-chains REVERT: A 130 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8168 (mm) REVERT: A 197 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7922 (tttt) REVERT: B 66 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7949 (tp) REVERT: C 66 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8059 (tp) REVERT: C 150 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7790 (mp) REVERT: C 269 GLU cc_start: 0.8076 (tt0) cc_final: 0.7678 (tt0) REVERT: D 5 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.6820 (tt) REVERT: D 61 MET cc_start: 0.8922 (mmm) cc_final: 0.8631 (mmt) REVERT: D 130 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8056 (mm) REVERT: E 15 GLN cc_start: 0.7815 (mt0) cc_final: 0.7596 (mt0) REVERT: E 66 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8118 (tp) REVERT: E 130 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8105 (mm) REVERT: E 269 GLU cc_start: 0.8080 (tt0) cc_final: 0.7538 (tt0) outliers start: 32 outliers final: 10 residues processed: 162 average time/residue: 1.1947 time to fit residues: 209.9898 Evaluate side-chains 168 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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 A residue 197 LYS 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 66 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 130 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 88 optimal weight: 0.5980 chunk 126 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3509 r_free = 0.3509 target = 0.123398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.108513 restraints weight = 11330.591| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.18 r_work: 0.3236 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11195 Z= 0.123 Angle : 0.475 5.067 15195 Z= 0.256 Chirality : 0.039 0.122 1850 Planarity : 0.004 0.037 1785 Dihedral : 7.014 59.599 1769 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.21 % Allowed : 14.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.22), residues: 1400 helix: 2.79 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 225 HIS 0.003 0.001 HIS E 18 PHE 0.011 0.002 PHE E 137 TYR 0.014 0.002 TYR D 100 ARG 0.006 0.000 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 844) hydrogen bonds : angle 3.43065 ( 2466) covalent geometry : bond 0.00269 (11190) covalent geometry : angle 0.47525 (15195) Misc. bond : bond 0.00009 ( 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 175 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.183 Fit side-chains REVERT: A 197 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7927 (tttt) REVERT: B 66 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7940 (tp) REVERT: C 66 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8063 (tp) REVERT: C 150 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7806 (mp) REVERT: C 269 GLU cc_start: 0.8073 (tt0) cc_final: 0.7667 (tt0) REVERT: C 283 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6535 (mm) REVERT: D 5 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.6798 (tt) REVERT: D 61 MET cc_start: 0.8926 (mmm) cc_final: 0.8660 (mmt) REVERT: D 130 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8064 (mm) REVERT: E 15 GLN cc_start: 0.7828 (mt0) cc_final: 0.7604 (mt0) REVERT: E 66 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8105 (tp) REVERT: E 130 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8165 (mm) REVERT: E 269 GLU cc_start: 0.8095 (tt0) cc_final: 0.7544 (tt0) outliers start: 24 outliers final: 11 residues processed: 160 average time/residue: 1.2697 time to fit residues: 220.5441 Evaluate side-chains 171 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 197 LYS 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 66 LEU Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 283 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 127 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 138 optimal weight: 0.0980 chunk 92 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 64 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3527 r_free = 0.3527 target = 0.124794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109953 restraints weight = 11288.858| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.18 r_work: 0.3255 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11195 Z= 0.109 Angle : 0.461 5.071 15195 Z= 0.248 Chirality : 0.039 0.121 1850 Planarity : 0.004 0.037 1785 Dihedral : 6.656 57.642 1769 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.12 % Allowed : 14.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.22), residues: 1400 helix: 2.91 (0.16), residues: 1015 sheet: None (None), residues: 0 loop : -0.63 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 225 HIS 0.003 0.001 HIS E 18 PHE 0.010 0.002 PHE D 137 TYR 0.012 0.002 TYR D 100 ARG 0.007 0.000 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 844) hydrogen bonds : angle 3.36525 ( 2466) covalent geometry : bond 0.00229 (11190) covalent geometry : angle 0.46149 (15195) Misc. bond : bond 0.00009 ( 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 175 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 152 time to evaluate : 1.293 Fit side-chains REVERT: A 269 GLU cc_start: 0.8242 (tt0) cc_final: 0.7966 (pt0) REVERT: C 66 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.8049 (tp) REVERT: C 150 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7809 (mp) REVERT: C 269 GLU cc_start: 0.8018 (tt0) cc_final: 0.7625 (tt0) REVERT: C 283 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6537 (mm) REVERT: D 5 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.6797 (tt) REVERT: D 61 MET cc_start: 0.8914 (mmm) cc_final: 0.8635 (mmt) REVERT: D 130 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8042 (mm) REVERT: E 15 GLN cc_start: 0.7786 (mt0) cc_final: 0.7563 (mt0) REVERT: E 66 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8086 (tp) REVERT: E 130 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8084 (mm) REVERT: E 269 GLU cc_start: 0.8069 (tt0) cc_final: 0.7557 (tt0) outliers start: 23 outliers final: 8 residues processed: 162 average time/residue: 1.5040 time to fit residues: 264.7734 Evaluate side-chains 165 residues out of total 1115 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain C residue 15 GLN 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 C residue 283 ILE Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 130 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 59 optimal weight: 1.9990 chunk 83 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3508 r_free = 0.3508 target = 0.123271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108557 restraints weight = 11323.417| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.17 r_work: 0.3233 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11195 Z= 0.131 Angle : 0.484 5.067 15195 Z= 0.260 Chirality : 0.040 0.124 1850 Planarity : 0.004 0.037 1785 Dihedral : 6.800 56.293 1767 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.47 % Allowed : 15.48 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.22), residues: 1400 helix: 2.78 (0.15), residues: 1015 sheet: None (None), residues: 0 loop : -0.68 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 225 HIS 0.002 0.001 HIS A 18 PHE 0.011 0.002 PHE D 22 TYR 0.015 0.002 TYR D 100 ARG 0.007 0.000 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 844) hydrogen bonds : angle 3.44593 ( 2466) covalent geometry : bond 0.00292 (11190) covalent geometry : angle 0.48426 (15195) Misc. bond : bond 0.00015 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8628.76 seconds wall clock time: 155 minutes 2.06 seconds (9302.06 seconds total)