Starting phenix.real_space_refine on Thu Feb 5 16:08:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n6i_23726/02_2026/7n6i_23726.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n6i_23726/02_2026/7n6i_23726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n6i_23726/02_2026/7n6i_23726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n6i_23726/02_2026/7n6i_23726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n6i_23726/02_2026/7n6i_23726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n6i_23726/02_2026/7n6i_23726.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 7 5.21 5 S 64 5.16 5 C 11744 2.51 5 N 3472 2.21 5 O 3597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18939 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 745 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 11, 'TRANS': 139} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'TRP:plan': 5, 'PHE:plan': 7, 'TYR:plan': 3, 'GLU:plan': 11, 'HIS:plan': 7, 'ARG:plan': 12, 'ASN:plan1': 3, 'GLN:plan1': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 297 Chain: "B" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 745 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 11, 'TRANS': 139} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'TRP:plan': 5, 'PHE:plan': 7, 'TYR:plan': 3, 'GLU:plan': 11, 'HIS:plan': 7, 'ARG:plan': 12, 'ASN:plan1': 3, 'GLN:plan1': 8, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 297 Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "L" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.33, per 1000 atoms: 0.23 Number of scatterers: 18939 At special positions: 0 Unit cell: (126.35, 143.64, 136.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 P 55 15.00 Mg 7 11.99 O 3597 8.00 N 3472 7.00 C 11744 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.45 Conformation dependent library (CDL) restraints added in 753.2 milliseconds 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 16 sheets defined 57.7% alpha, 4.3% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 61 through 74 removed outlier: 4.002A pdb=" N GLN A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 61 through 74 removed outlier: 4.002A pdb=" N GLN B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 removed outlier: 4.659A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 174 through 181 removed outlier: 4.120A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.610A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.523A pdb=" N LYS C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 257 Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 removed outlier: 4.007A pdb=" N ASP D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 175 through 181 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.522A pdb=" N LYS D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 257 Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.598A pdb=" N ASP E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.126A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.511A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.521A pdb=" N LYS E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 238 removed outlier: 4.345A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 257 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.856A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 134 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 174 through 181 removed outlier: 4.110A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.510A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 215 removed outlier: 3.521A pdb=" N LYS F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 257 Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 134 removed outlier: 4.658A pdb=" N ASP G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 174 through 181 removed outlier: 4.081A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS G 205 " --> pdb=" O GLY G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 238 removed outlier: 4.488A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 257 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.856A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.599A pdb=" N ASP H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 174 through 181 removed outlier: 4.111A pdb=" N ALA H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.602A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS H 205 " --> pdb=" O GLY H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 238 removed outlier: 4.487A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 257 Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 36 through 53 removed outlier: 3.817A pdb=" N GLY I 48 " --> pdb=" O ASP I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.657A pdb=" N ASP I 127 " --> pdb=" O SER I 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG I 128 " --> pdb=" O ASP I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 174 through 181 removed outlier: 4.091A pdb=" N ALA I 178 " --> pdb=" O ASP I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.533A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS I 205 " --> pdb=" O GLY I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 238 removed outlier: 4.490A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 257 Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'J' and resid 20 through 29 Processing helix chain 'J' and resid 36 through 53 Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 removed outlier: 4.657A pdb=" N ASP J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 128 " --> pdb=" O ASP J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 152 No H-bonds generated for 'chain 'J' and resid 150 through 152' Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 174 through 181 removed outlier: 4.118A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.527A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 215 removed outlier: 3.521A pdb=" N LYS J 205 " --> pdb=" O GLY J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 238 removed outlier: 4.481A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 257 Processing helix chain 'J' and resid 264 through 273 Processing sheet with id=AA1, first strand: chain 'C' and resid 171 through 173 removed outlier: 5.842A pdb=" N VAL C 58 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 172 through 173 removed outlier: 5.904A pdb=" N VAL D 58 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 171 through 172 removed outlier: 5.858A pdb=" N VAL E 58 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 171 through 172 removed outlier: 5.963A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 91 through 94 removed outlier: 7.051A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 171 through 172 removed outlier: 6.001A pdb=" N VAL G 58 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.649A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 171 through 172 removed outlier: 6.283A pdb=" N VAL H 58 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 171 through 172 removed outlier: 6.124A pdb=" N VAL I 58 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 171 through 172 removed outlier: 5.963A pdb=" N VAL J 58 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.637A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3118 1.31 - 1.44: 4801 1.44 - 1.56: 11152 1.56 - 1.69: 108 1.69 - 1.81: 96 Bond restraints: 19275 Sorted by residual: bond pdb=" C4 ATP J 300 " pdb=" C5 ATP J 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C4 ATP E 300 " pdb=" C5 ATP E 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP I 300 " pdb=" C5 ATP I 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP H 300 " pdb=" C5 ATP H 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP F 300 " pdb=" C5 ATP F 300 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.64e+01 ... (remaining 19270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 25530 4.13 - 8.26: 577 8.26 - 12.39: 44 12.39 - 16.53: 2 16.53 - 20.66: 14 Bond angle restraints: 26167 Sorted by residual: angle pdb=" PB ATP E 300 " pdb=" O3B ATP E 300 " pdb=" PG ATP E 300 " ideal model delta sigma weight residual 139.87 119.21 20.66 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP D 300 " pdb=" O3B ATP D 300 " pdb=" PG ATP D 300 " ideal model delta sigma weight residual 139.87 119.28 20.59 1.00e+00 1.00e+00 4.24e+02 angle pdb=" PB ATP H 300 " pdb=" O3B ATP H 300 " pdb=" PG ATP H 300 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP I 300 " pdb=" O3B ATP I 300 " pdb=" PG ATP I 300 " ideal model delta sigma weight residual 139.87 119.54 20.33 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PB ATP G 300 " pdb=" O3B ATP G 300 " pdb=" PG ATP G 300 " ideal model delta sigma weight residual 139.87 119.88 19.99 1.00e+00 1.00e+00 4.00e+02 ... (remaining 26162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 11463 31.41 - 62.81: 439 62.81 - 94.22: 70 94.22 - 125.63: 1 125.63 - 157.04: 3 Dihedral angle restraints: 11976 sinusoidal: 5152 harmonic: 6824 Sorted by residual: dihedral pdb=" N ARG B 30 " pdb=" C ARG B 30 " pdb=" CA ARG B 30 " pdb=" CB ARG B 30 " ideal model delta harmonic sigma weight residual 122.80 162.49 -39.69 0 2.50e+00 1.60e-01 2.52e+02 dihedral pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CA ARG A 30 " pdb=" CB ARG A 30 " ideal model delta harmonic sigma weight residual 122.80 162.46 -39.66 0 2.50e+00 1.60e-01 2.52e+02 dihedral pdb=" C ARG B 30 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " pdb=" CB ARG B 30 " ideal model delta harmonic sigma weight residual -122.60 -160.03 37.43 0 2.50e+00 1.60e-01 2.24e+02 ... (remaining 11973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 2950 0.347 - 0.693: 34 0.693 - 1.040: 4 1.040 - 1.387: 0 1.387 - 1.733: 2 Chirality restraints: 2990 Sorted by residual: chirality pdb=" CA ARG B 30 " pdb=" N ARG B 30 " pdb=" C ARG B 30 " pdb=" CB ARG B 30 " both_signs ideal model delta sigma weight residual False 2.51 0.78 1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CA ARG A 30 " pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CB ARG A 30 " both_signs ideal model delta sigma weight residual False 2.51 0.78 1.73 2.00e-01 2.50e+01 7.50e+01 chirality pdb=" CA TYR A 116 " pdb=" N TYR A 116 " pdb=" C TYR A 116 " pdb=" CB TYR A 116 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 2987 not shown) Planarity restraints: 3205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 92 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C MET A 92 " 0.054 2.00e-02 2.50e+03 pdb=" O MET A 92 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 93 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 92 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" C MET B 92 " 0.054 2.00e-02 2.50e+03 pdb=" O MET B 92 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 93 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 138 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C VAL H 138 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL H 138 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU H 139 " -0.014 2.00e-02 2.50e+03 ... (remaining 3202 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 14 2.17 - 2.85: 5309 2.85 - 3.53: 25822 3.53 - 4.22: 40896 4.22 - 4.90: 70849 Nonbonded interactions: 142890 Sorted by model distance: nonbonded pdb=" OD2 ASP I 245 " pdb=" O2' ATP I 300 " model vdw 1.484 3.040 nonbonded pdb=" OD2 ASP E 245 " pdb=" O2' ATP E 300 " model vdw 1.584 3.040 nonbonded pdb=" CB HIS B 34 " pdb=" OE2 GLU H 131 " model vdw 1.701 3.440 nonbonded pdb=" CB ARG B 155 " pdb=" NE ARG I 128 " model vdw 1.783 2.816 nonbonded pdb=" NZ LYS D 54 " pdb=" OE1 GLU E 250 " model vdw 1.823 3.120 ... (remaining 142885 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 19 through 275) selection = (chain 'E' and resid 19 through 275) selection = (chain 'F' and resid 19 through 275) selection = (chain 'G' and resid 19 through 275) selection = (chain 'H' and resid 19 through 275) selection = (chain 'I' and resid 19 through 275) selection = (chain 'J' and resid 19 through 275) } 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 group one per residue 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: 1.540 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.210 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 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 : 0.016 0.851 19279 Z= 1.315 Angle : 1.720 20.658 26167 Z= 1.347 Chirality : 0.126 1.733 2990 Planarity : 0.006 0.057 3205 Dihedral : 16.033 157.036 7556 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.45 % Allowed : 3.07 % Favored : 96.48 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.16), residues: 2338 helix: -0.21 (0.13), residues: 1262 sheet: -0.04 (0.51), residues: 96 loop : -0.28 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 116 TYR 0.007 0.000 TYR E 75 PHE 0.007 0.001 PHE H 125 TRP 0.021 0.001 TRP I 45 HIS 0.001 0.000 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.01379 (19275) covalent geometry : angle 1.71982 (26167) hydrogen bonds : bond 0.22452 ( 903) hydrogen bonds : angle 7.07007 ( 2663) Misc. bond : bond 0.58402 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 834 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LEU cc_start: 0.7135 (mt) cc_final: 0.6876 (mp) REVERT: C 39 VAL cc_start: 0.8217 (t) cc_final: 0.8000 (t) REVERT: C 42 LEU cc_start: 0.9103 (tp) cc_final: 0.8580 (tp) REVERT: C 194 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8253 (tt) REVERT: C 199 LEU cc_start: 0.7136 (mt) cc_final: 0.6831 (mt) REVERT: D 170 LEU cc_start: 0.8829 (tt) cc_final: 0.8628 (tt) REVERT: E 133 LEU cc_start: 0.8473 (mt) cc_final: 0.8249 (mt) REVERT: E 240 TYR cc_start: 0.8769 (m-80) cc_final: 0.8497 (m-80) REVERT: F 38 GLN cc_start: 0.7982 (tp40) cc_final: 0.7619 (tp40) REVERT: F 70 CYS cc_start: 0.7889 (m) cc_final: 0.7480 (m) REVERT: F 164 LEU cc_start: 0.8028 (mt) cc_final: 0.7790 (mt) REVERT: F 183 ASP cc_start: 0.6544 (t70) cc_final: 0.6313 (t70) REVERT: H 41 THR cc_start: 0.8869 (m) cc_final: 0.8589 (m) REVERT: H 163 ASP cc_start: 0.6463 (m-30) cc_final: 0.5805 (m-30) REVERT: I 77 HIS cc_start: 0.5999 (m-70) cc_final: 0.5776 (m-70) REVERT: I 204 PHE cc_start: 0.8420 (t80) cc_final: 0.7838 (t80) REVERT: J 100 CYS cc_start: 0.1713 (t) cc_final: 0.1494 (t) REVERT: J 211 TRP cc_start: 0.6531 (t-100) cc_final: 0.5893 (t-100) outliers start: 8 outliers final: 1 residues processed: 838 average time/residue: 0.1570 time to fit residues: 190.1580 Evaluate side-chains 401 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 399 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN C 185 GLN ** D 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 HIS ** F 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 38 GLN J 37 GLN ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN J 193 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.107812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075535 restraints weight = 61870.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.078124 restraints weight = 31574.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.079788 restraints weight = 20549.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.080864 restraints weight = 15605.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.081521 restraints weight = 13116.994| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 19279 Z= 0.177 Angle : 0.734 18.542 26167 Z= 0.382 Chirality : 0.044 0.233 2990 Planarity : 0.005 0.052 3205 Dihedral : 16.530 155.102 3240 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.79 % Allowed : 17.08 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.17), residues: 2338 helix: 1.07 (0.14), residues: 1284 sheet: 0.23 (0.54), residues: 96 loop : 0.14 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 128 TYR 0.021 0.002 TYR F 112 PHE 0.030 0.002 PHE D 125 TRP 0.029 0.002 TRP H 45 HIS 0.006 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00397 (19275) covalent geometry : angle 0.73378 (26167) hydrogen bonds : bond 0.05476 ( 903) hydrogen bonds : angle 4.83816 ( 2663) Misc. bond : bond 0.00339 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 431 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 TYR cc_start: 0.8979 (m-10) cc_final: 0.8599 (m-10) REVERT: C 163 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7711 (p0) REVERT: C 183 ASP cc_start: 0.8777 (t0) cc_final: 0.8563 (t0) REVERT: C 187 LEU cc_start: 0.9131 (pp) cc_final: 0.8792 (tt) REVERT: C 229 MET cc_start: 0.5754 (ptp) cc_final: 0.5460 (pmm) REVERT: D 70 CYS cc_start: 0.9147 (t) cc_final: 0.8924 (t) REVERT: D 75 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.8110 (t80) REVERT: D 150 LYS cc_start: 0.9321 (OUTLIER) cc_final: 0.9086 (mtmm) REVERT: D 159 ASP cc_start: 0.8031 (m-30) cc_final: 0.7600 (m-30) REVERT: D 170 LEU cc_start: 0.9276 (tt) cc_final: 0.8967 (tt) REVERT: D 187 LEU cc_start: 0.9267 (tp) cc_final: 0.8923 (tp) REVERT: D 210 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8676 (ttt) REVERT: E 55 SER cc_start: 0.8833 (m) cc_final: 0.8444 (p) REVERT: E 77 HIS cc_start: 0.7636 (m170) cc_final: 0.7413 (m170) REVERT: E 150 LYS cc_start: 0.8928 (tptp) cc_final: 0.8521 (tptp) REVERT: E 188 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8013 (mp0) REVERT: E 204 PHE cc_start: 0.8902 (t80) cc_final: 0.8355 (t80) REVERT: E 210 MET cc_start: 0.8700 (mmt) cc_final: 0.8444 (mmm) REVERT: E 223 ASN cc_start: 0.8428 (OUTLIER) cc_final: 0.8131 (p0) REVERT: E 233 LEU cc_start: 0.9631 (mt) cc_final: 0.9419 (mt) REVERT: E 246 GLU cc_start: 0.9360 (tp30) cc_final: 0.9152 (tp30) REVERT: F 62 SER cc_start: 0.8464 (m) cc_final: 0.8046 (t) REVERT: F 139 GLU cc_start: 0.8744 (mp0) cc_final: 0.8491 (mp0) REVERT: F 204 PHE cc_start: 0.9052 (t80) cc_final: 0.8839 (t80) REVERT: F 210 MET cc_start: 0.9118 (mmm) cc_final: 0.8867 (mmm) REVERT: F 263 ILE cc_start: 0.7959 (mt) cc_final: 0.7507 (mm) REVERT: G 29 LYS cc_start: 0.9223 (pttp) cc_final: 0.8917 (pttm) REVERT: G 124 ASP cc_start: 0.8445 (t0) cc_final: 0.8194 (t0) REVERT: G 159 ASP cc_start: 0.9017 (m-30) cc_final: 0.8749 (m-30) REVERT: G 229 MET cc_start: 0.9049 (mpp) cc_final: 0.8657 (pmm) REVERT: G 256 LEU cc_start: 0.9331 (mm) cc_final: 0.9109 (mm) REVERT: H 38 GLN cc_start: 0.8096 (tp40) cc_final: 0.7659 (tp40) REVERT: H 54 LYS cc_start: 0.8711 (tttp) cc_final: 0.8472 (tptp) REVERT: H 140 MET cc_start: 0.8627 (ttp) cc_final: 0.8212 (ttm) REVERT: H 159 ASP cc_start: 0.9271 (t0) cc_final: 0.9027 (t0) REVERT: H 195 ARG cc_start: 0.8129 (tpt170) cc_final: 0.7648 (ptt180) REVERT: H 214 MET cc_start: 0.9260 (mtm) cc_final: 0.8854 (mpp) REVERT: H 237 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8445 (p) REVERT: H 246 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8654 (mp0) REVERT: I 38 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: I 145 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8126 (mp0) REVERT: I 194 LEU cc_start: 0.7998 (tp) cc_final: 0.7775 (tt) REVERT: I 199 LEU cc_start: 0.7789 (tp) cc_final: 0.7127 (tp) REVERT: I 214 MET cc_start: 0.9039 (mtt) cc_final: 0.8827 (ptp) REVERT: I 229 MET cc_start: 0.9349 (mpp) cc_final: 0.8916 (pmm) REVERT: I 246 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8759 (mp0) REVERT: I 273 LYS cc_start: 0.9452 (mttt) cc_final: 0.8929 (tmtt) REVERT: J 38 GLN cc_start: 0.8698 (tp40) cc_final: 0.8473 (tp40) REVERT: J 93 TYR cc_start: 0.8190 (t80) cc_final: 0.7505 (t80) REVERT: J 116 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7286 (mtm-85) REVERT: J 214 MET cc_start: 0.9280 (mpp) cc_final: 0.8972 (mpp) REVERT: J 225 LYS cc_start: 0.9649 (pptt) cc_final: 0.9432 (mppt) REVERT: J 237 THR cc_start: 0.8625 (m) cc_final: 0.8186 (p) REVERT: J 267 VAL cc_start: 0.8829 (t) cc_final: 0.8211 (t) outliers start: 68 outliers final: 37 residues processed: 478 average time/residue: 0.1458 time to fit residues: 105.6603 Evaluate side-chains 381 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 336 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 150 LYS Chi-restraints excluded: chain D residue 210 MET Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 31 LYS Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 116 ARG Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 200 optimal weight: 4.9990 chunk 22 optimal weight: 0.0050 chunk 85 optimal weight: 0.3980 chunk 125 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 GLN E 38 GLN ** F 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN H 77 HIS I 77 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.107814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.076126 restraints weight = 61097.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078685 restraints weight = 31817.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.080326 restraints weight = 20905.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.081371 restraints weight = 15952.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.081934 restraints weight = 13428.427| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19279 Z= 0.133 Angle : 0.642 11.698 26167 Z= 0.332 Chirality : 0.042 0.222 2990 Planarity : 0.004 0.044 3205 Dihedral : 16.292 154.012 3238 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.62 % Allowed : 19.03 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.17), residues: 2338 helix: 1.29 (0.14), residues: 1292 sheet: 0.09 (0.53), residues: 96 loop : 0.25 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 258 TYR 0.018 0.001 TYR I 115 PHE 0.041 0.002 PHE I 125 TRP 0.026 0.002 TRP F 45 HIS 0.006 0.001 HIS I 77 Details of bonding type rmsd covalent geometry : bond 0.00296 (19275) covalent geometry : angle 0.64185 (26167) hydrogen bonds : bond 0.04513 ( 903) hydrogen bonds : angle 4.55472 ( 2663) Misc. bond : bond 0.00140 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 389 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 GLN cc_start: 0.9045 (mp10) cc_final: 0.8831 (pm20) REVERT: C 115 TYR cc_start: 0.8886 (m-10) cc_final: 0.8676 (m-10) REVERT: C 163 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7592 (p0) REVERT: C 183 ASP cc_start: 0.8623 (t0) cc_final: 0.8363 (t0) REVERT: C 229 MET cc_start: 0.5568 (ptp) cc_final: 0.5248 (pmm) REVERT: D 70 CYS cc_start: 0.9060 (t) cc_final: 0.8849 (t) REVERT: D 75 TYR cc_start: 0.8404 (OUTLIER) cc_final: 0.8056 (t80) REVERT: D 159 ASP cc_start: 0.8093 (m-30) cc_final: 0.7628 (m-30) REVERT: D 170 LEU cc_start: 0.9261 (tt) cc_final: 0.8884 (tt) REVERT: D 187 LEU cc_start: 0.9274 (tp) cc_final: 0.9011 (tp) REVERT: D 229 MET cc_start: 0.8860 (mpp) cc_final: 0.8192 (pmm) REVERT: D 246 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8503 (mp0) REVERT: E 38 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7750 (tp40) REVERT: E 55 SER cc_start: 0.8943 (m) cc_final: 0.8511 (p) REVERT: E 77 HIS cc_start: 0.7986 (m170) cc_final: 0.7536 (m-70) REVERT: E 179 VAL cc_start: 0.8934 (t) cc_final: 0.8621 (p) REVERT: E 246 GLU cc_start: 0.9348 (tp30) cc_final: 0.9096 (tp30) REVERT: F 46 LEU cc_start: 0.9614 (mt) cc_final: 0.9411 (mt) REVERT: F 62 SER cc_start: 0.8487 (m) cc_final: 0.8036 (t) REVERT: F 139 GLU cc_start: 0.8767 (mp0) cc_final: 0.8395 (mp0) REVERT: F 185 GLN cc_start: 0.8688 (mm-40) cc_final: 0.8419 (mm-40) REVERT: F 188 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8321 (mm-30) REVERT: F 210 MET cc_start: 0.8974 (mmm) cc_final: 0.8733 (mmm) REVERT: F 213 GLN cc_start: 0.8800 (mt0) cc_final: 0.8492 (mt0) REVERT: F 269 GLN cc_start: 0.9045 (mt0) cc_final: 0.8692 (mt0) REVERT: G 124 ASP cc_start: 0.8463 (t0) cc_final: 0.8173 (t0) REVERT: G 159 ASP cc_start: 0.8869 (m-30) cc_final: 0.8589 (m-30) REVERT: G 183 ASP cc_start: 0.8246 (t70) cc_final: 0.8039 (t70) REVERT: G 229 MET cc_start: 0.9143 (mpp) cc_final: 0.8603 (pmm) REVERT: G 256 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9084 (mm) REVERT: H 28 LEU cc_start: 0.9648 (mm) cc_final: 0.9365 (mp) REVERT: H 159 ASP cc_start: 0.9144 (t0) cc_final: 0.7885 (t0) REVERT: H 163 ASP cc_start: 0.7461 (m-30) cc_final: 0.6869 (m-30) REVERT: H 196 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.8135 (t80) REVERT: H 210 MET cc_start: 0.9386 (mpp) cc_final: 0.9057 (mpp) REVERT: H 246 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8712 (mp0) REVERT: I 38 GLN cc_start: 0.8504 (tp40) cc_final: 0.8226 (tt0) REVERT: I 145 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8304 (mp0) REVERT: I 156 ASP cc_start: 0.9483 (m-30) cc_final: 0.9262 (t0) REVERT: I 199 LEU cc_start: 0.7762 (tp) cc_final: 0.7108 (tp) REVERT: I 210 MET cc_start: 0.9404 (ttt) cc_final: 0.9093 (ttt) REVERT: I 212 GLU cc_start: 0.8575 (tt0) cc_final: 0.8123 (tt0) REVERT: I 229 MET cc_start: 0.9333 (mpp) cc_final: 0.8808 (pmm) REVERT: I 246 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8863 (mp0) REVERT: I 273 LYS cc_start: 0.9445 (mttt) cc_final: 0.8885 (tmtt) REVERT: J 38 GLN cc_start: 0.8615 (tp40) cc_final: 0.8145 (tt0) REVERT: J 75 TYR cc_start: 0.8724 (m-10) cc_final: 0.8454 (m-10) REVERT: J 104 ASP cc_start: 0.9218 (t70) cc_final: 0.8909 (t0) REVERT: J 223 ASN cc_start: 0.7968 (t0) cc_final: 0.7741 (t0) REVERT: J 224 LEU cc_start: 0.9267 (mt) cc_final: 0.8990 (mt) REVERT: J 246 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8865 (mm-30) outliers start: 47 outliers final: 26 residues processed: 418 average time/residue: 0.1239 time to fit residues: 80.7382 Evaluate side-chains 349 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 318 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 223 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 3 optimal weight: 50.0000 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 38 GLN I 38 GLN I 77 HIS I 185 GLN J 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.105231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073274 restraints weight = 62546.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.075701 restraints weight = 32644.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.077288 restraints weight = 21585.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.078293 restraints weight = 16565.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.078895 restraints weight = 14030.046| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19279 Z= 0.159 Angle : 0.628 12.314 26167 Z= 0.327 Chirality : 0.042 0.195 2990 Planarity : 0.004 0.041 3205 Dihedral : 16.075 153.803 3238 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.68 % Allowed : 19.53 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.17), residues: 2338 helix: 1.33 (0.14), residues: 1292 sheet: 0.13 (0.54), residues: 96 loop : 0.30 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 126 TYR 0.019 0.001 TYR I 115 PHE 0.046 0.002 PHE J 154 TRP 0.014 0.001 TRP F 45 HIS 0.005 0.001 HIS I 97 Details of bonding type rmsd covalent geometry : bond 0.00362 (19275) covalent geometry : angle 0.62794 (26167) hydrogen bonds : bond 0.04398 ( 903) hydrogen bonds : angle 4.54729 ( 2663) Misc. bond : bond 0.00166 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 340 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.2999 (mmtm) cc_final: 0.2652 (mmtm) REVERT: C 115 TYR cc_start: 0.9017 (m-80) cc_final: 0.8814 (m-10) REVERT: C 183 ASP cc_start: 0.8546 (t0) cc_final: 0.8297 (t0) REVERT: C 229 MET cc_start: 0.5785 (ptp) cc_final: 0.5441 (pmm) REVERT: D 75 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8127 (t80) REVERT: D 99 LYS cc_start: 0.8933 (mptt) cc_final: 0.8694 (mmtm) REVERT: D 159 ASP cc_start: 0.8145 (m-30) cc_final: 0.7679 (m-30) REVERT: D 170 LEU cc_start: 0.9296 (tt) cc_final: 0.8866 (tt) REVERT: D 229 MET cc_start: 0.8887 (mpp) cc_final: 0.8207 (pmm) REVERT: D 250 GLU cc_start: 0.9323 (tt0) cc_final: 0.8812 (tt0) REVERT: E 55 SER cc_start: 0.9050 (m) cc_final: 0.8718 (p) REVERT: E 145 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6967 (tp30) REVERT: E 163 ASP cc_start: 0.7121 (p0) cc_final: 0.6647 (p0) REVERT: E 179 VAL cc_start: 0.9008 (t) cc_final: 0.8642 (p) REVERT: F 134 LYS cc_start: 0.8902 (mtmm) cc_final: 0.8618 (mtmm) REVERT: F 139 GLU cc_start: 0.8786 (mp0) cc_final: 0.8467 (mp0) REVERT: F 144 ASP cc_start: 0.8982 (t0) cc_final: 0.8736 (t0) REVERT: F 145 GLU cc_start: 0.8244 (tp30) cc_final: 0.8022 (tp30) REVERT: F 159 ASP cc_start: 0.8148 (t70) cc_final: 0.7910 (t0) REVERT: F 185 GLN cc_start: 0.8655 (mm-40) cc_final: 0.8330 (mm-40) REVERT: F 213 GLN cc_start: 0.8712 (mt0) cc_final: 0.8511 (mt0) REVERT: F 269 GLN cc_start: 0.9095 (mt0) cc_final: 0.8715 (mt0) REVERT: G 124 ASP cc_start: 0.8449 (t0) cc_final: 0.8110 (t0) REVERT: G 159 ASP cc_start: 0.8768 (m-30) cc_final: 0.8361 (m-30) REVERT: G 183 ASP cc_start: 0.8317 (t70) cc_final: 0.8103 (t70) REVERT: G 213 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7611 (tm-30) REVERT: G 214 MET cc_start: 0.8854 (mmm) cc_final: 0.8381 (mmm) REVERT: G 229 MET cc_start: 0.9204 (mpp) cc_final: 0.8793 (pmm) REVERT: G 268 LEU cc_start: 0.9417 (mt) cc_final: 0.9127 (tp) REVERT: H 159 ASP cc_start: 0.8904 (t0) cc_final: 0.8312 (t0) REVERT: H 196 PHE cc_start: 0.8938 (OUTLIER) cc_final: 0.8714 (t80) REVERT: H 210 MET cc_start: 0.9387 (mpp) cc_final: 0.8970 (mpp) REVERT: H 214 MET cc_start: 0.9262 (mtm) cc_final: 0.8829 (mpp) REVERT: H 246 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8715 (mp0) REVERT: H 248 LEU cc_start: 0.9516 (OUTLIER) cc_final: 0.9312 (mm) REVERT: H 263 ILE cc_start: 0.7570 (mt) cc_final: 0.7360 (mm) REVERT: I 107 LYS cc_start: 0.9449 (ptmm) cc_final: 0.9163 (pptt) REVERT: I 145 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8366 (mp0) REVERT: I 156 ASP cc_start: 0.9406 (m-30) cc_final: 0.9064 (t0) REVERT: I 199 LEU cc_start: 0.7691 (tp) cc_final: 0.7107 (tp) REVERT: I 210 MET cc_start: 0.9376 (ttt) cc_final: 0.8990 (ttt) REVERT: I 212 GLU cc_start: 0.8660 (tt0) cc_final: 0.8371 (tt0) REVERT: I 214 MET cc_start: 0.8923 (mtp) cc_final: 0.8704 (ptp) REVERT: I 229 MET cc_start: 0.9376 (mpp) cc_final: 0.8676 (pmm) REVERT: I 246 GLU cc_start: 0.9359 (mm-30) cc_final: 0.8927 (mp0) REVERT: I 273 LYS cc_start: 0.9483 (mttt) cc_final: 0.8909 (tmtt) REVERT: J 38 GLN cc_start: 0.8673 (tp40) cc_final: 0.8418 (tp40) REVERT: J 75 TYR cc_start: 0.8750 (m-10) cc_final: 0.8434 (m-10) REVERT: J 104 ASP cc_start: 0.9288 (t70) cc_final: 0.8976 (t0) REVERT: J 246 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8862 (mm-30) outliers start: 66 outliers final: 41 residues processed: 380 average time/residue: 0.1295 time to fit residues: 77.6696 Evaluate side-chains 354 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 267 VAL Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 88 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 103 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 176 optimal weight: 8.9990 overall best weight: 1.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN E 223 ASN ** F 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 38 GLN ** I 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.104539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072761 restraints weight = 63355.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.075071 restraints weight = 34326.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076566 restraints weight = 23241.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.077495 restraints weight = 18096.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.078098 restraints weight = 15511.534| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19279 Z= 0.152 Angle : 0.628 12.106 26167 Z= 0.326 Chirality : 0.042 0.266 2990 Planarity : 0.004 0.040 3205 Dihedral : 15.858 154.028 3238 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.63 % Allowed : 20.54 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.18), residues: 2338 helix: 1.34 (0.15), residues: 1300 sheet: 0.07 (0.40), residues: 192 loop : 0.36 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 50 TYR 0.019 0.001 TYR F 112 PHE 0.044 0.002 PHE I 125 TRP 0.013 0.001 TRP C 20 HIS 0.002 0.001 HIS J 77 Details of bonding type rmsd covalent geometry : bond 0.00348 (19275) covalent geometry : angle 0.62768 (26167) hydrogen bonds : bond 0.04211 ( 903) hydrogen bonds : angle 4.51068 ( 2663) Misc. bond : bond 0.00154 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 329 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 GLN cc_start: 0.8999 (mp10) cc_final: 0.8791 (pm20) REVERT: C 29 LYS cc_start: 0.3119 (mmtm) cc_final: 0.2877 (mmtm) REVERT: C 115 TYR cc_start: 0.9044 (m-80) cc_final: 0.8809 (m-10) REVERT: C 131 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8432 (tm-30) REVERT: C 183 ASP cc_start: 0.8593 (t0) cc_final: 0.8313 (t70) REVERT: C 229 MET cc_start: 0.6299 (ptp) cc_final: 0.5872 (pmm) REVERT: D 55 SER cc_start: 0.9254 (m) cc_final: 0.8969 (p) REVERT: D 75 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.8151 (t80) REVERT: D 159 ASP cc_start: 0.8132 (m-30) cc_final: 0.7672 (m-30) REVERT: D 170 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8872 (tt) REVERT: D 229 MET cc_start: 0.9033 (mpp) cc_final: 0.8191 (pmm) REVERT: D 246 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8529 (mp0) REVERT: D 250 GLU cc_start: 0.9261 (tt0) cc_final: 0.8910 (tt0) REVERT: E 55 SER cc_start: 0.9080 (m) cc_final: 0.8784 (p) REVERT: E 210 MET cc_start: 0.9114 (mpp) cc_final: 0.8793 (mpp) REVERT: E 246 GLU cc_start: 0.9226 (tp30) cc_final: 0.9005 (tp30) REVERT: F 139 GLU cc_start: 0.8749 (mp0) cc_final: 0.8474 (mp0) REVERT: F 145 GLU cc_start: 0.8418 (tp30) cc_final: 0.8179 (tp30) REVERT: F 159 ASP cc_start: 0.8083 (t70) cc_final: 0.7836 (t0) REVERT: F 185 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8209 (mm-40) REVERT: F 209 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8800 (pt0) REVERT: F 214 MET cc_start: 0.9102 (mmm) cc_final: 0.8604 (mmm) REVERT: F 229 MET cc_start: 0.8942 (pmm) cc_final: 0.8387 (pmm) REVERT: G 124 ASP cc_start: 0.8482 (t0) cc_final: 0.8150 (t0) REVERT: G 159 ASP cc_start: 0.8656 (m-30) cc_final: 0.8318 (m-30) REVERT: G 213 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7649 (tm-30) REVERT: G 214 MET cc_start: 0.8653 (mmm) cc_final: 0.7961 (mmm) REVERT: G 229 MET cc_start: 0.9186 (mpp) cc_final: 0.8780 (pmm) REVERT: H 196 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.8844 (t80) REVERT: H 214 MET cc_start: 0.9259 (mtm) cc_final: 0.9021 (mtm) REVERT: H 248 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9372 (mm) REVERT: H 263 ILE cc_start: 0.7721 (mt) cc_final: 0.7519 (mm) REVERT: I 107 LYS cc_start: 0.9403 (ptmm) cc_final: 0.9097 (pptt) REVERT: I 145 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8367 (mp0) REVERT: I 156 ASP cc_start: 0.9321 (m-30) cc_final: 0.9007 (t0) REVERT: I 160 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9042 (mp) REVERT: I 199 LEU cc_start: 0.7694 (tp) cc_final: 0.7085 (tp) REVERT: I 210 MET cc_start: 0.9381 (ttt) cc_final: 0.8965 (ttt) REVERT: I 212 GLU cc_start: 0.8748 (tt0) cc_final: 0.8529 (tt0) REVERT: I 214 MET cc_start: 0.8945 (mtp) cc_final: 0.8726 (ptp) REVERT: I 229 MET cc_start: 0.9372 (mpp) cc_final: 0.8867 (pmm) REVERT: I 246 GLU cc_start: 0.9297 (mm-30) cc_final: 0.8857 (mp0) REVERT: I 273 LYS cc_start: 0.9513 (mttt) cc_final: 0.8922 (tmtt) REVERT: J 75 TYR cc_start: 0.8726 (m-10) cc_final: 0.8337 (m-10) REVERT: J 104 ASP cc_start: 0.9379 (t70) cc_final: 0.9108 (t0) outliers start: 65 outliers final: 41 residues processed: 374 average time/residue: 0.1300 time to fit residues: 76.7125 Evaluate side-chains 356 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 309 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 209 GLU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 66 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 206 optimal weight: 20.0000 chunk 32 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 210 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 219 optimal weight: 30.0000 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 38 GLN ** F 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS J 193 HIS ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.104107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072427 restraints weight = 62849.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074707 restraints weight = 34168.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.076170 restraints weight = 23177.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.077111 restraints weight = 18113.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.077681 restraints weight = 15511.298| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19279 Z= 0.133 Angle : 0.609 10.585 26167 Z= 0.317 Chirality : 0.042 0.200 2990 Planarity : 0.004 0.039 3205 Dihedral : 15.689 154.270 3238 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.85 % Allowed : 20.76 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.18), residues: 2338 helix: 1.34 (0.15), residues: 1300 sheet: -0.03 (0.39), residues: 192 loop : 0.34 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 175 TYR 0.018 0.001 TYR F 112 PHE 0.044 0.002 PHE I 125 TRP 0.010 0.001 TRP H 45 HIS 0.007 0.001 HIS J 193 Details of bonding type rmsd covalent geometry : bond 0.00300 (19275) covalent geometry : angle 0.60919 (26167) hydrogen bonds : bond 0.03936 ( 903) hydrogen bonds : angle 4.41849 ( 2663) Misc. bond : bond 0.00135 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 337 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 TYR cc_start: 0.9034 (m-80) cc_final: 0.8803 (m-10) REVERT: C 131 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 139 GLU cc_start: 0.8061 (mp0) cc_final: 0.7780 (mp0) REVERT: C 183 ASP cc_start: 0.8527 (t0) cc_final: 0.8228 (t70) REVERT: C 210 MET cc_start: 0.9173 (ptp) cc_final: 0.8077 (ptm) REVERT: C 214 MET cc_start: 0.8926 (mtm) cc_final: 0.8699 (mpp) REVERT: C 229 MET cc_start: 0.6332 (ptp) cc_final: 0.5916 (pmm) REVERT: D 55 SER cc_start: 0.9245 (m) cc_final: 0.9003 (p) REVERT: D 75 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.8172 (t80) REVERT: D 156 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8317 (t70) REVERT: D 159 ASP cc_start: 0.8181 (m-30) cc_final: 0.7742 (m-30) REVERT: D 170 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8855 (tt) REVERT: D 210 MET cc_start: 0.9203 (mtp) cc_final: 0.8682 (ttt) REVERT: D 229 MET cc_start: 0.9020 (mpp) cc_final: 0.8477 (pmm) REVERT: D 250 GLU cc_start: 0.9259 (tt0) cc_final: 0.8840 (tt0) REVERT: E 55 SER cc_start: 0.9098 (m) cc_final: 0.8789 (p) REVERT: E 163 ASP cc_start: 0.7377 (p0) cc_final: 0.7027 (p0) REVERT: E 185 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7458 (tp-100) REVERT: E 210 MET cc_start: 0.9093 (mpp) cc_final: 0.8773 (mpp) REVERT: E 246 GLU cc_start: 0.9230 (tp30) cc_final: 0.9016 (tp30) REVERT: F 139 GLU cc_start: 0.8697 (mp0) cc_final: 0.8469 (mp0) REVERT: F 159 ASP cc_start: 0.8037 (t70) cc_final: 0.7791 (t0) REVERT: F 185 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8121 (mm-40) REVERT: G 124 ASP cc_start: 0.8490 (t0) cc_final: 0.8165 (t0) REVERT: G 159 ASP cc_start: 0.8653 (m-30) cc_final: 0.8268 (m-30) REVERT: G 213 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7659 (tm-30) REVERT: G 214 MET cc_start: 0.8677 (mmm) cc_final: 0.7982 (mmm) REVERT: G 229 MET cc_start: 0.9169 (mpp) cc_final: 0.8807 (pmm) REVERT: G 268 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9068 (tp) REVERT: H 103 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8356 (ttmm) REVERT: H 196 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8816 (t80) REVERT: H 203 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8924 (t0) REVERT: H 214 MET cc_start: 0.9254 (mtm) cc_final: 0.9006 (mtm) REVERT: H 229 MET cc_start: 0.7816 (mmt) cc_final: 0.7362 (mmt) REVERT: H 248 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9310 (mm) REVERT: H 263 ILE cc_start: 0.7800 (mt) cc_final: 0.7593 (mm) REVERT: I 38 GLN cc_start: 0.8623 (tp40) cc_final: 0.8382 (tp40) REVERT: I 107 LYS cc_start: 0.9416 (ptmm) cc_final: 0.9140 (pptt) REVERT: I 145 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8412 (mm-30) REVERT: I 156 ASP cc_start: 0.9287 (m-30) cc_final: 0.9010 (t0) REVERT: I 160 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9040 (mp) REVERT: I 199 LEU cc_start: 0.7750 (tp) cc_final: 0.7189 (tp) REVERT: I 210 MET cc_start: 0.9397 (ttt) cc_final: 0.8943 (ttt) REVERT: I 214 MET cc_start: 0.8975 (mtp) cc_final: 0.8733 (ptp) REVERT: I 273 LYS cc_start: 0.9522 (mttt) cc_final: 0.8946 (tmtt) REVERT: J 38 GLN cc_start: 0.8911 (tp40) cc_final: 0.8468 (tt0) REVERT: J 75 TYR cc_start: 0.8741 (m-10) cc_final: 0.8341 (m-10) REVERT: J 104 ASP cc_start: 0.9403 (t70) cc_final: 0.9079 (t0) outliers start: 69 outliers final: 42 residues processed: 382 average time/residue: 0.1340 time to fit residues: 80.2274 Evaluate side-chains 362 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 312 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 268 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 267 VAL Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 0.0470 chunk 213 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 200 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.100458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.068614 restraints weight = 64473.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070752 restraints weight = 35374.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072136 restraints weight = 24227.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.073000 restraints weight = 19109.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073522 restraints weight = 16502.214| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19279 Z= 0.196 Angle : 0.669 15.050 26167 Z= 0.346 Chirality : 0.043 0.222 2990 Planarity : 0.004 0.037 3205 Dihedral : 15.644 155.093 3238 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.52 % Allowed : 20.65 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2338 helix: 1.31 (0.15), residues: 1300 sheet: -0.48 (0.34), residues: 232 loop : 0.24 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 231 TYR 0.026 0.002 TYR F 112 PHE 0.040 0.003 PHE I 125 TRP 0.010 0.001 TRP G 20 HIS 0.010 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00445 (19275) covalent geometry : angle 0.66852 (26167) hydrogen bonds : bond 0.04534 ( 903) hydrogen bonds : angle 4.58841 ( 2663) Misc. bond : bond 0.00156 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 305 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.2856 (mmtm) cc_final: 0.2597 (mmtm) REVERT: C 115 TYR cc_start: 0.9088 (m-80) cc_final: 0.8755 (m-10) REVERT: C 139 GLU cc_start: 0.8103 (mp0) cc_final: 0.7719 (mp0) REVERT: C 140 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.7766 (mpp) REVERT: C 183 ASP cc_start: 0.8590 (t0) cc_final: 0.8302 (t0) REVERT: C 199 LEU cc_start: 0.8924 (pt) cc_final: 0.8718 (pt) REVERT: C 210 MET cc_start: 0.9219 (ptp) cc_final: 0.8372 (ptp) REVERT: D 54 LYS cc_start: 0.8906 (mmmt) cc_final: 0.8560 (mmtm) REVERT: D 75 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8211 (t80) REVERT: D 145 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8245 (mm-30) REVERT: D 156 ASP cc_start: 0.8804 (OUTLIER) cc_final: 0.8348 (t70) REVERT: D 159 ASP cc_start: 0.8340 (m-30) cc_final: 0.7849 (m-30) REVERT: D 170 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9002 (tt) REVERT: D 229 MET cc_start: 0.9048 (mpp) cc_final: 0.7986 (pmm) REVERT: D 250 GLU cc_start: 0.9302 (tt0) cc_final: 0.8966 (tt0) REVERT: E 46 LEU cc_start: 0.9577 (mt) cc_final: 0.9215 (tp) REVERT: E 163 ASP cc_start: 0.7515 (p0) cc_final: 0.7111 (p0) REVERT: E 185 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7631 (tp-100) REVERT: E 210 MET cc_start: 0.9104 (mpp) cc_final: 0.8828 (mpp) REVERT: E 238 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8464 (mp0) REVERT: E 246 GLU cc_start: 0.9189 (tp30) cc_final: 0.8902 (tp30) REVERT: F 125 PHE cc_start: 0.9318 (m-80) cc_final: 0.9009 (m-80) REVERT: F 159 ASP cc_start: 0.8068 (t70) cc_final: 0.7803 (t0) REVERT: F 185 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8137 (mm-40) REVERT: G 124 ASP cc_start: 0.8590 (t0) cc_final: 0.8238 (t0) REVERT: G 229 MET cc_start: 0.9239 (mpp) cc_final: 0.8850 (pmm) REVERT: G 256 LEU cc_start: 0.9324 (mm) cc_final: 0.9025 (mm) REVERT: H 38 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8452 (tt0) REVERT: H 51 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8742 (mmmt) REVERT: H 54 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8650 (tttt) REVERT: H 103 LYS cc_start: 0.9166 (ttpt) cc_final: 0.8649 (ttmm) REVERT: H 196 PHE cc_start: 0.9230 (OUTLIER) cc_final: 0.8653 (t80) REVERT: H 248 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9372 (mm) REVERT: I 38 GLN cc_start: 0.8763 (tp40) cc_final: 0.8559 (tp40) REVERT: I 107 LYS cc_start: 0.9421 (ptmm) cc_final: 0.9132 (pptt) REVERT: I 145 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8403 (mp0) REVERT: I 160 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9000 (mp) REVERT: I 199 LEU cc_start: 0.8063 (tp) cc_final: 0.7092 (tp) REVERT: I 210 MET cc_start: 0.9444 (ttt) cc_final: 0.8870 (ttt) REVERT: I 214 MET cc_start: 0.8963 (mtp) cc_final: 0.8695 (ptp) REVERT: I 224 LEU cc_start: 0.9418 (mm) cc_final: 0.9214 (mp) REVERT: I 229 MET cc_start: 0.9339 (pmm) cc_final: 0.8873 (pmm) REVERT: I 246 GLU cc_start: 0.9196 (mm-30) cc_final: 0.8733 (mp0) REVERT: I 273 LYS cc_start: 0.9583 (mttt) cc_final: 0.9040 (tmtt) REVERT: J 75 TYR cc_start: 0.8763 (m-10) cc_final: 0.8327 (m-10) REVERT: J 104 ASP cc_start: 0.9465 (t70) cc_final: 0.9212 (t0) outliers start: 81 outliers final: 52 residues processed: 360 average time/residue: 0.1324 time to fit residues: 74.9781 Evaluate side-chains 341 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 281 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 125 PHE Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 124 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 253 ILE Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 160 ILE Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 131 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 120 optimal weight: 0.2980 chunk 176 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.102007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.070257 restraints weight = 63771.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.072464 restraints weight = 35044.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073885 restraints weight = 23884.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.074788 restraints weight = 18717.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.075226 restraints weight = 16065.677| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.7292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19279 Z= 0.130 Angle : 0.651 12.652 26167 Z= 0.333 Chirality : 0.043 0.220 2990 Planarity : 0.004 0.037 3205 Dihedral : 15.486 155.533 3238 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.01 % Allowed : 22.32 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2338 helix: 1.32 (0.15), residues: 1312 sheet: -0.23 (0.39), residues: 192 loop : 0.27 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 243 TYR 0.016 0.001 TYR F 112 PHE 0.042 0.002 PHE I 125 TRP 0.010 0.001 TRP H 45 HIS 0.004 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00292 (19275) covalent geometry : angle 0.65143 (26167) hydrogen bonds : bond 0.03854 ( 903) hydrogen bonds : angle 4.42475 ( 2663) Misc. bond : bond 0.00118 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 49 LYS cc_start: 0.9368 (tppt) cc_final: 0.9117 (tppt) REVERT: C 54 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8642 (mtpt) REVERT: C 107 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9134 (tptp) REVERT: C 139 GLU cc_start: 0.8070 (mp0) cc_final: 0.7666 (mp0) REVERT: C 140 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.7751 (mpp) REVERT: C 183 ASP cc_start: 0.8489 (t0) cc_final: 0.8197 (t70) REVERT: C 199 LEU cc_start: 0.8914 (pt) cc_final: 0.8705 (pt) REVERT: D 156 ASP cc_start: 0.8744 (OUTLIER) cc_final: 0.8227 (t70) REVERT: D 159 ASP cc_start: 0.8374 (m-30) cc_final: 0.7928 (m-30) REVERT: D 162 GLU cc_start: 0.9122 (tp30) cc_final: 0.8673 (tt0) REVERT: D 170 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8916 (tt) REVERT: D 210 MET cc_start: 0.9231 (mtp) cc_final: 0.8767 (ttt) REVERT: D 229 MET cc_start: 0.8960 (mpp) cc_final: 0.8468 (mmt) REVERT: E 127 ASP cc_start: 0.8608 (p0) cc_final: 0.7968 (p0) REVERT: E 163 ASP cc_start: 0.7515 (p0) cc_final: 0.7056 (p0) REVERT: E 185 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7511 (tp40) REVERT: E 210 MET cc_start: 0.9064 (mpp) cc_final: 0.8712 (mpp) REVERT: E 238 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8443 (mp0) REVERT: E 246 GLU cc_start: 0.9184 (tp30) cc_final: 0.8679 (tp30) REVERT: F 125 PHE cc_start: 0.9282 (m-80) cc_final: 0.8985 (m-80) REVERT: F 127 ASP cc_start: 0.8402 (OUTLIER) cc_final: 0.8187 (p0) REVERT: F 139 GLU cc_start: 0.8710 (mp0) cc_final: 0.8375 (pm20) REVERT: F 159 ASP cc_start: 0.8058 (t70) cc_final: 0.7825 (t0) REVERT: F 185 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8178 (mm-40) REVERT: F 188 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8374 (mm-30) REVERT: F 214 MET cc_start: 0.9039 (mmm) cc_final: 0.8649 (mmm) REVERT: G 37 GLN cc_start: 0.7727 (pp30) cc_final: 0.7511 (pp30) REVERT: G 124 ASP cc_start: 0.8548 (t0) cc_final: 0.8194 (t0) REVERT: G 152 GLU cc_start: 0.8952 (mp0) cc_final: 0.8537 (pm20) REVERT: G 229 MET cc_start: 0.9271 (mpp) cc_final: 0.8854 (pmm) REVERT: H 78 LYS cc_start: 0.7398 (mmmt) cc_final: 0.7072 (ttpp) REVERT: H 103 LYS cc_start: 0.9080 (ttpt) cc_final: 0.8561 (ttmm) REVERT: H 196 PHE cc_start: 0.9114 (OUTLIER) cc_final: 0.8884 (t80) REVERT: H 214 MET cc_start: 0.9318 (mtm) cc_final: 0.9059 (mtm) REVERT: H 248 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9322 (mm) REVERT: I 38 GLN cc_start: 0.8689 (tp40) cc_final: 0.8347 (tp40) REVERT: I 107 LYS cc_start: 0.9426 (ptmm) cc_final: 0.9125 (pptt) REVERT: I 145 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8492 (mm-30) REVERT: I 199 LEU cc_start: 0.7975 (tp) cc_final: 0.6907 (tp) REVERT: I 210 MET cc_start: 0.9414 (ttt) cc_final: 0.9146 (ttt) REVERT: I 214 MET cc_start: 0.8949 (mtp) cc_final: 0.8709 (ptp) REVERT: I 229 MET cc_start: 0.9348 (pmm) cc_final: 0.8955 (pmm) REVERT: I 273 LYS cc_start: 0.9567 (mttt) cc_final: 0.9009 (tmtt) REVERT: J 75 TYR cc_start: 0.8704 (m-10) cc_final: 0.8267 (m-10) REVERT: J 104 ASP cc_start: 0.9502 (t70) cc_final: 0.9283 (t0) REVERT: J 211 TRP cc_start: 0.9282 (t-100) cc_final: 0.8927 (t-100) outliers start: 54 outliers final: 40 residues processed: 353 average time/residue: 0.1333 time to fit residues: 73.0827 Evaluate side-chains 336 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 289 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 129 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 85 optimal weight: 0.0670 chunk 180 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 189 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN J 38 GLN ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.101933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.070246 restraints weight = 63825.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.072418 restraints weight = 35050.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073871 restraints weight = 23963.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074772 restraints weight = 18765.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075300 restraints weight = 16133.205| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.7434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 19279 Z= 0.131 Angle : 0.679 16.529 26167 Z= 0.343 Chirality : 0.043 0.236 2990 Planarity : 0.004 0.036 3205 Dihedral : 15.351 155.610 3238 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.35 % Allowed : 22.49 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.18), residues: 2338 helix: 1.27 (0.15), residues: 1316 sheet: -0.22 (0.39), residues: 192 loop : 0.22 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 148 TYR 0.018 0.001 TYR F 112 PHE 0.040 0.002 PHE I 125 TRP 0.012 0.001 TRP H 45 HIS 0.004 0.001 HIS J 77 Details of bonding type rmsd covalent geometry : bond 0.00302 (19275) covalent geometry : angle 0.67890 (26167) hydrogen bonds : bond 0.03781 ( 903) hydrogen bonds : angle 4.45538 ( 2663) Misc. bond : bond 0.00112 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 301 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 GLU cc_start: 0.8006 (mp0) cc_final: 0.7590 (mp0) REVERT: C 140 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.7790 (mpp) REVERT: C 183 ASP cc_start: 0.8468 (t0) cc_final: 0.8193 (t70) REVERT: C 196 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8710 (t80) REVERT: D 140 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7908 (ttm) REVERT: D 156 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8320 (t0) REVERT: D 159 ASP cc_start: 0.8363 (m-30) cc_final: 0.7923 (m-30) REVERT: D 162 GLU cc_start: 0.9142 (tp30) cc_final: 0.8700 (tt0) REVERT: D 170 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8931 (tt) REVERT: D 210 MET cc_start: 0.9225 (mtp) cc_final: 0.8828 (ttt) REVERT: D 229 MET cc_start: 0.8959 (mpp) cc_final: 0.8473 (mmt) REVERT: D 250 GLU cc_start: 0.9341 (tt0) cc_final: 0.8704 (tt0) REVERT: E 185 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7778 (tp-100) REVERT: E 210 MET cc_start: 0.9049 (mpp) cc_final: 0.8708 (mpp) REVERT: E 238 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8460 (mp0) REVERT: F 125 PHE cc_start: 0.9284 (m-80) cc_final: 0.8983 (m-80) REVERT: F 127 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8167 (p0) REVERT: F 145 GLU cc_start: 0.8382 (tt0) cc_final: 0.8006 (tm-30) REVERT: F 159 ASP cc_start: 0.8065 (t70) cc_final: 0.7755 (t0) REVERT: F 185 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8185 (mm-40) REVERT: F 188 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8391 (mm-30) REVERT: F 214 MET cc_start: 0.9028 (mmm) cc_final: 0.8633 (mmm) REVERT: F 250 GLU cc_start: 0.8828 (tt0) cc_final: 0.8228 (tm-30) REVERT: G 37 GLN cc_start: 0.7755 (pp30) cc_final: 0.7512 (pp30) REVERT: G 124 ASP cc_start: 0.8573 (t0) cc_final: 0.8227 (t0) REVERT: G 152 GLU cc_start: 0.8976 (mp0) cc_final: 0.8541 (pm20) REVERT: G 180 ILE cc_start: 0.8970 (tt) cc_final: 0.8763 (pt) REVERT: G 229 MET cc_start: 0.9278 (mpp) cc_final: 0.8860 (pmm) REVERT: G 256 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9019 (mm) REVERT: H 78 LYS cc_start: 0.7347 (mmmt) cc_final: 0.7093 (ttpp) REVERT: H 103 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8583 (ttmm) REVERT: H 188 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7799 (mm-30) REVERT: H 214 MET cc_start: 0.9314 (mtm) cc_final: 0.9041 (mtm) REVERT: H 248 LEU cc_start: 0.9592 (OUTLIER) cc_final: 0.9318 (mm) REVERT: I 38 GLN cc_start: 0.8721 (tp40) cc_final: 0.8128 (tp40) REVERT: I 107 LYS cc_start: 0.9407 (ptmm) cc_final: 0.9161 (tptp) REVERT: I 145 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8489 (mm-30) REVERT: I 199 LEU cc_start: 0.7966 (tp) cc_final: 0.6902 (tp) REVERT: I 210 MET cc_start: 0.9368 (ttt) cc_final: 0.9113 (ttt) REVERT: I 229 MET cc_start: 0.9383 (pmm) cc_final: 0.8894 (pmm) REVERT: I 246 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8597 (mp0) REVERT: I 273 LYS cc_start: 0.9573 (mttt) cc_final: 0.9013 (tmtt) REVERT: J 75 TYR cc_start: 0.8672 (m-10) cc_final: 0.8240 (m-10) REVERT: J 104 ASP cc_start: 0.9508 (t70) cc_final: 0.9272 (t0) outliers start: 60 outliers final: 40 residues processed: 341 average time/residue: 0.1258 time to fit residues: 67.1075 Evaluate side-chains 338 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 290 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 140 MET Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 171 optimal weight: 0.6980 chunk 153 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 25 optimal weight: 50.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.101268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.069717 restraints weight = 63322.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.071870 restraints weight = 34672.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073283 restraints weight = 23637.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074171 restraints weight = 18548.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074715 restraints weight = 15947.045| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19279 Z= 0.138 Angle : 0.686 13.445 26167 Z= 0.349 Chirality : 0.043 0.223 2990 Planarity : 0.004 0.036 3205 Dihedral : 15.217 155.844 3238 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.07 % Allowed : 22.99 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2338 helix: 1.24 (0.15), residues: 1316 sheet: -0.43 (0.34), residues: 232 loop : 0.18 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 148 TYR 0.019 0.001 TYR H 112 PHE 0.039 0.002 PHE I 125 TRP 0.011 0.001 TRP H 45 HIS 0.003 0.001 HIS G 77 Details of bonding type rmsd covalent geometry : bond 0.00318 (19275) covalent geometry : angle 0.68596 (26167) hydrogen bonds : bond 0.03841 ( 903) hydrogen bonds : angle 4.47849 ( 2663) Misc. bond : bond 0.00118 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 282 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 54 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8318 (mtpp) REVERT: C 139 GLU cc_start: 0.7924 (mp0) cc_final: 0.7529 (mp0) REVERT: C 140 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.7840 (mpp) REVERT: C 183 ASP cc_start: 0.8398 (t0) cc_final: 0.8141 (t0) REVERT: C 196 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8818 (t80) REVERT: C 229 MET cc_start: 0.6423 (pmm) cc_final: 0.6201 (pmm) REVERT: D 156 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8201 (t70) REVERT: D 159 ASP cc_start: 0.8327 (m-30) cc_final: 0.7892 (m-30) REVERT: D 162 GLU cc_start: 0.9129 (tp30) cc_final: 0.8723 (tt0) REVERT: D 170 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8964 (tt) REVERT: D 187 LEU cc_start: 0.9316 (tt) cc_final: 0.9035 (mt) REVERT: D 210 MET cc_start: 0.9160 (mtp) cc_final: 0.8704 (ttt) REVERT: D 214 MET cc_start: 0.8878 (mmt) cc_final: 0.8608 (mmm) REVERT: D 229 MET cc_start: 0.8965 (mpp) cc_final: 0.8514 (mmt) REVERT: D 250 GLU cc_start: 0.9233 (tt0) cc_final: 0.8471 (tt0) REVERT: E 185 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7643 (tp-100) REVERT: E 238 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8481 (mp0) REVERT: F 125 PHE cc_start: 0.9272 (m-80) cc_final: 0.8970 (m-80) REVERT: F 145 GLU cc_start: 0.8401 (tt0) cc_final: 0.8047 (tm-30) REVERT: F 159 ASP cc_start: 0.8059 (t70) cc_final: 0.7753 (t0) REVERT: F 185 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8055 (mm-40) REVERT: F 188 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8419 (mm-30) REVERT: F 214 MET cc_start: 0.8961 (mmm) cc_final: 0.8549 (mmm) REVERT: F 250 GLU cc_start: 0.8744 (tt0) cc_final: 0.8256 (tm-30) REVERT: G 124 ASP cc_start: 0.8575 (t0) cc_final: 0.8244 (t0) REVERT: G 229 MET cc_start: 0.9228 (mpp) cc_final: 0.8816 (pmm) REVERT: G 256 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8925 (mm) REVERT: H 97 HIS cc_start: 0.7809 (m-70) cc_final: 0.7582 (m170) REVERT: H 103 LYS cc_start: 0.9146 (ttpt) cc_final: 0.8915 (ttmm) REVERT: H 188 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7835 (mm-30) REVERT: H 214 MET cc_start: 0.9275 (mtm) cc_final: 0.9012 (mtm) REVERT: H 248 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9339 (mm) REVERT: I 38 GLN cc_start: 0.8723 (tp40) cc_final: 0.8151 (tp40) REVERT: I 107 LYS cc_start: 0.9396 (ptmm) cc_final: 0.9153 (tptp) REVERT: I 145 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8511 (mm-30) REVERT: I 199 LEU cc_start: 0.8052 (tp) cc_final: 0.7050 (tp) REVERT: I 229 MET cc_start: 0.9321 (pmm) cc_final: 0.8889 (pmm) REVERT: I 246 GLU cc_start: 0.9190 (mm-30) cc_final: 0.8560 (mp0) REVERT: I 273 LYS cc_start: 0.9579 (mttt) cc_final: 0.9047 (tmtt) REVERT: J 75 TYR cc_start: 0.8680 (m-10) cc_final: 0.8244 (m-10) REVERT: J 104 ASP cc_start: 0.9519 (t70) cc_final: 0.9218 (t0) REVERT: J 204 PHE cc_start: 0.9446 (OUTLIER) cc_final: 0.8953 (m-80) outliers start: 55 outliers final: 41 residues processed: 317 average time/residue: 0.1205 time to fit residues: 59.9906 Evaluate side-chains 321 residues out of total 2042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 273 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 140 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 20 TRP Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 256 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 204 PHE Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 269 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 193 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.100836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069329 restraints weight = 64070.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071466 restraints weight = 35017.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072870 restraints weight = 23888.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.073782 restraints weight = 18716.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074219 restraints weight = 16078.666| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19279 Z= 0.141 Angle : 0.684 12.069 26167 Z= 0.348 Chirality : 0.043 0.331 2990 Planarity : 0.004 0.037 3205 Dihedral : 15.134 156.235 3238 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.96 % Allowed : 22.94 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.18), residues: 2338 helix: 1.24 (0.15), residues: 1316 sheet: -0.43 (0.34), residues: 232 loop : 0.18 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 148 TYR 0.019 0.001 TYR F 112 PHE 0.039 0.002 PHE I 125 TRP 0.010 0.001 TRP H 45 HIS 0.003 0.001 HIS E 97 Details of bonding type rmsd covalent geometry : bond 0.00325 (19275) covalent geometry : angle 0.68357 (26167) hydrogen bonds : bond 0.03795 ( 903) hydrogen bonds : angle 4.50727 ( 2663) Misc. bond : bond 0.00126 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3804.99 seconds wall clock time: 66 minutes 15.84 seconds (3975.84 seconds total)